TitleAuthor(s)VenueYear
Wastewater surveillance for public health Levy JI, Andersen KG, Knight R, Karthikeyan S Science2023
Stability of the fecal and oral microbiome over two years at -80°C for multiple collection methods Zouiouich S, Byrd DA, Hua X, Karwa S, Wan Y, Shi J, Humphrey GC, Ackermann GL, Knight R, Abnet CC, Vogtmann E, Sinha R Cancer Epidemiol Biomarkers Prev2023
Association of subjective and objective measures of sleep with gut microbiota composition and diversity in older men: The Osteoporotic Fractures in Men (MrOS) study Estaki M, Langsetmo L, Shardell M, Mischel A, Jiang L, Zhong Y, Kaufmann C, Knight R, Stone K, Kado D J Gerontol A Biol Sci Med Sci2023
Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A, Mazmanian SK Mov Disord2023
Insulin-regulated serine and lipid metabolism drive peripheral neuropathyHandzlik MK, Gengatharan JM, Frizzi KE, McGregor GH, Martino C, Rahman G, Gonzalez A, Moreno AM, Green CR, Guernsey LS, Lin T, Tseng P, Ideguchi Y, Fallon RJ, Chaix A, Panda S, Mali P, Wallace M, Knight R, Gantner ML, Calcutt NA, Metallo CM Nature2023
The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin Melnik AV, Callewaert C, Dorrestein K, Broadhead R, Minich JJ, Ernst M, Humphrey G, Ackermann G, Gathercole R, Aksenov AA, Knight R, Dorrestein PC mSystems2023
Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades Kodera SM, Sharma A, Martino C, Dsouza M, Grippo M, Lutz HL, Knight R, Gilbert JA, Negri C, Allard SM Environ Microbiome2023
Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritisBrewer RC, Lanz TV, Hale CR, Sepich-Poore GD, Martino C, Swafford AD, Carroll TS, Kongpachith S, Blum LK, Elliott SE, Blachere NE, Parveen S, Fak J, Yao V, Troyanskaya O, Frank MO, Bloom MS, Jahanbani S, Gomez AM, Iyer R, Ramadoss NS, Sharpe O, Chandrasekaran S, Kelmenson LB, Wang Q, Wong H, Torres HL, Wiesen M, Graves DT, Deane KD, Holers VM, Knight R, Darnell RB, Robinson WH, Orange DE Sci Transl Med2023
Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies Usyk M, Peters BA, Karthikeyan S, McDonald D, Sollecito CC, Vazquez-Baeza Y, Shaffer JP, Gellman MD, Talavera GA, Daviglus ML, Thyagarajan B, Knight R, Qi Q, Kaplan R, Burk RD Cell Rep Methods2023
Diet Quality and the Fecal Microbiota in Adults in the American Gut Project Baldeon AD, McDonald D, Gonzalez A, Knight R, Holscher HD J Nutr2023
The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases Fogelson KA, Dorrestein PC, Zarrinpar A, Knight RGastroenterology2023
SEARCH. “Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schoolsFielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R Lancet Reg Health Am2023
Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol Pendergraft MA, Belda-Ferre P, Petras D, Morris CK, Mitts BA, Aron AT, Bryant M, Schwartz T, Ackermann G, Humphrey G, Kaandorp E, Dorrestein PC, Knight R, Prather KA Environ Sci Technol2023
Healthy dietary patterns are associated with the gut microbiome in the Hispanic Community Health Study/Study of Latinos Peters BA, Xing J, Chen GC, Usyk M, Wang Z, McClain AC, Thyagarajan B, Daviglus ML, Sotres-Alvarez D, Hu FB, Knight R, Burk RD, Kaplan RC, Qi Q Am J Clin Nutr2023
Association of the gut microbiome with kidney function and damage in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) Peters BA, Qi Q, Usyk M, Daviglus ML, Cai J, Franceschini N, Lash JP, Gellman MD, Yu B, Boerwinkle E, Knight R, Burk RD, Kaplan RC Gut Microbes2023
Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A, Mazmanian SK Mov Disord2023
Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic GP, Kovalick G, Chopyk J, Kuo P, Huang L, Ghatbale P, Das P, Realegeno S, Knight R, Gilbert JA, Pride DT Sah Microbiol Spectr2023
Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease Dilmore AH, Martino C, Neth BJ, West KA, Zemlin J, Rahman G, Panitchpakdi M, Meehan MJ, Weldon KC, Blach C, Schimmel L, Kaddurah-Daouk R, Dorrestein PC, Knight R, Craft S; Alzheimer's Gut Microbiome Project Consortium Alzheimers Dement2023
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? Mutalova R, Sarrazin-Gendron R, Cai E, Richard G, Ghasemloo Gheidari P, Caisse S, Knight R, Blanchette M, Szantner A, Waldispühl J CHI '23: Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems2023
Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity Liu H, Ling W, Hua X, Moon JY, Williams-Nguyen JS, Zhan X, Plantinga AM, Zhao N, Zhang A, Knight R, Qi Q, Burk RD, Kaplan RC, Wu MC Microbiome2023
Sequence-structure-function relationships in the microbial protein universe Koehler Leman J, Szczerbiak P, Renfrew PD, Gligorijevic V, Berenberg D, Vatanen T, Taylor BC, Chandler C, Janssen S, Pataki A, Carriero N, Fisk I, Xavier RJ, Knight R, Bonneau R, Kosciolek T Nat Commun2023
Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome Taylor BC, Sheikh Andalibi M, Wandro S, Weldon KC, Sepich-Poore GD, Carpenter CS, Fraraccio S, Franklin D, Iudicello JE, Letendre S, Gianella S, Grant I, Ellis RJ, Heaton RK, Knight R, Swafford AD Microorganisms2023
Implementation of Practical Surface SARS-CoV-2 Surveillance in School SettingsCantú VJ, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Sanders K, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, Crescini ES, De Hoff P, Eisner E, Hakim A, Kapadia B, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Sathe S, Seaver P, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R mSystems2022
A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R Biotechniques2022
The molecular impact of life in an indoor environment Aksenov AA, Salido RA, Melnik AV, Brennan C, Brejnrod A, Caraballo-Rodríguez AM, Gauglitz JM, Lejzerowicz F, Farmer DK, Vance ME, Knight R, Dorrestein PC Sci Adv.2022
Context-aware deconvolution of cell-cell communication with Tensor-cell2cell Armingol E, Baghdassarian HM, Martino C, Perez-Lopez A, Aamodt C, Knight R, Lewis NEJ Nat Commun2022
Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome Dantas Machado AC, Brown SD, Lingaraju A, Sivaganesh V, Martino C, Chaix A, Zhao P, Pinto AFM, Chang MW, Richter RA, Saghatelian A, Saltiel AR, Knight R, Panda S, Zarrinpar A Cell Rep2022
The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health StudyWu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA, Vogtmann E Int J Cancer2022
Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course iMSMS Consortium Cell2022
Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactionsNarunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadiani M, Gal-Yam EN, Patel SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R Cell2022
The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps Hanes D, Nowinski B, Lamb JJ, Larson IA, McDonald D, Knight R, Song SJ, Patno N Front Nutr2022
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmissionKarthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R Nature2022
Enhancing untargeted metabolomics using metadata-based source annotationGauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP Jr, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC Nat Biotechnol2022
Baseline microbiome and metabolome are associated with response to ITIS diet in an exploratory trial in patients with rheumatoid arthritisCoras R, Martino C, Gauglitz JM, Cedola F, Tripathi A, Jarmusch AK, Alharthi M, Fernandez-Bustamante M, Agustin-Perez M, Singh A, Choi SI, Rivera T, Nguyen K, Shekhtman T, Holt T, Lee S, Golshan S, Dorrestein PC, Knight R, Guma M Clin Transl Med2022
Microbiota succession throughout life from the cradle to the grave Martino C, Dilmore AH, Burcham ZM, Metcalf JL, Jeste D, Knight R Nat Rev Microbiol2022
Intestinal transgene delivery with native E. coli chassis allows persistent physiological changesRussell BJ, Brown SD, Siguenza N, Mai I, Saran AR, Lingaraju A, Maissy ES, Dantas Machado AC, Pinto AFM, Sanchez C, Rossitto LA, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Gonzalez DJ, Saghatelian A, Knight R, Zarrinpar A Cell2022
Acetate reprograms gut microbiota during alcohol consumption Martino C, Zaramela LS, Gao B, Embree M, Tarasova J, Parker SJ, Wang Y, Chu H, Chen P, Lee KC, Galzerani DD, Gengatharan JM, Lekbua A, Neal M, Knight R, Tsukamoto H, Metallo CM, Schnabl B, Zengler K Nat Commun2022
Oral Progenitor Cell Line-Derived Small Extracellular Vesicles as a Treatment for Preferential Wound Healing Outcome Knight R, Board-Davies E, Brown H, Clayton A, Davis T, Karatas B, Burston J, Tabi Z, Falcon-Perez JM, Paisey S, Stephens P Stem Cells Transl Med2022
Location-specific signatures of Crohn's disease at a multi-omics scale Gonzalez CG, Mills RH, Zhu Q, Sauceda C, Knight R, Dulai PS, Gonzalez DJ Microbiome2022
Limited microbiome differences in captive and semi-wild primate populations consuming similar diets Kuthyar S, Watson K, Huang S, Brent LJN, Platt M, Horvath J, Gonzalez-Martinez J, Martínez M, Godoy-Vitorino F, Knight R, Dominguez-Bello MG, Amato KR FEMS Microbiol Ecol2022
Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References Hakim D, Wandro S, Zengler K, Zaramela LS, Nowinski B, Swafford A, Zhu Q, Song SJ, Gonzalez A, McDonald D, Knight R mSystems2022
Generation of Functional Immortalized Human Corneal Stromal Stem Cells Dos Santos A, Lyu N, Balayan A, Knight R, Zhuo KS, Sun Y, Xu J, Funderburgh ML, Funderburgh JL, Deng SX Int J Mol Sci2022
A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing miceAbdel-Haq R, Schlachetzki JCM, Boktor JC, Cantu-Jungles TM, Thron T, Zhang M, Bostick JW, Khazaei T, Chilakala S, Morais LH, Humphrey G, Keshavarzian A, Katz JE, Thomson M, Knight R, Gradinaru V, Hamaker BR, Glass CK, Mazmanian SK Elife2022
Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, Kunselman E, Shane MA, Perry DS, Gonzalez A, McDonald D, Knight R, Michael TP, Allen EE Nat Commun2022
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project 500 (EMP500) Consortium Nat Microbiol2022
Representative oral microbiome data for the US population: the National Health and Nutrition Examination Survey Vogtmann E, Chaturvedi AK, Blaser MJ, Bokulich NA, Caporaso JG, Gillison ML, Hua X, Hullings AG, Knight R, Purandare V, Shi J, Wan Y, Freedman ND, Abnet CC Lancet Microbe2022
Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses Kumar T, Bryant M, Cantrell K, Song SJ, McDonald D, Tubb HM, Farmer S, Lukacz ES, Brubaker L, Knight R mSystems2022
Stool multi-omics for the study of host-microbe interactions in inflammatory bowel disease Sauceda C, Bayne C, Sudqi K, Gonzalez A, Dulai PS, Knight R, Gonzalez DJ, Gonzalez CG Gut Microbes2022
The gut microbiome is a significant risk factor for future chronic lung disease Liu Y, Teo SM, Méric G, Tang HHF, Zhu Q, Sanders JG, Vázquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V, Inouye M J Allergy Clin Immunol2022
Using All Our Genomes: Blood-based Liquid Biopsies for the Early Detection of Cancer Adams E, Sepich-Poore GD, Miller-Montgomery S, Knight R View (Beijing)2022
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohortQin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brożyńska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Méric G Nat Genet 2022
A gut-derived metabolite alters brain activity and anxiety behaviour in miceNeedham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, Guo Y, Zhu Q, Griffiths JA, Knight R, Bjorkman PJ, Shapiro MG, Geschwind DH, Holschneider DP, Fischbach MA, Mazmanian SK Nature 2022
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data Armstrong G, Rahman G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R Front Bioinform2022
Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R Bioessays2022
Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides Aleti G, Kohn JN, Troyer EA, Weldon K, Huang S, Tripathi A, Dorrestein PC, Swafford AD, Knight R, Hong S BMC Microbiol2022
Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity IncreasesArmstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R mSystems2022
The ViReflow pipeline enables user friendly large scale viral consensus genome Moshiri N, Fisch KM, Birmingham A, DeHoff P, Yeo GW, Jepsen K, Laurent LC, Knight RreconstructionSci2022
Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boostingLiu Y, Méric G, Havulinna AS, Teo SM, Åberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vázquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M Cell Metab2022
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing TaxonomyZhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight RmSystems2022
The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis PatientsGonzalez CG, Mills RH, Kordahi MC, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey JC Jr, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS Cell Mol Gastroenterol Hepatol2022
Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos Peters BA, Lin J, Qi Q, Usyk M, Isasi CR, Mossavar-Rahmani Y, Derby CA, Santoro N, Perreira KM, Daviglus ML, Kominiarek MA, Cai J, Knight R, Burk RD, Kaplan RC mSystems2022
Unlocking capacities of genomics for the COVID-19 response and future pandemicsKnyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S Nat Methods2022
The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study) Bai-Tong SS, Thoemmes MS, Weldon KC, Motazavi D, Kitsen J, Hansen S, Furst A, Geng B, Song SJ, Gilbert JA, Bode L, Dorrestein PC, Knight R, Leibel SA, Leibel SL Sci Rep2022
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS Marotz C, Molinsky R, Martino C, Bohn B, Roy S, Rosenbaum M, Desvarieux M, Yuzefpolskaya M, Paster BJ, Jacobs DR, Colombo PC, Papapanou PN, Knight R, Demmer RT NPJ Biofilms Microbiomes2022
Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, Knight R mSystems2022
The Impact of Exclusive Enteral Nutrition on the Gut Microbiome of Children with Medical Complexity Beauchamp-Walters J, Aleti G, Herrera L, Debelius J, Lima N, Dalal P, Hong S, Knight R, Rhee KE JPEN J Parenter Enteral Nutr2022
Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS Goh CE, Bohn B, Marotz C, Molinsky R, Roy S, Paster BJ, Chen CY, Rosenbaum M, Yuzefpolskaya M, Colombo PC, Desvarieux M, Papapanou PN, Jacobs DR Jr, Knight R, Demmer RT J Am Heart Assoc2022
SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Casas Maya M, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Ostrander RT, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R mSystems2022
A Prebiotic Diet Alters the Fecal Microbiome and Improves Sleep in Response to Sleep Disruption in Rats Bowers SJ, Summa KC, Thompson RS, González A, Vargas F, Olker C, Jiang P, Lowry CA, Dorrestein PC, Knight R, Wright KP Jr, Fleshner M, Turek FW, Vitaterna MH Front Neurosci2022
Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase Sfiligoi I, Armstrong G, Gonzalez A, McDonald D, Knight R mSystems2022
Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention Orchanian SB, Gauglitz JM, Wandro S, Weldon KC, Doty M, Stillwell K, Hansen S, Jiang L, Vargas F, Rhee KE, Lumeng JC, Dorrestein PC, Knight R, Kim JH, Song SJ, Swafford AD Adv Biol 2022
The oral microbiome and breast cancer and non-malignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health StudyWu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA Int J Cancer2022
Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling Hu Y, Amir A, Huang X, Li Y, Huang S, Wolfe E, Weiss S, Knight R, Xu ZZ Genome Res2022
Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School SettingsCantú VJ, Sanders K, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, De Hoff P, Eisner E, Hakim A, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Plascencia A, Sathe S, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R mSystems2022
Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish AdultsRuuskanen MO, Erawijantari PP, Havulinna AS, Liu Y, Méric G, Tuomilehto J, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ Diabetes Care 2022
A gut-derived metabolite alters brain activity and anxiety behaviour in miceNeedham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, Guo Y, Zhu Q, Griffiths JA, Knight R, Bjorkman PJ, Shapiro MG, Geschwind DH, Holschneider DP, Fischbach MA, Mazmanian SK Nature 2022
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data Armstrong G, Rahman G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R Front Bioinform2022
Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R Bioessays2022
Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides Aleti G, Kohn JN, Troyer EA, Weldon K, Huang S, Tripathi A, Dorrestein PC, Swafford AD, Knight R, Hong S BMC Microbiol2022
Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity IncreasesArmstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R mSystems2022
The ViReflow pipeline enables user friendly large scale viral consensus genome Moshiri N, Fisch KM, Birmingham A, DeHoff P, Yeo GW, Jepsen K, Laurent LC, Knight RreconstructionSci2022
Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boostingLiu Y, Méric G, Havulinna AS, Teo SM, Åberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vázquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M Cell Metab2022
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing TaxonomyZhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight RmSystems2022
The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis PatientsGonzalez CG, Mills RH, Kordahi MC, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey JC Jr, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS Cell Mol Gastroenterol Hepatol2022
Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos Peters BA, Lin J, Qi Q, Usyk M, Isasi CR, Mossavar-Rahmani Y, Derby CA, Santoro N, Perreira KM, Daviglus ML, Kominiarek MA, Cai J, Knight R, Burk RD, Kaplan RC mSystems2022
Unlocking capacities of genomics for the COVID-19 response and future pandemicsKnyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S Nat Methods2022
The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study) Bai-Tong SS, Thoemmes MS, Weldon KC, Motazavi D, Kitsen J, Hansen S, Furst A, Geng B, Song SJ, Gilbert JA, Bode L, Dorrestein PC, Knight R, Leibel SA, Leibel SL Sci Rep2022
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS Marotz C, Molinsky R, Martino C, Bohn B, Roy S, Rosenbaum M, Desvarieux M, Yuzefpolskaya M, Paster BJ, Jacobs DR, Colombo PC, Papapanou PN, Knight R, Demmer RT NPJ Biofilms Microbiomes2022
Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, Knight R mSystems2022
The Impact of Exclusive Enteral Nutrition on the Gut Microbiome of Children with Medical Complexity Beauchamp-Walters J, Aleti G, Herrera L, Debelius J, Lima N, Dalal P, Hong S, Knight R, Rhee KE JPEN J Parenter Enteral Nutr2022
Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS Goh CE, Bohn B, Marotz C, Molinsky R, Roy S, Paster BJ, Chen CY, Rosenbaum M, Yuzefpolskaya M, Colombo PC, Desvarieux M, Papapanou PN, Jacobs DR Jr, Knight R, Demmer RT J Am Heart Assoc2022
SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Casas Maya M, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Ostrander RT, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R mSystems2022
A Prebiotic Diet Alters the Fecal Microbiome and Improves Sleep in Response to Sleep Disruption in Rats Bowers SJ, Summa KC, Thompson RS, González A, Vargas F, Olker C, Jiang P, Lowry CA, Dorrestein PC, Knight R, Wright KP Jr, Fleshner M, Turek FW, Vitaterna MH Front Neurosci2022
Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase Sfiligoi I, Armstrong G, Gonzalez A, McDonald D, Knight R mSystems2022
Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention Orchanian SB, Gauglitz JM, Wandro S, Weldon KC, Doty M, Stillwell K, Hansen S, Jiang L, Vargas F, Rhee KE, Lumeng JC, Dorrestein PC, Knight R, Kim JH, Song SJ, Swafford AD Adv Biol (Weinh)2022
The oral microbiome and breast cancer and non-malignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health StudyWu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA Vogtmann E. Int J Cancer2022
Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling Hu Y, Amir A, Huang X, Li Y, Huang S, Wolfe E, Weiss S, Knight R, Xu ZZ Genome Res2022
Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School SettingsCantú VJ, Sanders K, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, De Hoff P, Eisner E, Hakim A, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Plascencia A, Sathe S, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R mSystems2022
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severityMills RH, Dulai PS, Vázquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K, Humphrey G, Carrillo-Terrazas M, Goldasich LD, Bryant M, Raffatellu M, Quinn RA, Gewirtz AT, Chassaing B, Chu H, Sandborn WJ, Dorrestein PC, Knight R, Gonzalez DJ Nat Microbiol 2022
Predicting fungal infection rate and severity with skin-associated microbial communities on amphibiansChen MY, Kueneman JG, González A, Humphrey G, Knight R, McKenzie VJ Mol Ecol 2022
Mapping the human brain metabolome and influences of gut microbiomeBatra R, Heinken A, Karu N, Arnold M, Kastenmüller G, Hankemeier T, Bennett DA, Knight R, Krumsiek J. Thiele I, Kaddurah-Daouk RF Alzheimer's Dement 2021
The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum DisorderDilmore AH, McDonald D, Nguyen TT, Adams JB, Krajmalnik-Brown R, Elijah E, Dorrestein PC, Knight R mSystems 2021
Class Ib MHC-Mediated Immune Interactions Play a Critical Role in Maintaining Mucosal Homeostasis in the Mammalian Large IntestineDasgupta S, Maricic I, Tang J, Wandro S, Weldon K, Carpenter CS, Eckmann L, Rivera-Nieves J, Sandborn W, Knight R, Dorrestein P, Swafford AD, Kumar VImmunohorizons 2021
Clean room microbiome complexity impacts planetary protection bioburdenHendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran KMicrobiome 2021
Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohortsWu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R, Vogtmann E BMC Microbiol 2021
Reporting guidelines for human microbiome research: the STORMS checklistMirzayi C, Renson A; Genomic Standards Consortium; Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L Nat Med 2021
The Gut Microbiome Modifies the Association between a Mediterranean Diet and Diabetes in US Hispanic / Latino PopulationWang DD, Qi Q, Wang Z, Usyk M, Sotres-Alvarez D, Mattei J, Tamez M, Gellman MD, Daviglus M, Hu FB, Stampfer MJ, Huttenhower C, Knight R, Burk RD, Kaplan RC J Clin Endocrinol Metab 2021
Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs Salido RA, Cantú VJ, Clark AE, Leibel SL, Foroughishafiei A, Saha A, Hakim A, Nouri A, Lastrella AL, Castro-Martínez A, Plascencia A, Kapadia BK, Xia B, Ruiz CA, Marotz CA, Maunder D, Lawrence ES, Smoot EW, Eisner E, Crescini ES, Kohn L, Franco Vargas L, Chacón M, Betty M, Machnicki M, Wu MY, Baer NA, Belda-Ferre P, De Hoff P, Seaver P, Ostrander RT, Tsai R, Sathe S, Aigner S, Morgan SC, Ngo TT, Barber T, Cheung W, Carlin AF, Yeo GW, Laurent LC, Fielding-Miller R, Knight R mSystems 2021
Skin inflammation activates intestinal stromal fibroblasts and promotes colitisDokoshi T, Seidman JS, Cavagnero KJ, Li F, Liggins MC, Taylor BC, Olvera J, Knight R, Chang JT, Salzman NH, Gallo RL J Clin Invest 2021
Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS ACS Sens 2021
Fecal Microbiome Composition Does Not Predict Diet-Induced TMAO Production in Healthy Adults”Ferrell M, Bazeley P, Wang Z, Levison BS, Li XS, Jia X, Krauss RM, Knight R, Lusis AJ, Garcia-Garcia JC, Hazen SL, Tang WHW J Am Heart Assoc 2021
Markers of Gut Barrier Function and Microbial Translocation Associate with Lower Gut Microbial Diversity in People with HIV”Ellis RJ, Iudicello JE, Heaton RK, Isnard S, Lin J, Routy JP, Gianella S, Hoenigl M, Knight R Viruses 2021
A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project”Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song SJ, Knight R, Derrien M, Veiga P Am J Clin Nutr 2021
Individuals with substance use disorders have a distinct oral microbiome pattern”Guetterman HM, Huey SL, Knight R, Fox AM, Mehta S, Finkelstein JLAdv Nutr 2021
Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data”Armstrong G, Martino C, Rahman G, Gonzalez A, Vázquez-Baeza Y, Mishne G, Knight R mSystems 2021
Individuals with substance use disorders have a distinct oral microbiome pattern”Kosciolek T, Victor TA, Kuplicki R, Rossi M, Estaki M, Ackermann G; Tulsa 1000 Investigators, Knight R, Paulus MP Brain Behav Immun Health 2021
Reduced Gut Microbiome Diversity in People With HIV Who Have Distal Neuropathic PainEllis RJ, Heaton RK, Gianella S, Rahman G, Knight R J Pain 2021
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomesArmstrong GW, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck K, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vázquez-Baeza Y, Knight R Genome Res 2021
Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern CaliforniaAlderete TL, Jones RB, Shaffer JP, Holzhausen EA, Patterson WB, Kazemian E, Chatzi L, Knight R, Plows JF, Berger PK, Goran MI Gut Microbes 2021
Host DNA Depletion in Saliva Samples for Improved Shotgun MetagenomicsMarotz C, Zuniga C, Zaramela L, Knight R, Zengler KMethods Mol Biol 2021
Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University CampusKarthikeyan S, Nguyen A, McDonald D, Zong Y, Ronquillo N, Ren J, Zou J, Farmer S, Humphrey G, Henderson D, Javidi T, Messer K, Anderson C, Schooley R, Martin NK, Knight R mSystems 2021
Emergence of an early SARS-CoV-2 epidemic in the United StatesSnyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G Jr, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KGCell 2021
Nutritional Interventions and the Gut Microbiome in ChildrenMehta S, Huey SL, McDonald D, Knight R, Finkelstein JL Annu Rev Nutr 2021
A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial DecompositionDeel H, Emmons AL, Kiely J, Damann FE, Carter DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf JL mSphere 2021
A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome DiversityJing G, Zhang Y, Liu L, Wang Z, Sun Z, Knight R, Su X, Xu J mSystems 2021
Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythmsThompson RS, Gaffney M, Hopkins S, Kelley T, Gonzalez A, Bowers SJ, Hotz Vitaterna M, Turek FW, Foxx CL, Lowry CA, Vargas F, Dorrestein PC, Wright KP Jr, Knight R, Fleshner M Brain Behav Immun 2021
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiomeHuang S, Jiang S, Huo D, Allaband C, Estaki M, Cantu V, Belda-Ferre P, Vázquez-Baeza Y, Zhu Q, Ma C, Li C, Zarrinpar A, Liu YY, Knight R, Zhang J Microbiome 2021
Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and MetabolomeAllaband C, Lingaraju A, Martino C, Russell B, Tripathi A, Poulsen O, Dantas Machado AC, Zhou D, Xue J, Elijah E, Malhotra A, Dorrestein PC, Knight R, Haddad GG, Zarrinpar A mSystems 2021
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshopsDillon MR, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RRM, Sanchez A, Simard A, Vázquez-Baeza Y, Ziemski M, Miwa HE, Kerere TA, Coote C, Bonneau R, Knight R, Oliveira G, Gopalasingam P, Kaehler BD, Cope EK, Metcalf JL, Robeson Ii MS, Bokulich NA, Caporaso JGPLoS Comput Biol 2021
Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seedingSong SJ, Wang J, Martino C, Jiang LJ, Thompson WK, Shenhav L, McDonald D, Marotz C, Harris PR, Hernandez CD, Henderson N, Ackley E, Nardella D, Gillihan C, Montacuti V, Schweizer W, Jay M, Combellick J, Sun H, Garcia-Mantrana I, Gil Raga F, Collado MC, Rivera-Vinas JI, Campos-Rivera M, Ruiz-Calderon JF, Knight R, Dominguez-Bello MGMed 2021
Host and gut microbial tryptophan metabolism and type 2 diabetes: an integrative analysis of host genetics, diet, gut microbiome and circulating metabolites in cohort studiesQi Q, Li J, Yu B, Moon JY, Chai JC, Merino J, Hu J, Ruiz-Canela M, Rebholz C, Wang Z, Usyk M, Chen GC, Porneala BC, Wang W, Nguyen NQ, Feofanova EV, Grove ML, Wang TJ, Gerszten RE, Dupuis J, Salas-Salvadó J, Bao W, Perkins DL, Daviglus ML, Thyagarajan B, Cai J, Wang T, Manson JE, Martínez-González MA, Selvin E, Rexrode KM, Clish CB, Hu FB, Meigs JB, Knight R, Burk RD, Boerwinkle E, Kaplan RC Gut 2021
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environmentMarotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM Microbiome 2021
Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkersZhu Q, Hou Q, Huang S, Ou Q, Huo D, Vázquez-Baeza Y, Cen C, Cantu V, Estaki M, Chang H, Belda-Ferre P, Kim HC, Chen K, Knight R, Zhang J ISME J 2021
Individuals with substance use disorders have a distinct oral microbiome patternKosciolek T, Victor TA, Kuplicki R, Rossi M, Estaki M, Ackermann G, Tulsa 1000 Investigators, Knight R, Paulus MP Brain Behav Immun 2021
Nonalcoholic Steatohepatitis and HCC in a Hyperphagic Mouse Accelerated by Western Diet Ganguly S, Muench GA, Shang L, Rosenthal SB, Rahman G, Wang R, Wang Y, Kwon HC, Diomino AM, Kisseleva T, Soorosh P, Hosseini M, Knight R, Schnabl B, Brenner DA, Dhar D Cell Mol Gastroenterol Hepatol 2021
Associations of healthy food choices with gut microbiota profiles Koponen KK, Salosensaari A, Ruuskanen MO, Havulinna AS, Männistö S, Jousilahti P, Palmu J, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Meric G, Cheng S, Inouye M, Jain M, Niiranen TJ, Valsta LM, Knight R, Salomaa VV Am J Clin Nutr 2021
Challenges in benchmarking metagenomic profilers Sun Z, Huang S, Zhang M, Zhu Q, Haiminen N, Carrieri AP, Vázquez-Baeza Y, Parida L, Kim HC, Knight R, Liu YY Nat Methods 2021
Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection Jung CE, Estaki M, Chopyk J, Taylor BC, Gonzalez A, McDonald D, Shin J, Ferrante K, Wasenda E, Lippmann Q, Knight R, Pride D, Lukacz ES Female Pelvic Med Reconstr Surg 2021
Taxonomic signatures of cause-specific mortality risk in human gut microbiome Salosensaari A, Laitinen V, Havulinna AS, Meric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous JD, Long T, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti L, Niiranen T Nat Commun 2021
Intratumoral bacteria generate a new class of therapeutically relevant tumor antigens in melanoma Sepich-Poore GD, Carter H, Knight R Cancer Cell 2021
METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection Marotz C, Cavagnero KJ, Song SJ, McDonald D, Wandro S, Humphrey G, Bryant M, Ackermann G, Diaz E, Knight R Cell Rep 2021
Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria Jiao JY, Fu L, Hua ZS, Liu L, Salam N, Liu PF, Lv AP, Wu G, Xian WD, Zhu Q, Zhou EM, Fang BZ, Oren A, Hedlund BP, Jiang HC, Knight R, Cheng L, Li WJ ISME J 2021
Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M Genome Res 2021
Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data Jiang L, Haiminen N, Carrieri AP, Huang S, Vã Zquez-Baeza Y, Parida L, Kim HC, Swafford AD, Knight R, Natarajan L Biometrics 2021
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition Marotz C, Cavagnero KJ, Song SJ, McDonald D, Wandro S, Humphrey G, Bryant M, Ackermann G, Diaz E, Knight R mSystems 2021
Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome Xue J, Allaband C, Zhou D, Poulsen O, Martino C, Jiang L, Tripathi A, Elijah E, Dorrestein PC, Knight R, Zarrinpar A, Haddad GG Front Physiol 2021
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Schiabor Barrett KM, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM 3rd, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, MacCannell D, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu CY, Suchard MA, Lu JT, Lee W, Andersen KG Cell 2021
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection Mu A, McDonald D, Jarmusch AK, Martino C, Brennan C, Bryant M, Humphrey GC, Toronczak J, Schwartz T, Nguyen D, Ackermann G, D'Onofrio A, Strathdee SA, Schooley RT, Dorrestein PC, Knight R, Aslam S Microbiome 2021
Association of Loneliness and Wisdom With Gut Microbial Diversity and Composition: An Exploratory Study Nguyen TT, Zhang X, Wu TC, Liu J, Le C, Tu XM, Knight R, Jeste DV Front Psychiatry 2021
Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study Sinha R, Zhao N, Goedert JJ, Byrd DA, Wan Y, Hua X, Hullings AG, Knight R, Breda SV, Mathijs K, de Kok TM, Ward MH; PHYTOME consortium members Environ Res 2021
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R mSystems 2021
Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos Mei Z, Chen GC, Wang Z, Usyk M, Yu B, Baeza YV, Humphrey G, Benitez RS, Li J, Williams-Nguyen JS, Daviglus ML, Hou L, Cai J, Zheng Y, Knight R, Burk RD, Boerwinkle E, Kaplan RC, Qi Q Am J Clin Nutr 2021
SARS-CoV-2 Screening Among Symptom-Free Healthcare Workers Demmer RT, Ulrich AK, Wiggen TD, Strickland A, Naumchik BM, Kulasingam S, Stovitz SD, Marotz C, Belda-Ferre P, Humphrey G, De Hoff P, Laurent L, Kline S, Knight R Infect Control Hosp Epidemiol 2021
Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing Bhagwat G, Zhu Q, O'Connor W, Subashchandrabose S, Grainge I, Knight R, Palanisami T Environ Sci Technol 2021
High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County Karthikeyan S, Ronquillo N, Belda-Ferre P, Alvarado D, Javidi T, Longhurst CA, Knight R mSystems 2021
Links between gut microbiome composition and fatty liver disease in a large population sample Ruuskanen MO, Åberg F, Männistö V, Havulinna AS, Méric G, Liu Y, Loomba R, Vázquez-Baeza Y, Tripathi A, Valsta LM, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ Gut Microbes 2021
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R Biotechniques 2021
Absence of CCR2 reduces spontaneous intestinal tumorigenesis in the ApcMin /+ mouse model Jala VR, Bodduluri SR, Ghosh S, Chheda Z, Singh R, Smith ME, Chilton PM, Fleming CJ, Mathis SP, Sharma RK, Knight R, Yan J, Haribabu B Int J Cancer 2021
Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a "Two Hit" Stressor Model Foxx CL, Heinze JD, González A, Vargas F, Baratta MV, Elsayed AI, Stewart JR, Loupy KM, Arnold MR, Flux MC, Sago SA, Siebler PH, Milton LN, Lieb MW, Hassell JE, Smith DG, Lee KAK, Appiah SA, Schaefer EJ, Panitchpakdi M, Sikora NC, Weldon KC, Stamper CE, Schmidt D, Duggan DA, Mengesha YM, Ogbaselassie M, Nguyen KT, Gates CA, Schnabel K, Tran L, Jones JD, Vitaterna MH, Turek FW, Fleshner M, Dorrestein PC, Knight R, Wright KP, Lowry CA Front Physiol 2021
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD Microbiome 2021
Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a "Two Hit" Stressor Model Foxx CL, Heinze JD, González A, Vargas F, Baratta MV, Elsayed AI, Stewart JR, Loupy KM, Arnold MR, Flux MC, Sago SA, Siebler PH, Milton LN, Lieb MW, Hassell JE, Smith DG, Lee KAK, Appiah SA, Schaefer EJ, Panitchpakdi M, Sikora NC, Weldon KC, Stamper CE, Schmidt D, Duggan DA, Mengesha YM, Ogbaselassie M, Nguyen KT, Gates CA, Schnabel K, Tran L, Jones JD, Vitaterna MH, Turek FW, Fleshner M, Dorrestein PC, Knight R, Wright KP, Lowry CA Front Physiol 2021
Large-scale association analyses identify host factors influencing human gut microbiome composition Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A Nat Genet 2021
Associations of fecal microbial profiles with breast cancer and non-malignant breast disease in the Ghana Breast Health Study SByrd DA, Vogtmann E, Wu Z, Han Y, Wan Y, Clegg-Lamptey JN, Yarney J, Wiafe-Addai B, Wiafe S, Awuah B, Ansong D, Nyarko K, Hullings AG, Hua X, Ahearn T, Goedert JJ, Shi J, Knight R, Figueroa JD, Brinton LA, Garcia-Closas M, Sinha R Int J Cancer 2021
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing Karst SM, Ziels RM, Kirkegaard RH, Sørensen EA, McDonald D, Zhu Q, Knight R, Albertsen M Nat Methods 2021
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L Mar Drugs 2021
Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Pogliano J, Nizet V, Feist AM, Palsson BO Gigascience 2021
Reply to: Examining microbe-metabolite correlations by linear methods Morton JT, McDonald D, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R Nat Methods 2021
Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 LaPelusa M, Donoviel D, Branzini SE, Carlson PE Jr, Culler S, Cheema AK, Kaddurah-Daouk R, Kelly D, de Cremoux I, Knight R, Krajmalnik-Brown R, Mayo SL, Mazmanian SK, Mayer EA, Petrosino JF, Garrison K Microbiome 2020
Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota Sabey KA, Song SJ, Jolles A, Knight R, Ezenwa VO ISME J 2020
The Gut Microbiome, Aging, and Longevity: A Systematic Review Badal VD, Vaccariello ED, Murray ER, Yu KE, Knight R, Jeste DV, Nguyen TT Nutrients 2020
Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus Microbiome Centers Consortium COVID Committee mSystems 2020
Vitamin D metabolites and the gut microbiome in older men Thomas RL, Jiang L, Adams JS, Xu ZZ, Shen J, Janssen S, Ackermann G, Vanderschueren D, Pauwels S, Knight R, Orwoll ES, Kado DM Nat Commun 2020
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules Baker JL, Morton JT, Dinis M, Alvarez R, Tran NC, Knight R, Edlund A Genome Res 2020
Triclosan leads to dysregulation of the metabolic regulator FGF21 exacerbating high fat diet-induced nonalcoholic fatty liver disease Yueh MF, He F, Chen C, Vu C, Tripathi A, Knight R, Karin M, Chen S, Tukey RH Proc Natl Acad Sci U S A. 2020
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC Nat Chem Biol 2020
Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL 2nd, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K Nat Biotechnol 2020
Host variables confound gut microbiota studies of human disease Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y Nature 2020
Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients Salido RA, Morgan SC, Rojas MI, Magallanes CG, Marotz C, DeHoff P, Belda-Ferre P, Aigner S, Kado DM, Yeo GW, Gilbert JA, Laurent L, Rohwer F, Knight R mSystems 2020
Expanding magnetic organelle biogenesis in the domain Bacteria Lin W, Zhang W, Paterson GA, Zhu Q, Zhao X, Knight R, Bazylinski DA, Roberts AP, Pan Y Microbiome 2020
Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis The iMSMS Consortium Mult Scler 2020
Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk Nguyen TT, Kosciolek T, Daly RE, Vázquez-Baeza Y, Swafford A, Knight R, Jeste DV Brain Behav Immun 2020
Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV Taylor BC, Weldon KC, Ellis RJ, Franklin D, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Iudicello J, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R mSystems 2020
Early-life gut dysbiosis linked to juvenile mortality in ostriches Videvall E, Song SJ, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK Microbiome 2020
Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome DiversityFang X, Vázquez-Baeza Y, Elijah E, Vargas F, Ackermann G, Humphrey G, Lau R, Weldon KC, Sanders JG, Panitchpakdi M, Carpenter C, Jarmusch AK, Neill J, Miralles A, Dulai P, Singh S, Tsai M, Swafford AD, Smarr L, Boyle DL, Palsson BO, Chang JT, Dorrestein PC, Sandborn WJ, Knight R, Boland BS Inflamm Bowel Dis 2020
Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of AntibioticVrbanac A, Patras KA, Jarmusch AK, Mills RH, Shing SR, Quinn RA, Vargas F, Gonzalez DJ, Dorrestein PC, Knight R, Nizet V mSystems 2020
Fecal Microbiota Transplant is Highly Effective in Real-World Practice: Initial Results from the FMT National RegistryKelly CR, Yen EF, Grinspan AM, Kahn SA, Atreja A, Lewis JD, Moore TA, Rubin DT, Kim AM, Serra S, Nersesova Y, Fredell L, Hunsicker D, McDonald D, Knight R, Allegretti JR, Pekow J, Absah I, Hsu R, Vincent J, Khanna S, Tangen L, Crawford CV, Mattar MC, Chen LA, Fischer M, Arsenescu RI, Feuerstadt P, Goldstein J, Kerman D, Ehrlich AC, Wu GD, Laine L Gastroenterology 2020
A Distinct Microbiome Signature in Posttreatment Lyme Disease PatientsMorrissette M, Pitt N, González A, Strandwitz P, Caboni M, Rebman AW, Knight R, D'Onofrio A, Aucott JN, Soloski MJ, Lewis K mBio 2020
Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome Taylor BC, Weldon KC, Ellis RJ, Franklin D, Groth T, Gentry EC, Tripathi A, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Oliveira MF, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R mSystems 2020
Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans Ha CWY, Martin A, Sepich-Poore GD, Shi B, Wang Y, Gouin K, Humphrey G, Sanders K, Ratnayake Y, Chan KSL, Hendrick G, Caldera JR, Arias C, Moskowitz JE, Ho Sui SJ, Yang S, Underhill D, Brady MJ, Knott S, Kaihara K, Steinbaugh MJ, Li H, McGovern DPB, Knight R, Fleshner P, Devkota S Cell 2020
The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite TreatmentMinich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B, Allen EE Microbiol 2020
Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infectionLabarta-Bajo L, Nilsen SP, Humphrey G, Schwartz T, Sanders K, Swafford A, Knight R, Turner JR, Zúñiga EI J Exp Med 2020
Leveling up citizen scienceWaldispühl J, Szantner A, Knight R, Caisse S, Pitchford R Nat Biotechnol 2020
Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India Huey SL, Jiang L, Fedarko MW, McDonald D, Martino C, Ali F, Russell DG, Udipi SA, Thorat A, Thakker V, Ghugre P, Potdar RD, Chopra H, Rajagopalan K, Haas JD, Finkelstein JL, Knight R, Mehta S mSphere 2020
CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infectionLabarta-Bajo L, Gramalla-Schmitz A, Gerner RR, Kazane KR, Humphrey G, Schwartz T, Sanders K, Swafford A, Knight R, Raffatellu M, Zúñiga EI Proc Natl Acad Sci U S A 2020
Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic SignaturesWozniak JM, Mills RH, Olson J, Caldera JR, Sepich-Poore GD, Carrillo-Terrazas M, Tsai CM, Vargas F, Knight R, Dorrestein PC, Liu GY, Nizet V, Sakoulas G, Rose W, Gonzalez DJ Cell 2020
Context-aware dimensionality reduction deconvolutes gut microbial community dynamicsMartino C, Shenhav L, Marotz CA, Armstrong G, McDonald D, Vázquez-Baeza Y, Morton JT, Jiang L, Dominguez-Bello MG, Swafford AD, Halperin E, Knight R Nat Biotechnol 2020
Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort Loftfield E, Herzig KH, Caporaso JG, Derkach A, Wan Y, Byrd DA, Vogtmann E, Männikkö M, Karhunen V, Knight R, Gunter MJ, Jӓrvelin MR, Sinha R Cancer Epidemiol Biomarkers Prev 2020
Fructose stimulated de novo lipogenesis is promoted by inflammation Todoric J, Di Caro G, Reibe S, Henstridge DC, Green CR, Vrbanac A, Ceteci F, Conche C, McNulty R, Shalapour S, Taniguchi K, Meikle PJ, Watrous JD, Moranchel R, Najhawan M, Jain M, Liu X, Kisseleva T, Diaz-Meco MT, Moscat J, Knight R, Greten FR, Lau LF, Metallo CM, Febbraio MA, Karin M Nat Metab 2020
Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium Mu A, Carter GP, Li L, Isles NS, Vrbanac AF, Morton JT, Jarmusch AK, De Souza DP, Narayana VK, Kanojia K, Nijagal B, McConville MJ, Knight R, Howden BP, Stinear TP mSystems 2020
Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes JYoshino M, Kayser BD, Yoshino J, Stein RI, Reeds D, Eagon JC, Eckhouse SR, Watrous JD, Jain M, Knight R, Schechtman K, Patterson BW, Klein S N Engl J Med 2020
ReDU: a framework to find and reanalyze public mass spectrometry data Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL 2nd, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. Nat Methods 2020
Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals Palmu J, Salosensaari A, Havulinna AS, Cheng S, Inouye M, Jain M, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Vartiainen E, Laatikainen T, Jousilahti P, Salomaa V, Knight R, Lahti L, Niiranen TJ. J Am Heart Assoc 2020
A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis Oh TG, Kim SM, Caussy C, Fu T, Guo J, Bassirian S, Singh S, Madamba EV, Bettencourt R, Richards L, Raffatellu M, Dorrestein PC, Yu RT, Atkins AR, Huan T, Brenner DA, Sirlin CB, Knight R, Downes M, Evans RM, Loomba R Cell Metab 2020
Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice Dethloff F, Vargas F, Elijah E, Quinn R, Park DI, Herzog DP, Müller MB, Gentry EC, Knight R, Gonzalez A, Dorrestein PC, Turck CW Front Psychiatry 2020
High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy Raghuvanshi R, Vasco K, Vázquez-Baeza Y, Jiang L, Morton JT, Li D, Gonzalez A, DeRight Goldasich L, Humphrey G, Ackermann G, Swafford AD, Conrad D, Knight R, Dorrestein PC, Quinn RA mSystems 2020
Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. Genome Res 2020
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes Ma B, Wang Y, Ye S, Liu S, Stirling E, Gilbert JA, Faust K, Knight R, Jansson JK, Cardona C, Röttjers L, Xu J Microbiome 2020
Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen EE mSphere 2020
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. Nat Commun 2020
Visualizing 'omic feature rankings and log-ratios using QurroFedarko MW, Martino C, Morton JT, González A, Rahman G, Marotz CA, Minich JJ, Allen EE, Knight R. NAR Genom Bioinform 2020
QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. Curr Protoc Bioinformatics 2020
SHOGUN: a modular, accurate, and scalable framework for microbiome quantification Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Knight R, Knights D. Bioinformatics 2020
Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, Allen EE Appl Environ Microbiol 2020
Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: a Pharmacokinetic, Microbiome and Untargeted Metabolomics Study Jarmusch AK, Vrbanac A, Momper JD, Ma JD, Alhaja M, Liyanage M, Knight R, Dorrestein PC, Tsunoda SM Clin Transl Sci 2020
Microbiome analyses of blood and tissues suggest cancer diagnostic approach Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R. Nature 2020
Multiple-Disease Detection and Classification across Cohorts via Microbiome Search Su X, Jing G, Sun Z, Liu L, Xu Z, McDonald D, Wang Z, Wang H, Gonzalez A, Zhang Y, Huang S, Huttley G, Knight R, Xu J mSystems 2020
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R mSystems 2020
Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs Gauglitz JM, Morton JT, Tripathi A, Hansen S, Gaffney M, Carpenter C, Weldon KC, Shah R, Parampil A, Fidgett AL, Swafford AD, Knight R, Dorrestein PC mSystems 2020
Longitudinal survey of microbiome associated with particulate matter in a megacity Qin N, Liang P, Wu C, Wang G, Xu Q, Xiao X, Wang T, Zolfo M, Segata N, Qin H, Knight R, Gilbert JA, Zhu TF Genome Biol 2020
Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing Fouladi F, Bailey MJ, Patterson WB, Sioda M, Blakley IC, Fodor AA, Jones RB, Chen Z, Kim JS, Lurmann F, Martino C, Knight R, Gilliland FD, Alderete TL Environ Int 2020
Global chemical effects of the microbiome include new bile-acid conjugations Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC Nature 2020
Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome Bowers SJ, Vargas F, González A, He S, Jiang P, Dorrestein PC, Knight R, Wright KP Jr, Lowry CA, Fleshner M, Vitaterna MH, Turek FW PLoS One 2020
Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults Kohn JN, Kosciolek T, Marotz C, Aleti G, Guay-Ross RN, Hong SH, Hansen S, Swafford A, Knight R, Hong S Brain Behav Immu 2020
The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months Ordiz MI, Janssen S, Humphrey G, Ackermann G, Stephenson K, Agapova S, Divala O, Kaimila Y, Maleta K, Zhong C, Knight R, Trehan I, Tarr PI, Rusconi B, Manary MJ Am J Clin Nutr 2020
Human Skin, Oral, and Gut Microbiomes Predict Chronological Age Huang S, Haiminen N, Carrieri AP, Hu R, Jiang L, Parida L, Russell B, Allaband C, Zarrinpar A, Vázquez-Baeza Y, Belda-Ferre P, Zhou H, Kim HC, Swafford AD, Knight R, Xu ZZ mSystems 2020
A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice Sampson TR, Challis C, Jain N, Moiseyenko A, Ladinsky MS, Shastri GG, Thron T, Needham BD, Horvath I, Debelius JW, Janssen S, Knight R, Wittung-Stafshede P, Gradinaru V, Chapman M, Mazmanian SK Elife 2020
Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study Burcham ZM, Garneau NL, Comstock SS, Tucker RM, Knight R, Metcalf JL; Genetics of Taste Lab Citizen Scientists Sci Rep 2020
Organ-level protein networks as a reference for the host effects of the microbiome Mills RH, Wozniak JM, Vrbanac A, Campeau A, Chassaing B, Gewirtz A, Knight R, Gonzalez DJ Genome Res 2020
Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations: Statistical Power for Microbiome Studies Casals-Pascual C, González A, Vázquez-Baeza Y, Song SJ, Jiang L, Knight R Gastroenterology 2020
Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats Song SJ, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, Humphrey G, Gilbert JA, Hackett SJ, White KP, Skeen HR, Kurtis SM, Withrow J, Braile T, Miller M, McCracken KG, Maley JM, Ezenwa VO, Williams A, Blanton JM, McKenzie VJ, Knight R mBio 2020
Using microbiome tools for estimating the postmortem interval Deel H, Bucheli S, Belk A, Ogden S, Lynne A, O Carter D, Knight R, Metcalf JL Microbial Forensics 2020
Oral probiotic versus placebo and the maternal microbiome during pregnancy: A randomized controlled trial Conturie C, Thorson C, Su C, Perry K, Humphrey G, Hansen S, Knight R, Song SJ, Swafford A, Laurent L Am J Obstet Gynecol 2020
Mass spectrometry searches using MASST Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC Nat Biotechnol 2020
Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates Yan Y, Maurer-Alcalá XX, Knight R, Kosakovsky Pond SL, Katz LA mBio 10(6) 2019
Effects of the microalgae Chlamydomonas on gastrointestinal health Fields FJ, Lejzerowicz F, Schroeder D, Ngoi SM, Tran M, McDonald D, Jiang L, Chang JT, Knight R, Mayfield S Journal of Functional Foods 2019
The emergence of microbiome centres Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL Nat Microbiol 2020
Microbial biogeography and ecology of the mouth and implications for periodontal diseases Proctor DM, Shelef KM, Gonzalez A, Davis CL, Dethlefsen L, Burns AR, Loomer PM, Armitage GC, Ryder MI, Millman ME, Knight R, Holmes SP, Relman DA Periodontol 2000 2020
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J Sci Data 2019
The Microbiome and Its Potential for Pharmacology Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R Handb Exp Pharmacol 2019
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R Nat Commun 2019
Three-dimensional culture of oral progenitor cells: Effects on small extracellular vesicles production and proliferative function Yang Y, Knight R, Stephens P, Zhang Y. J Oral Pathol Med 2019
Neighborhoods to Nucleotides-Advances and Gaps for an Obesity Disparities Systems Epidemiology Model Jankowska MM, Gaulton K, Knight R, Patrick K, Sears DD Current Epidemiology Reports 2019
Altered Gut Microbiota and Host Metabolite Profiles in HIV-infected Women Wang Z, Usyk M, Sollecito CC, Qiu Y, Williams-Nguyen J, Hua S, Gradissimo A, Wang T, Xue X, Kurland IJ, Ley K, Landay AL, Anastos K, Knight R, Kaplan RC, Burk RD, Qi Q Clin Infect Dis 2019
Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations Byrd DA, Chen J, Vogtmann E, Hullings A, Song SJ, Amir A, Kibriya MG, Ahsan H, Chen Y, Nelson H, Knight R, Shi J, Chia N, Sinha R. PLoS One 2019
Learning representations of microbe-metabolite interactionsMorton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R.Nat Methods 2019
Home chemical and microbial transitions across urbanizationMcCall LI, Callewaert C, Zhu Q, Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG.Nat Microbiol. 2019
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short readsSanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R.Genome Biol 2019
Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesityKaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD.Genome Biol 2019
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H.Cell Syst. 2019
Species abundance information improves sequence taxonomy classification accuracyKaehler BD, Bokulich NA, McDonald D, Knight R, Caporaso JG, Huttley GA.Nat Commun. 2019
Voices in methods developmentAnikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X.Nat Methods 2019
Challenges in the construction of knowledge bases for human microbiome-disease associationsBadal VD, Wright D, Katsis Y, Kim HC, Swafford AD, Knight R, Hsu CN.Microbiome 2019
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogenyAmato KR, Mallott EK, McDonald D, Dominy NJ, Goldberg T, Lambert JE, Swedell L, Metcalf JL, Gomez A, Britton GAO, Stumpf RM, Leigh SR, Knight R.Genome Biol 2019
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic FibrosisMelnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. mSystems2019
Benchmarking urine storage and collection conditions for evaluating the female urinary microbiomeJung CE, Chopyk J, Shin JH, Lukacz ES, Brubaker L, Schwanemann LK, Knight R, Wolfe AJ, Pride DT Sci Rep2019
Gut microbiome in serious mental illnesses: A systematic review and critical evaluation. Nguyen TT, Hathaway H, Kosciolek T, Knight R, Jeste DV.Schizophr Res 2019
Expanding the scope and scale of microbiome research. Knight R, Ley RE, Raes J, Grice EA.Genome Biol 2019
A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children. Sun Z, Huang S, Zhu P, Yue F, Zhao H, Yang M, Niu Y, Jing G, Su X, Li H, Callewaert C, Knight R, Liu J, Smith E, Wei K, Xu J.mSystems 2019
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.Nat Biotechnol 2019
Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy". Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J.MBio 2019
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, Knight R, Moshiri N, Nguyen MH, Rosenthal SB, Pérez F, Rose PW.PLoS Comput Biol. 2019
Associations of the fecal microbial proteome composition and proneness to diet-induced obesity. Tran HQ, Mills RH, Peters NV, Holder MK, de Vries GJ, Knight R, Chassaing B, Gonzalez DJ, Gewirtz AT.Mol Cell Proteomics 2019
IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis.Callewaert C, Nakatsuji T, Knight R, Kosciolek T, Vrbanac A, Kotol P, Ardeleanu M, Hultsch T, Guttman-Yassky E, Bissonnette R, Silverberg JI, Krueger J, Menter A, Graham NMH, Pirozzi G, Hamilton JD, Gallo RL.J Invest Dermatol 2019
redbiom: a Rapid Sample Discovery and Feature Characterization System.McDonald D, Kaehler B, Gonzalez A, DeReus J, Ackermann G, Marotz C, Huttley G, Knight R.mSystems 2019
Quantifying and Understanding Well-to-Well Contamination in Microbiome Research. Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. mSystems 2019
Diet and the Gut Microbiome in 10-18-Month-Old Children Living in Urban Slums of Mumbai, India (OR01-08-19).Huey S, Rajagopalan K, Venkatramanan S, Udipi S, Thakker V, Thorat A, Potdar R, Haas J, Finkelstein J, Knight R, Mehta S.Curr Dev Nutr 2019
Establishing microbial composition measurement standards with reference frames.Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, Zengler K, Knight R.Nat Commun 2019
Early-Career Scientists Shaping the WorldCristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J.mSystems 2019
Farm-like indoor microbiota in non-farm homes protects children from asthma development. Kirjavainen PV, Karvonen AM, Adams RI, Täubel M, Roponen M, Tuoresmäki P, Loss G, Jayaprakash B, Depner M, Ege MJ, Renz H, Pfefferle PI, Schaub B, Lauener R, Hyvärinen A, Knight R, Heederik DJJ, von Mutius E, Pekkanen J.Nature Medicine 2019
The impact of skin care products on skin chemistry and microbiome dynamics.Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC.BMC Biology 2019
Ground beef microbiome changes with antimicrobial decontamination interventions and product storage.Weinroth MD, Britton BC, McCullough KR, Martin JN, Geornaras I, Knight R, Belk KE, Metcalf JL.PLOS ONE 2019
Is there convergence of gut microbes in blood-feeding vertebrates? Song SJ, Sanders JG, Baldassarre DT, Chaves JA, Johnson NS, Piaggio AJ, Stuckey MJ, Nováková E, Metcalf JL, Chomel BB, Aguilar-Setién A, Knight R, McKenzie VJ. Philos Trans R Soc Lond B Biol Sci. 2019
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. Cell 2019
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA 3rd; IBDMDB Investigators, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Nature 2019
Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary. Marotz C, Sharma A, Humphrey G, Gottel N, Daum C, Gilbert JA, Eloe-Fadrosh E, Knight R Biotechniques 2019
Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi. Hale VL, Tan CL, Niu K, Yang Y, Zhang Q, Knight R, Amato KR Am J Primatol 2019
Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R, Thackray VG mSystems 2019
Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment. Sprecher KE, Ritchie HK, Burke TM, Depner CM, Smits AN, Dorrestein PC, Fleshner M, Knight R, Lowry CA, Turek FW, Vitaterna MH, Wright KP Jr. Sleep 2019
Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems. Tripathi A, Xu ZZ, Xue J, Poulsen O, Gonzalez A, Humphrey G, Meehan MJ, Melnik AV, Ackermann G, Zhou D, Malhotra A, Haddad GG, Dorrestein PC, Knight R. mSystems 2019
Consent insufficient for data release-Response. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Science 2019
Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM Sci Data 2019
Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes. Thompson LR, Haroon MF, Shibl AA, Cahill MJ, Ngugi DK, Williams GJ, Morton JT, Knight R, Goodwin KD, Stingl U Appl Environ Microbiol 2019
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Checinska Sielaff A, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, Minich J, McDonald D, Mayer T, Knight R, Karouia F, Fox GE, Venkateswaran K. Microbiome 2019
A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease. Caussy C, Tripathi A, Humphrey G, Bassirian S, Singh S, Faulkner C, Bettencourt R, Rizo E, Richards L, Xu ZZ, Downes MR, Evans RM, Brenner DA, Sirlin CB, Knight R, Loomba R. Nat Commun 2019
Major shifts in gut microbiota during development and its relationship to growth in ostriches. Videvall E, Song SJ, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK. Mol Ecol 2019
The genetic basis for adaptation of model-designed syntrophic co-cultures. Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM. Exp PLoS Comput Biol 2019
Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month. Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, González A, Midtvedt T, Eggesbø M Microbiome 2019
FXR Regulates Intestinal Cancer Stem Cell Proliferation. Fu T, Coulter S, Yoshihara E, Oh TG, Fang S, Cayabyab F, Zhu Q, Zhang T, Leblanc M, Liu S, He M, Waizenegger W, Gasser E, Schnabl B, Atkins AR, Yu RT, Knight R, Liddle C, Downes M, Evans RM. Cell 2019
Engineering the microbiome for animal health and conservation. Jin Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. Exp Biol Med (Maywood) 2019
Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome. Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC. Microbiome 2019
Calour: an Interactive, Microbe-Centric Analysis Tool. Xu ZZ, Amir A, Sanders J, Zhu Q, Morton JT, Bletz MC, Tripathi A, Huang S, McDonald D, Jiang L, Knight R mSystems 2019
Toward unrestricted use of public genomic data DAmann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.Science 2019
Role of the microbiome in human development. Dominguez-Bello MG, Godoy-Vitorino F, Knight R, Blaser MJGut 2019
GABA-modulating bacteria of the human gut microbiota. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K.Nat Microbiol 2018
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS.Trends Microbiol 2018
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017. Sinha R, Ahsan H, Blaser M, Caporaso JG, Carmical JR, Chan AT, Fodor A, Gail MH, Harris CC, Helzlsouer K, Huttenhower C, Knight R, Kong HH, Lai GY, Hutchinson DLS, Le Marchand L, Li H, Orlich MJ, Shi J, Truelove A, Verma M, Vogtmann E, White O, Willett W, Zheng W, Mahabir S, Abnet C.Microbiome 2018
The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus. Vrbanac A, Riestra AM, Coady A, Knight R, Nizet V, Patras KA.BMC Microbiol 2018
Evaluating the Information Content of Shallow Shotgun Metagenomics. Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D.mSystems 2018
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L.Front Microbiol. 2018
Identifying and Predicting Novelty in Microbiome Studies. Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J.mBio 2018
Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria. Cekanaviciute E, Pröbstel AK, Thomann A, Runia TF, Casaccia P, Katz Sand I, Crabtree E, Singh S, Morrissey J, Barba P, Gomez R, Knight R, Mazmanian S, Graves J, Cree BAC, Zamvil SS, Baranzini SE.mSystems 2018
High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R.mSystems 2018
Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. Kodama WA, Xu Z, Metcalf JL, Song SJ, Harrison N, Knight R, Carter DO, Happy CB.J Forensic Sci 2018
Striped UniFrac: enabling microbiome analysis at unprecedented scale. McDonald D, Vázquez-Baeza Y, Koslicki D, McClelland J, Reeve N, Xu Z, Gonzalez A, Knight R.Nat Methods 2018
Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort. Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, Knight R, Lozupone CA, Eggesbø M.MBio 2018
Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis. Maricic I, Marrero I, Eguchi A, Nakamura R, Johnson CD, Dasgupta S, Hernandez CD, Nguyen PS, Swafford AD, Knight R, Feldstein AE, Loomba R, Kumar V J Immunol 2018
Preserving microbial diversity. Bello MGD, Knight R, Gilbert JA, Blaser MJ Science 2018
Qiita: rapid, web-enabled microbiome meta-analysis. Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R Nat Methods 2018
Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects. Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R, Jeste DV Schizophr Res. 2018
Niche partitioning of a pathogenic microbiome driven by chemical gradients. Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC Sci Adv. 2018
Comparison of oral collection methods for studies of microbiota. Vogtmann E, Chen J, Kibriya MG, Amir A, Shi J, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Barmon B, Knight R, Chia N, Ahsan H, Abnet CC, Sinha R Cancer Epidemiol Biomarkers Prev 2018
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R Clin Gastroenterol Hepatol. 2018
Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R Microbiologyopen 2018
Regional variation limits applications of healthy gut microbiome reference ranges and disease models. He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW Nat Med. 2018
Links between environment, diet, and the hunter-gatherer microbiome Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL Gut Microbes 2018
Are microbiome studies ready for hypothesis-driven research? Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R. Curr Opin Microbiol. 2018
Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Zarrinpar A, Chaix A, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S. Nat Commun. 2018
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. Nat Commun. 2018
Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. Amato KR, G Sanders J, Song SJ, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S. ISME J 2018
Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi Q, Knight R, Glavina Del Rio T, Tringe SG, Buckler ES, Dangl JL, Ley RE. Proc Natl Acad Sci U S A 2018
Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus. Lavrinienko A, Mappes T, Tukalenko E, Mousseau TA, Møller AP, Knight R, Morton JT, Thompson LR, Watts PC. ISME J 2018
The gut-liver axis and the intersection with the microbiome. Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, Knight R. Nat Rev Gastroenterol Hepatol 2018
Best practices for analysing microbiomes. Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. Nat Rev Microbiol 2018
Ancient Thali Diet: Gut Microbiota, Immunity, and Health. Shondelmyer K, Knight R, Sanivarapu A, Ogino S, Vanamala JKP. Yale J Biol Med 2018
Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'omics. Maurer-Alcalá XX, Yan Y, Pilling O, Knight R, Katz LA Genome Biol Evol. 2018
Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome. Tripathi A, Melnik AV, Xue J, Poulsen O, Meehan MJ, Humphrey G, Jiang L, Ackermann G, McDonald D, Zhou D, Knight R, Dorrestein PC, Haddad GG mSystems 2018
The gut microbiome of nonhuman primates: Lessons in ecology and evolution. Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ Am J Primatol. 2018
Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis. He Y, Kosciolek T, Tang J, Zhou Y, Li Z, Ma X, Zhu Q, Yuan N, Yuan L, Li C, Jin K, Knight R, Tsuang MT, Chen X Eur Psychiatry. 2018
Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. Kharbush JJ, Thompson LR, Haroon MF, Knight R, Aluwihare LI FEMS Microbiol Ecol. 2018
Methods for phylogenetic analysis of microbiome data. Washburne AD, Morton JT, Sanders J, McDonald D, Zhu Q, Oliverio AM, Knight R Nat Microbiol. 2018
Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. Lapek JD Jr, Mills RH, Wozniak JM, Campeau A, Fang RH, Wei X, van de Groep K, Perez-Lopez A, van Sorge NM, Raffatellu M, Knight R, Zhang L, Gonzalez DJ Nat Cell Syst. 2018
Best practices for analysing microbiomes. Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC Nat Rev Microbiol 2018
Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Michaud JM, Thompson LR, Kaul D, Espinoza JL, Richter RA, Xu ZZ, Lee C, Pham KM, Beall CM, Malfatti F, Azam F, Knight R, Burkart MD, Dupont CL, Prather KA Nat Commun 2018
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J Microbiome 2018
American Gut: an Open Platform for Citizen Science Microbiome Research. McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R. mSystems 2018
The gut-liver axis and the intersection with the microbiome. Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, Knight R Nat Rev Gastroenterol Hepatol 2018
Exposure to toxic metals triggers unique responses from the rat gut microbiota. Richardson JB, Dancy BCR, Horton CL, Lee YS, Madejczyk MS, Xu ZZ, Ackermann G, Humphrey G, Palacios G, Knight R, Lewis JA Sci Rep 2018
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R mSystems 2018
Hopanoid-producing bacteria in the Red Sea include the major marine nitrite-oxidizers Kharbush JJ, Thompson LR, Haroon MF, Knight R, Aluwihare LI. FEMS Microbiol Ecol. 2018
Earth Microbiome Project and Global Systems Biology Gilbert JA, Jansson JK, Knight R mSystems 2018
Current understanding of the human microbiome Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R Nat Med 2018
Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space Knight R Breastfeed Med 2018
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R mSystems 2018
Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome McCall LI, Tripathi A, Vargas F, Knight R, Dorrestein PC, Siqueira-Neto JLPLoS Negl Trop Dis. 2018
Bacterial density rather than diversity correlates with hatching success across different avian species Peralta-Sánchez JM, Martín-Platero AM, Wegener-Parfrey L, Martínez-Bueno M, Rodríguez-Ruano S, Navas-Molina JA, Vázquez-Baeza Y, Martín-Gálvez D, Martín-Vivaldi M, Ibáñez-Álamo JD, Knight R, Soler JJFEMS Microbiol Ecol 2018
Creating a 3D microbial and chemical snapshot of a human habitat Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PCSci Rep 2018
Improving saliva shotgun metagenomics by chemical host DNA depletion Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler KMicrobiome 2018
Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models Belk A, Xu ZZ, Carter DO, Lynne A, Bucheli S, Knight R, Metcalf JLGenes (Basel)2018
Coprolites reveal ecological interactions lost with the extinction of New Zealand birds Boast AP, Weyrich LS, Wood JR, Metcalf JL, Knight R, Cooper AProc Natl Acad Sci U S A 2018
Bacterial density rather than diversity correlates with hatching success across different avian species Peralta-Sánchez JM, Martín-Platero AM, Wegener-Parfrey L, Martínez-Bueno M, Rodríguez-Ruano S, Navas-Molina JA, Vázquez-Baeza Y, Martín-Gálvez D, Martín-Vivaldi M, Ibáñez-Álamo JD, Knight R, Soler JJFEMS Microbiol Ecol 2018
Expanding our Understanding of the Role of the Microbiome in Health and Disease Knight, R Arch Med Res 2018
Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction Zhou Y, Xu ZZ, He Y, Yang Y, Liu L, Lin Q, Nie Y, Li M, Zhi F, Liu S, Amir A, González A, Tripathi A, Chen M, Wu GD, Knight R, Zhou H, Chen Y. mSystems 2018
Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics) Maurer-Alcalá XX, Knight R, Katz LAMBio 2018
The human microbiome in evolution Davenport ER, Sanders JG, Song SJ, Amato KR, Clark AG, Knight RBMC Biol 2017
Enterotypes in the landscape of gut microbial community composition Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.Nat Microbiol 2017
Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality Raulo A, Ruokolainen L, Lane A, Amato K, Knight R, Leigh S, Stumpf R, White B, Nelson KE, Baden AL, Tecot SR. J Anim Ecol 2017
Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes Jiang L, Amir A, Morton JT, Heller R, Arias-Castro E, Knight R mSystems 2017
Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M Nature 2017
Evaluating the impact of domestication and captivity on the horse gut microbiomeMetcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L Sci Rep. 2017
Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human LungGarg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC Cell Host Microbe 2017
A Communal Catalogue Reveals Earth's Multiscale Microbial DiversityThompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. Nature 2017
Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and StreptococcusDahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, Knight R, Stigum H, Eggesbø M. PLoS One 2017
Guiding longitudinal sampling in IBD cohortsVázquez-Baeza Y, Gonzalez A, Xu ZZ, Washburne A, Herfarth HH, Sartor RB, Knight R. Gut 2017
Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and MetabolomeMaier TV, Lucio M, Lee LH, VerBerkmoes NC, Brislawn CJ, Bernhardt J, Lamendella R, McDermott JE, Bergeron N, Heinzmann SS, Morton JT, González A, Ackermann G, Knight R, Riedel K, Krauss RM, Schmitt-Kopplin P, Jansson JK. mSystems 2017
Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their MetabolitesReddivari L, Veeramachaneni DNR, Walters WA, Lozupone C, Palmer J, Hewage MKK, Bhatnagar R, Amir A, Kennett MJ, Knight R, Vanamala JKP mSystems 2017
Impacts of the Human Gut Microbiome on TherapeuticsVázquez-Baeza Y, Callewaert C, Debelius J, Hyde E, Marotz C, Morton JT, Swafford A, Vrbanac A, Dorrestein PC, Knight R. Annu Rev Pharmacol Toxicol 2017
Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest AntsSanders JG, Lukasik P, Frederickson ME, Russell JA, Koga R, Knight R, Pierce NE Integr Comp Biol. 2017
The sponge microbiome projectMoitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T Gigascience 2017
The Effects of Captivity on the Mammalian Gut MicrobiomeMcKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore A, Seguin-Orlando A, Feh C, Orlando L, Mendelson JR, Sanders J, Knight R. Integr Comp Biol 2017
Strains, functions and dynamics in the expanded Human Microbiome ProjectLloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. Nature 2017
Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse modelsCekanaviciute E, Yoo BB, Runia TF, Debelius JW, Singh S, Nelson CA, Kanner R, Bencosme Y, Lee YK, Hauser SL, Crabtree-Hartman E, Sand IK, Gacias M, Zhu Y, Casaccia P, Cree BAC, Knight R, Mazmanian SK, Baranzini SE Proc Natl Acad Sci U S A 2017
Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic InfectionMcCall L.I., Morton J.T., Bernatchez J.A., Siquiera-Neto J.L., Knight R., Dorrestein P.C., McKerrow J.H. Anal Chem. 2017
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of TanzaniaSmits S.A., Leach J., Sonnenburg E.D., Gonzalez C.G., Lichtman J.S., Reid G., Knight R., Manjurano A., Changalucha J., Elias J.E., Dominguez-Bello M.G., Sonnenburg J.L. Science: Vol. 357, Issue 6353, pp. 802-8062017
Genetic influences on the human oral microbiomeDemmitt B.A., Corley R.P., Huibregtse B.M., Keller M.C., Hewitt J.K., McQueen M.B., Knight R., McDermott I., Krauter K.S. BMC Genomics 201718:6592017
The sponge microbiome projectMoitinho-Silva L., Nielsen S., Amir A., Gonzalez A., Ackermann G., Cerrano C., Astudillo-Garcia C., Easson C., Sipkema D., Liu F., Steinert G., Kotoulas G., McCormack G.P., Feng G., Bell J.J., Vicente J., Björk J.R., Montoya J.M., Olson J.B., Reveillaud J., Steindler L., Pineda M., Marra M.V., Ilan M., Taylor M.W., Polymenakou P., Erwin P.M., Schupp P.J., Simister R.L., Knight R., Thacker R.W., Costa R., Hill R.T., Lopez-Legentil S., Dailianis T., Ravasi T., Hentschel U., Li Z., Webster N.S., Thomas T.GigaScience2017
Leukotriene B4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progressionJala V.R., Maturu P., Bodduluri S.R., Krishnan E., Mathis S., Subbarao K., Wang M., Jenson A.B., Proctor M.L., Rouchka E.C., Knight R., Haribabu B.OncoImmunology2017
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. R. M. Bowers, N. C. Kypides, R. Stepanauskas, M. Harmon-Smith, D. Doud, T. B. K. Reddy, F. Schulz, J. Jarett, A. R. Rivers, E. A Eloe-Fadrosh, S. G. Tringe, N. N. Ivanova, A. Copeland, A. Clum, E. D. Becraft, R. R. Malstrom, B. Birren, M. Podar, P. Bork, G. M. Weinstock, G. M. Garrity, J. A. Dodsworth, S. Yooseph, G. Sutton, F. O. Glöckner, J. A. Gilbert, W. C. Nelson, S. J. Hallam, S. P. Jungbluth, T. J. G. Ettema, S. Tighe, K. T. Konstantinidis, W. Liu, B. J. Baker, T. Rattei, J. A. Eisen, B. Hedlund, K. D. McMahon, N. Fierer, R. Knight, R. Finn, G. Cochrane, I. Karsch-Mizrachi, G. W. Tyson, C. Rinke, A. Lapidus, F. Meyer, P. Yilmaz, D. H. Parks, A. M. Eren, L. Schriml, J. F. Banfield, P. Hugenholtz, T. WolkeNat Biotechnol2017
Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey SpeciesV. L. Hale, C. L. Tan, K. Niu, Y. Yang, R. Knight, Q. Zhang, D. Cui and K. R. AmatoMicrob Ecol 2017
The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory StudyS. M. J. Hemmings, S. Malan-Muller, L. L. van den Heuvel, B. A. Demmitt, M. A. Stanislawski, D. G. Smith, A. D. Bohr, C. E. Stamper, E. R. Hyde, J. T. Morton, C. A. Marotz, P. H. Siebler, M. Braspenning, W. Van Criekinge, A. J. Hoisington, L. A. Brenner, T. T. Postolache, M. B. McQueen, K. S. Krauter, R. Knight, S. Seedat and C. A. LowryPsychosom Med 2017
Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes"A. M. Linz, B. C. Crary, A. Shade, S. Owens, J. A. Gilbert, R. Knight and K. D. McMahonmSphere 2, (4) 2017
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal SamplesA. V. Melnik, R. R. da Silva, E. R. Hyde, A. A. Aksenov, F. Vargas, A. Bouslimani, I. Protsyuk, A. K. Jarmusch, A. Tripathi, T. Alexandrov, R. Knight and P. C. DorresteinAnal Chem 89, (14) 7549-75592017
Intermittent Hypoxia and Hypercapnia Accelerate Atherosclerosis, Partially via Trimethylamine-OxideJ. Xue, D. Zhou, O. Poulsen, T. Imamura, Y. H. Hsiao, T. H. Smith, A. Malhotra, P. Dorrestein, R. Knight and G. G. HaddadAm J Respir Cell Mol Biol 20172017
Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin ResistanceV. Charepalli, L. Reddivari, S. Radhakrishnan, E. Eriksson, X. Xiao, S. W. Kim, F. Shen, M. Vijay-Kumar, Q. Li, V. B. Bhat, R. Knight and J. K. P. Vanamala Cancer Prev Res (Phila) 2017
The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory StudyS. M. J. Hemmings, S. Malan-Muller, L. L. van den Heuvel, B. A. Demmitt, M. A. Stanislawski, D. G. Smith, A. D. Bohr, C. E. Stamper, E. R. Hyde, J. T. Morton, C. A. Marotz, P. H. Siebler, M. Braspenning, W. Van Criekinge, A. J. Hoisington, L. A. Brenner, T. T. Postolache, M. B. McQueen, K. S. Krauter, R. Knight, S. Seedat and C. A. LowryPsychosom Med2017
Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog LakesA. M. Linz, B. C. Crary, A. Shade, S. Owens, J. A. Gilbert, R. Knight and K. D. McMahonmSphere 2, (3) 2017
DNA extraction for streamlined metagenomics of diverse environmental samplesC. Marotz, A. Amir, G. Humphrey, J. Gaffney, G. Gogul and R. KnightBiotechniques 62, (6) 290-2932017
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal SamplesA. V. Melnik, R. R. da Silva, E. R. Hyde, A. A. Aksenov, F. Vargas, A. Bouslimani, I. Protsyuk, A. K. Jarmusch, A. Tripathi, T. Alexandrov, R. Knight and P. C. DorresteinAnal Chem 2017
Significant Impacts of Increasing Aridity on the Arid Soil MicrobiomeJ. W. Neilson, K. Califf, C. Cardona, A. Copeland, W. van Treuren, K. L. Josephson, R. Knight, J. A. Gilbert, J. Quade, J. G. Caporaso and R. M. MaiermSystems 2, (3) 22017
Bacterial colonization and succession in a newly opened hospitalS. Lax, N. Sangwan, D. Smith, P. Larsen, K. M. Handley, M. Richardson, K. Guyton, M. Krezalek, B. D. Shogan, J. Defazio, I. Flemming, B. Shakhsheer, S. Weber, E. Landon, S. Garcia-Houchins, J. Siegel, J. Alverdy, R. Knight, B. Stephens and J. A. GilbertScience Translational Medicine 9(391)2017
Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big DataJ. Xu, B. Ma, X. Su, S. Huang, X. Xu, X. Zhou, W. E. Huang and R. KnightEngineering 3, (1) 66-702017
Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping A. Amir, D. McDonald, J. A. Navas-Molina, J. Debelius, J. T. Morton, E. Hyde, A. Robbins-Pianka and R. Knight mSystems 2, (2) 2017
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns A. Amir, D. McDonald, J. A. Navas-Molina, E. Kopylova, J. T. Morton, Z. Zech Xu, E. P. Kightley, L. R. Thompson, E. R. Hyde, A. Gonzalez and R. Knight mSystems 2, (2)2017
Mass Spectrometry Based Molecular 3D-Cartography of Plant Metabolites D. J. Floros, D. Petras, C. A. Kapono, A. V. Melnik, T. J. Ling, R. Knight and P. C. Dorrestein Front Plant Sci 8, 4292017
A Microbiome Foundation for the Study of Crohn's Disease D. Gevers, S. Kugathasan, D. Knights, A. D. Kostic, R. Knight and R. J. Xavier Cell Host Microbe 21, (3) 301-3042017
Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome E. M. Hill-Burns, J. W. Debelius, J. T. Morton, W. T. Wissemann, M. R. Lewis, Z. D. Wallen, S. D. Peddada, S. A. Factor, E. Molho, C. P. Zabetian, R. Knight and H. Payami Mov Disord 32, (5) 739-7492017
Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease S. Khanna, Y. Vazquez-Baeza, A. Gonzalez, S. Weiss, B. Schmidt, D. A. Muniz-Pedrogo, J. F. Rainey, 3rd, P. Kammer, H. Nelson, M. Sadowsky, A. Khoruts, S. L. Farrugia, R. Knight, D. S. Pardi and P. C. Kashyap Microbiome 5, (1) 552017
Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape H. C. King, T. Khera-Butler, P. James, B. B. Oakley, G. Erenso, A. Aseffa, R. Knight, E. M. Wellington and O. Courtenay PLoS One 12, (3) e01738112017
The Microbiome and Human Biology R. Knight, C. Callewaert, C. Marotz, E. R. Hyde, J. W. Debelius, D. McDonald and M. L. Sogin Annu Rev Genomics Hum Genet 2017
Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algaeT. Luzzatto Knaan, N. Garg, M. Wang, E. Glukhov, Y. Peng, G. Ackermann, A. Amir, B. M. Duggan, S. Ryazanov, L. Gerwick, R. Knight, T. Alexandrov, N. Bandeira, W. H. Gerwick and P. C. Dorrestein Elife 62017
Microbiome Tools for Forensic Science J. L. Metcalf, Z. Z. Xu, A. Bouslimani, P. Dorrestein, D. O. Carter and R. Knight Trends Biotechnol 2017
Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus E. Novakova, D. C. Woodhams, S. M. Rodriguez-Ruano, R. M. Brucker, J. W. Leff, A. Maharaj, A. Amir, R. Knight and J. Scott Front Microbiol 8, 5262017
Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh E. Vogtmann, J. Chen, M. G. Kibriya, Y. Chen, T. Islam, M. Eunes, A. Ahmed, J. Naher, A. Rahman, A. Amir, J. Shi, C. C. Abnet, H. Nelson, R. Knight, N. Chia, H. Ahsan and R. Sinha Appl Environ Microbiol 83, (10) 2017
An Elegan(t) Screen for Drug-Microbe Interactions A. Vrbanac, J. W. Debelius, L. Jiang, J. T. Morton, P. Dorrestein and R. Knight Cell Host Microbe 21, (5) 555-5562017
Normalization and microbial differential abundance strategies depend upon data characteristics S. Weiss, Z. Z. Xu, S. Peddada, A. Amir, K. Bittinger, A. Gonzalez, C. Lozupone, J. R. Zaneveld, Y. Vazquez-Baeza, A. Birmingham, E. R. Hyde and R. Knight Microbiome 5, (1) 272017
Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical PrimateK. R. Amato, S. Van Belle, A. Di Fiore, A. Estrada, R. Stumpf, B. White, K. E. Nelson, R. Knight and S. R. LeighMicrobial Ecology 1-92017
Dynamics of the human gut microbiome in inflammatory bowel diseaseJ. Halfvarson, C. J. Brislawn, R. Lamendella, Y. Vázquez-Baeza, W. A. Walters, L. M. Bramer, M. D'Amato, F. Bonfiglio, D. McDonald and A. GonzalezNature Microbiology 2, 170042017
Origin of microbial biomineralization and magnetotaxis during the ArcheanW. Lin, G. A. Paterson, Q. Zhu, Y. Wang, E. Kopylova, Y. Li, R. Knight, D. A. Bazylinski, R. Zhu and J. L. KirschvinkProceedings of the National Academy of Sciences 2016146542017
Balance Trees Reveal Microbial Niche DifferentiationJ. T. Morton, J. Sanders, R. A. Quinn, D. McDonald, A. Gonzalez, Y. Vázquez-Baeza, J. A. Navas-Molina, S. J. Song, J. L. Metcalf and E. R. HydemSystems 2, (1) e00162-162017
Uncovering the Horseshoe Effect in Microbial AnalysesJ. T. Morton, L. Toran, A. Edlund, J. L. Metcalf, C. Lauber and R. KnightmSystems 2, (1) e00166-162017
Gut Instinct: Creating scientific theories with online learnersV. Pandey, A. Amir, J. Debelius, E. R. Hyde, T. Kosciolek, R. Knight and S. Klemmer2017
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopesL. R. Thompson, K. Nikolakakis, S. Pan, J. Reed, R. Knight and E. G. RubyEnvironmental Microbiology2017
Bringing the Dynamic Microbiome to Life with AnimationsY. Vázquez-Baeza, A. Gonzalez, L. Smarr, D. McDonald, J. T. Morton, J. A. Navas-Molina and R. KnightCell Host Microbe 21, (1) 7-102017
Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD riskN. Bergeron, P. T. Williams, R. Lamendella, N. Faghihnia, A. Grube, X. Li, Z. Wang, R. Knight, J. K. Jansson, S. L. Hazen and R. M. KraussBr J Nutr 116, (12) 2020-20292016
Lifestyle chemistries from phones for individual profilingA. Bouslimani, A. V. Melnik, Z. Xu, A. Amir, R. R. da Silva, M. Wang, N. Bandeira, T. Alexandrov, R. Knight and P. C. DorresteinProceedings of the National Academy of Sciences 113, (48) E7645-E76542016
Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co‐utilization in Escherichia coliJ. Groot, S. C. Cepress‐Mclean, A. Robbins‐Pianka, R. Knight and R. T. GillBiotechnology and Bioengineering2016
Antibiotic discovery is a walk in the parkL.-F. Nothias, R. Knight and P. C. DorresteinProceedings of the National Academy of Sciences 113, (51) 14477-144792016
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s DiseaseT. R. Sampson, J. W. Debelius, T. Thron, S. Janssen, G. G. Shastri, Z. E. Ilhan, C. Challis, C. E. Schretter, S. Rocha and V. GradinaruCell 167, (6) 1469-1480. e122016
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's DiseaseT. R. Sampson, J. W. Debelius, T. Thron, S. Janssen, G. G. Shastri, Z. E. Ilhan, C. Challis, C. E. Schretter, S. Rocha, V. Gradinaru, M. F. Chesselet, A. Keshavarzian, K. M. Shannon, R. Krajmalnik-Brown, P. Wittung-Stafshede, R. Knight and S. K. MazmanianCell 167, (6) 1469-1480.e122016
Intestinal adaptation in proximal and distal segments: Two epithelial responses diverge after intestinal separationK. Schall, K. Holoyda, M. Isani, C. Schlieve, T. Salisbury, T. Khuu, J. Debelius, R. Moats, H. Pollack and C. LienSurgery2016
Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha DiversityR. S. Thompson, R. Roller, A. Mika, B. N. Greenwood, R. Knight, M. Chichlowski, B. M. Berg and M. FleshnerFront Behav Neurosci 10, 2402016
Comparison of collection methods for fecal samples in microbiome studiesE. Vogtmann, J. Chen, A. Amir, J. Shi, C. C. Abnet, H. Nelson, R. Knight, N. Chia and R. SinhaAmerican Journal of Epidemiology2016
Using machine learning to identify major shifts in human gut microbiome protein family abundance in diseaseM. Yazdani, B. C. Taylor, J. W. Debelius, W. Li, R. Knight and L. SmarrBig Data (Big Data), 2016 IEEE International Conference on2016
Using the gut microbiota as a novel tool for examining colobine primate GI healthK. R. Amato, J. L. Metcalf, S. J. Song, V. L. Hale, J. Clayton, G. Ackermann, G. Humphrey, K. Niu, D. Cui and H. ZhaoGlobal Ecology and Conservation 7, 225-2372016
Heritable components of the human fecal microbiome are associated with visceral fatM. Beaumont, J. K. Goodrich, M. A. Jackson, I. Yet, E. R. Davenport, S. Vieira-Silva, J. Debelius, T. Pallister, M. Mangino and J. RaesGenome Biol 17, (1) 1892016
Precision Medicine in Alcoholic and Non-Alcoholic Fatty Liver Disease via Modulating the Gut MicrobiotaS. Bluemel, B. Williams, R. Knight and B. SchnablAmerican Journal of Physiology-Gastrointestinal and Liver Physiology ajpgi. 00245.20162016
Tiny microbes, enormous impacts: what matters in gut microbiome studies?J. Debelius, S. J. Song, Y. Vazquez-Baeza, Z. Z. Xu, A. Gonzalez and R. KnightGenome Biol 17, (1) 2172016
Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project CohortA. Gonzalez, E. Hyde, N. Sangwan, J. A. Gilbert, E. Viirre and R. KnightmSystems 1, (5) e00105-162016
Effects of field conditions on fecal microbiotaV. L. Hale, C. L. Tan, K. Niu, Y. Yang, D. Cui, H. Zhao, R. Knight and K. R. AmatoJ Microbiol Methods 130, 180-1882016
The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their HabitatE. R. Hyde, J. A. Navas-Molina, S. J. Song, J. G. Kueneman, G. Ackermann, C. Cardona, G. Humphrey, D. Boyer, T. Weaver and J. R. MendelsonmSystems 1, (4) e00046-162016
Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivityJ. G. Kueneman, D. C. Woodhams, R. Harris, H. M. Archer, R. Knight and V. J. McKenzieProc. R. Soc. B2016
Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic StudiesE. Loftfield, E. Vogtmann, J. N. Sampson, S. C. Moore, H. Nelson, R. Knight, N. Chia and R. SinhaCancer Epidemiology and Prevention Biomarkers2016
Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intakeS. Mandal, K. M. Godfrey, D. McDonald, W. V. Treuren, J. V. Bjørnholt, T. Midtvedt, B. Moen, K. Rudi, R. Knight and A. L. BrantsæterMicrobiome 4, (1) 552016
Culturing: Looking it up in our gutC. Marotz and R. KnightNature Microbiology 1, 161692016
Let researchers try new pathsT. Oni, F. Sciarrino, G. Adesso and R. KnightNature 538, (7626) 451-4532016
Integrating citizen science with online learning to ask better questionsV. Pandey, S. Klemmer, A. Amir, J. Debelius, E. R. Hyde, T. Kosciolek and R. KnightarXiv preprint arXiv:1609.057632016
Mass Spectrometry-Based Visualization of Molecules Associated with Human HabitatsD. Petras, L.-F. Nothias, R. A. Quinn, T. Alexandrov, N. Bandeira, A. Bouslimani, G. Castro-Falcón, L. Chen, T. Dang and D. J. FlorosAnalytical Chemistry2016
Prevalence and genetic diversity of Blastocystis in family units living in the United StatesP. D. Scanlan, R. Knight, S. J. Song, G. Ackermann and P. D. CotterInfection, Genetics and Evolution 45, 95-972016
Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networksY. Vázquez-Baeza, E. R. Hyde, J. S. Suchodolski and R. KnightNature Microbiology 1, 161772016
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular NetworkingM. Wang, J. J. Carver, V. V. Phelan, L. M. Sanchez, N. Garg, Y. Peng, D. D. Nguyen, J. Watrous, C. A. Kapono and T. Luzzatto-KnaanNat Biotechnol 34, (8) 828-8372016
Role of the microbiome, probiotics, and ‘dysbiosis therapy’in critical illnessP. E. Wischmeyer, D. McDonald and R. KnightCurrent Opinion in Critical Care 22, (4) 347-3532016
Microbiome-wide association studies link dynamic microbial consortia to diseaseJ. A. Gilbert, R. A. Quinn, J. Debelius, Z. Z. Xu, J. Morton, N. Garg, J. K. Jansson, P. C. Dorrestein and R. KnightNature 535, (7610) 94-1032016
The Microbiota, Immunoregulation, and Mental Health: Implications for Public HealthC. A. Lowry, D. G. Smith, P. H. Siebler, D. Schmidt, C. E. Stamper, J. E. Hassell, Jr., P. S. Yamashita, J. H. Fox, S. O. Reber, L. A. Brenner, A. J. Hoisington, T. T. Postolache, K. A. Kinney, D. Marciani, M. Hernandez, S. M. Hemmings, S. Malan-Muller, K. P. Wright, R. Knight, C. L. Raison and G. A. RookCurr Environ Health Rep2016
Microbiology of deathJ. L. Metcalf, D. O. Carter and R. KnightCurrent Biology 26, (13) R561-R5632016
Metagenomic covariation along densely sampled environmental gradients in the Red SeaL. R. Thompson, G. J. Williams, M. F. Haroon, A. Shibl, P. Larsen, J. Shorenstein, R. Knight and U. StinglIsme journal2016
Extreme Dysbiosis of the Microbiome in Critical IllnessP. Wischmeyer, G. Ackermann, D. Mcdonald, C. Baird, D. Heyland and R. KnightLIPPINCOTT WILLIAMS & WILKINS2016
Host age, social group, and habitat type influence the gut microbiota of wild ring?tailed lemurs (Lemur catta)G. Bennett, M. Malone, M. L. Sauther, F. P. Cuozzo, B. White, K. E. Nelson, R. M. Stumpf, R. Knight, S. R. Leigh and K. R. AmatoAmerican Journal of Primatology 20162016
Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century ChallengesM. J. Blaser, Z. G. Cardon, M. K. Cho, J. L. Dangl, T. J. Donohue, J. L. Green, R. Knight, M. E. Maxon, T. R. Northen and K. S. PollardMBio 7, (3) e00714-162016
mockrobiota: a public resource for microbiome bioinformatics benchmarkingN. A. Bokulich, J. R. Rideout, W. G. Mercurio, B. Wolfe, C. F. Maurice, R. J. Dutton, P. J. Turnbaugh, R. Knight and J. G. CaporasoPeerJ Preprints2016
Microbial Skin Inhabitants: Friends ForeverP. C. Dorrestein, R. L. Gallo and R. KnightCell 165, (4) 771-7722016
Avoiding Pandemic Fears in the Subway and Conquering the PlatypusA. Gonzalez, Y. Vázquez-Baeza, J. Pettengill, A. Ottesen, D. McDonald and R. KnightmSystems 1, (3) e00050-162016
Genetic Determinants of the Gut Microbiome in UK TwinsJ. K. Goodrich, E. R. Davenport, M. Beaumont, M. A. Jackson, R. Knight, C. Ober, T. D. Spector, J. T. Bell, A. G. Clark and R. E. LeyCell Host Microbe 19, (5) 731-432016
Stress response, gut microbial diversity and sexual signals correlate with social interactionsI. I. Levin, D. M. Zonana, B. K. Fosdick, S. J. Song, R. Knight and R. J. SafranBiology Letters 12, (6) 201603522016
Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in miceS. O. Reber, P. H. Siebler, N. C. Donner, J. T. Morton, D. G. Smith, J. M. Kopelman, K. R. Lowe, K. J. Wheeler, J. H. Fox and J. E. HassellProceedings of the National Academy of Sciences 2016003242016
Fecal Microbiome in Epidemiologic Studies—ResponseR. Sinha, E. Vogtmann, J. Chen, A. Amir, J. Shi, J. Sampson, R. Flores, R. Knight and N. ChiaCancer Epidemiology Biomarkers & Prevention 25, (5) 870-8712016
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field StudiesS. J. Song, A. Amir, J. L. Metcalf, K. R. Amato, Z. Z. Xu, G. Humphrey and R. KnightmSystems 1, (3) e00021-162016
Diversity, structure and convergent evolution of the global sponge microbiomeT. Thomas, L. Moitinho-Silva, M. Lurgi, J. R. Bjork, C. Easson, C. Astudillo-Garcia, J. B. Olson, P. M. Erwin, S. Lopez-Legentil, H. Luter, A. Chaves-Fonnegra, R. Costa, P. J. Schupp, L. Steindler, D. Erpenbeck, J. Gilbert, R. Knight, G. Ackermann, J. Victor Lopez, M. W. Taylor, R. W. Thacker, J. M. Montoya, U. Hentschel and N. S. WebsterNat Commun 7, 118702016
The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic diseaseM. M. Wieck, J. W. Debelius, R. G. Spurrier, A. Trecartin, R. Knight and T. C. GrikscheitSurgery2016
Role of the microbiome, probiotics, and ‘dysbiosis therapy’in critical illnessP. E. Wischmeyer, D. McDonald and R. KnightCurrent Opinion in Critical Care 22, (4) 347-3532016
From Sample to Multi-Omics Conclusions in under 48 HoursR. A. Quinn, J. A. Navas-Molina, E. R. Hyde, S. J. Song, Y. Vázquez-Baeza, G. Humphrey, J. Gaffney, J. J. Minich, A. V. Melnik and J. HerschendmSystems 1, (2)2016
Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate speciesK. R. Amato, R. Martinez-Mota, N. Righini, M. Raguet-Schofield, F. P. Corcione, E. Marini, G. Humphrey, G. Gogul, J. Gaffney, E. Lovelace, L. Williams, A. Luong, M. G. Dominguez-Bello, R. M. Stumpf, B. White, K. E. Nelson, R. Knight and S. R. LeighOecologia 180, (3) 717-332016
The impact of kinship and social contact on the gut microbiota of wild, black howler monkeys (Alouatta pigra)K. R. Amato, S. Van Belle, A. Di Fiore, A. Estrada, R. Stumpf, B. White, K. Nelson, R. Knight and S. R. LeighJ Microbiol Biol Educ. 2016 Mar; 17(1): 46–50.2016
Tools for the Microbiome: Nano and BeyondJ. S. Biteen, P. C. Blainey, Z. G. Cardon, M. Chun, G. M. Church, P. C. Dorrestein, S. E. Fraser, J. A. Gilbert, J. K. Jansson, R. Knight, J. F. Miller, A. Ozcan, K. A. Prather, S. R. Quake, E. G. Ruby, P. A. Silver, S. Taha, G. van den Engh, P. S. Weiss, G. C. Wong, A. T. Wright and T. D. YoungACS Nano 10, (1) 6-372016
Geography and location are the primary drivers of office microbiome compositionJ. H. Chase, J. Fouquier, M. Zare, D. L. Sonderegger, R. Knight, S. Kelley, J. A. Siegel and J. G. CaporasoPeerJ Preprints2016
Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut ProjectJ. W. Debelius, Y. Vazquez-Baeza, D. McDonald, Z. Xu, E. Wolfe and R. KnightJ Microbiol Biol Educ 17, (1) 46-502016
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transferM. G. Dominguez-Bello, K. M. De Jesus-Laboy, N. Shen, L. M. Cox, A. Amir, A. Gonzalez, N. A. Bokulich, S. J. Song, M. Hoashi, J. I. Rivera-Vinas, K. Mendez, R. Knight and J. C. ClementeNat Med 22, (3) 250-32016
ghost-tree: creating hybrid-gene phylogenetic trees for diversity analysesJ. Fouquier, J. R. Rideout, E. Bolyen, J. Chase, A. Shiffer, D. McDonald, R. Knight, J. G. Caporaso and S. T. KelleyMicrobiome 4, (1) 112016
Les grands pouvoirs des bactériesR. Knight and B. BuhlerMarabout2016
Open-Source Sequence Clustering Methods Improve the State Of the ArtE. Kopylova, J. A. Navas-Molina, C. Mercier, Z. Z. Xu, F. Mahé, Y. He, H.-W. Zhou, T. Rognes, J. G. Caporaso and R. KnightmSystems 1, (1)3-152016
Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas)J. G. Kueneman, D. C. Woodhams, W. Van Treuren, H. M. Archer, R. Knight and V. J. McKenzieIsme j 10, (4) 934-442016
Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander SkinA. H. Loudon, A. Venkataraman, W. Van Treuren, D. C. Woodhams, L. W. Parfrey, V. J. McKenzie, R. Knight, T. M. Schmidt and R. N. HarrisFront Microbiol 72016
Microbial community assembly and metabolic function during mammalian corpse decompositionJ. L. Metcalf, Z. Z. Xu, S. Weiss, S. Lax, W. Van Treuren, E. R. Hyde, S. J. Song, A. Amir, P. Larsen, N. Sangwan, D. Haarmann, G. C. Humphrey, G. Ackermann, L. R. Thompson, C. Lauber, A. Bibat, C. Nicholas, M. J. Gebert, J. F. Petrosino, S. C. Reed, J. A. Gilbert, A. M. Lynne, S. R. Bucheli, D. O. Carter and R. KnightScience 351, (6269) 158-622016
Keemei: cloud-based validation of tabular bioinformatics file formats in Google SheetsJ. R. Rideout, J. H. Chase, E. Bolyen, G. Ackermann, A. Gonzalez, R. Knight and J. G. CaporasoPeerJ PrePrints 42016
Walls talk: Microbial biogeography of homes spanning urbanizationJ. F. Ruiz-Calderon, H. Cavallin, S. J. Song, A. Novoselac, L. R. Pericchi, J. N. Hernandez, R. Rios, O. H. Branch, H. Pereira, L. C. Paulino, M. J. Blaser, R. Knight and M. G. Dominguez-BelloSci Adv 2, (2)2016
"Fecal microbiome in epidemiologic studies" - ResponseR. Sinha, E. Vogtmann, J. Chen, A. Amir, J. Shi, J. N. Sampson, R. Flores, R. Knight and N. ChiaCancer Epidemiol Biomarkers Prev2016
Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon EnvironmentsL. K. Ursell, A. Robbins-Pianka, N. Scott, A. Gonzalez, D. Knights, J. R. Rideout, A. Kshatriya, J. G. Caporaso and R. KnightSpringer Protocols Handbooks2016
Carcass mass has little influence on the structure of gravesoil microbial communitiesS. Weiss, D. O. Carter, J. L. Metcalf and R. KnightInt J Legal Med 130, (1) 253-2632016
Correlation detection strategies in microbial data sets vary widely in sensitivity and precisionS. Weiss, W. Van Treuren, C. Lozupone, K. Faust, J. Friedman, Y. Deng, L. C. Xia, Z. Z. Xu, L. Ursell, E. J. Alm, A. Birmingham, J. A. Cram, J. A. Fuhrman, J. Raes, F. Sun, J. Zhou and R. KnightIsme Journal2016
Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coliS. J. Weiss, T. J. Mansell, P. Mortazavi, R. Knight and R. T. GillPLoS One 11(1)2016
Associations between human milk oligosaccharides and infant body composition in the first 6 mo of lifeT. L. Alderete, C. Autran, B. E. Brekke, R. Knight, L. Bode, M. I. Goran and D. A. FieldsAm J Clin Nutr 102, (6) 1381-82015
MICROBIOME. A unified initiative to harness Earth's microbiomesA. P. Alivisatos, M. J. Blaser, E. L. Brodie, M. Chun, J. L. Dangl, T. J. Donohue, P. C. Dorrestein, J. A. Gilbert, J. L. Green, J. K. Jansson, R. Knight, M. E. Maxon, M. J. McFall-Ngai, J. F. Miller, K. S. Pollard, E. G. Ruby and S. A. TahaScience 350, (6260) 507-82015
Determinants of the gut microbiota of Mesoamerican howler monkeys (Alouatta pigra and A. palliata)K. R. Amato, M. Raguet-Schofield, N. Righini, R. Martinez-Mota, R. Knight, R. M. Stumpf, K. E. Nelson, B. A. White and S. R. LeighAmerican Journal of Physical Anthropology2015
Variable responses of human and non-human primate gut microbiomes to a Western dietK. R. Amato, C. J. Yeoman, G. Cerda, C. A. Schmitt, J. D. Cramer, M. E. Miller, A. Gomez, T. R. Turner, B. A. Wilson, R. M. Stumpf, K. E. Nelson, B. A. White, R. Knight and S. R. LeighMicrobiome 3, 532015
Microbiome Studies of Carrion DecompositionM. E. Benbow, J. K. Tomberlin, A. M. Tarone, J. L. Metcalf, D. O. Carter and R. KnightCarrion Ecology, Evolution, and Their Applications2015
Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic YogurtJ. E. Bisanz, M. K. Enos, G. PrayGod, S. Seney, J. M. Macklaim, S. Chilton, D. Willner, R. Knight, C. Fusch, G. Fusch, G. B. Gloor, J. P. Burton and G. ReidAppl Environ Microbiol 81, (15) 4965-752015
Molecular cartography of the human skin surface in 3DA. Bouslimani, C. Porto, C. M. Rath, M. Wang, Y. Guo, A. Gonzalez, D. Berg-Lyon, G. Ackermann, G. J. Moeller Christensen, T. Nakatsuji, L. Zhang, A. W. Borkowski, M. J. Meehan, K. Dorrestein, R. L. Gallo, N. Bandeira, R. Knight, T. Alexandrov and P. C. DorresteinProc Natl Acad Sci U S A 112, (17)2015
Seasonal variation of postmortem microbial communitiesD. O. Carter, J. L. Metcalf, A. Bibat and R. KnightForensic Sci Med Pathol 11, (2) 202-72015
The microbiome of uncontacted AmerindiansJ. C. Clemente, E. C. Pehrsson, M. J. Blaser, K. Sandhu, Z. Gao, B. Wang, M. Magris, G. Hidalgo, M. Contreras, O. Noya-Alarcon, O. Lander, J. McDonald, M. Cox, J. Walter, P. L. Oh, J. F. Ruiz, S. Rodriguez, N. Shen, S. J. Song, J. Metcalf, R. Knight, G. Dantas and M. G. Dominguez-BelloSci Adv 1, (3)2015
Short Course in the MicrobiomeK. Falana, R. Knight, C. R. Martin, R. Goldszmid, K. L. Greathouse, J. Gere, H. Young and W. P. KuoJournal of Circulating Biomarkers2015
Cross-biome comparison of microbial association networksK. Faust, G. Lima-Mendez, J.-S. Lerat, J. F. Sathirapongsasuti, R. Knight, C. Huttenhower, T. Lenaerts and J. RaesFront Microbiol 62015
Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial TraitsE. F. Freed, J. D. Winkler, S. J. Weiss, A. D. Garst, V. K. Mutalik, A. P. Arkin, R. Knight and R. T. GillACS Synth Biol 4, (11) 1244-532015
Conceptualizing a Genomics Software Institute (GSI)J. A. Gilbert, C. Catlett, N. Desai, R. Knight, O. White, R. Robbins, R. Sankaran, S.-A. Sansone, D. Field and F. MeyerStandards in genomic sciences 6, (1) 1362015
Euphorbia plant latex is inhabited by diverse microbial communitiesM. Gunawardana, E. R. Hyde, S. Lahmeyer, B. L. Dorsey, T. P. La Val, M. Mullen, J. Yoo, R. Knight and M. M. BaumAm J Bot 102, (12) 1966-19772015
Microbiota and Host Nutrition across Plant and Animal KingdomsS. Hacquard, R. Garrido-Oter, A. Gonzalez, S. Spaepen, G. Ackermann, S. Lebeis, A. C. McHardy, J. L. Dangl, R. Knight, R. Ley and P. Schulze-LefertCell Host Microbe 17, (5) 603-162015
Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8weeksV. L. Hale, C. L. Tan, R. Knight and K. R. AmatoJ Microbiol Methods 113, 16-262015
Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversityY. He, J. G. Caporaso, X.-T. Jiang, H.-F. Sheng, S. M. Huse, J. R. Rideout, R. C. Edgar, E. Kopylova, W. A. Walters and R. KnightMicrobiome 3, (1) 12015
Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversityY. He, J. G. Caporaso, X. T. Jiang, H. F. Sheng, S. M. Huse, J. R. Rideout, R. C. Edgar, E. Kopylova, W. A. Walters, R. Knight and H. W. Zhou2015
Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidisW. M. Holden, S. M. Hanlon, D. C. Woodhams, T. M. Chappell, H. L. Wells, S. M. Glisson, V. J. McKenzie, R. Knight, M. J. Parris and L. A. Rollins-SmithBiological Conservation 187, 91-1022015
Why microbiome treatments could pay off soonR. KnightNature 5182015
Follow Your Gut: The Enormous Impact of Tiny MicrobesR. KnightSimon and Schuster2015
Wir sind viele: TED BooksR. Knight and B. BuhlerS. Fischer Verlag2015
Microbiome based systems, Apparatus and methods for the exploration and production of HydrocarbonsR. Knight, A. Kshatriya, J. Ely, J. Prestidge Jr, P. Henshaw, C. Lauber, G. J. Caporaso, D. Knights, R. Gill and J. Moxley2015
Microbiome based systems, Apparatus and methods for monitoring and controlling industrial processes and systemsR. Knight, A. Kshatriya, C. Lauber, G. J. Caporaso, D. Knights, R. Gill and J. Moxley2015
New Tools for Understanding, Composition and Dynamics of Microbial Communities, ProjectR. Knight, M. E. Lladser, A. P. Martin and S. E. BrennerEncyclopedia of Metagenomics: Environmental Metagenomics 457-4572015
Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river waterA. Korajkic, L. W. Parfrey, B. R. McMinn, Y. V. Baeza, W. VanTeuren, R. Knight and O. C. ShanksWater Res 69, 30-392015
Satellite remote sensing data can be used to model marine microbial metabolite turnoverP. E. Larsen, N. Scott, A. F. Post, D. Field, R. Knight, Y. Hamada and J. A. GilbertIsme Journal 9, (1) 166-1792015
The unifrac significance test is sensitive to tree topologyC. A. Lozupone and R. KnightBMC Bioinformatics 16, (1) 2112015
ConStrains identifies microbial strains in metagenomic datasetsC. Luo, R. Knight, H. Siljander, M. Knip, R. J. Xavier and D. GeversNat Biotechnol 33, (10) 1045-10522015
Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experimentC. A. Macdonald, M. J. Crawley, D. J. Wright, J. Kuczynski, L. Robinson, R. Knight, W. A. Al-Soud, S. J. Sorensen, Y. Deng, J. Zhou and B. K. SinghEnviron Microbiol 17, (3) 841-542015
Changes in vaginal microbiota following antimicrobial and probiotic therapyJ. M. Macklaim, J. C. Clemente, R. Knight, G. B. Gloor and G. ReidMicrob Ecol Health Dis 262015
Analysis of composition of microbiomes: a novel method for studying microbial compositionS. Mandal, W. Van Treuren, R. A. White, M. Eggesbo, R. Knight and S. D. PeddadaMicrob Ecol Health Dis 262015
Context and the human microbiomeD. McDonald, A. Birmingham and R. KnightMicrobiome 3, (1) 1-82015
Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patientsD. McDonald, M. Hornig, C. Lozupone, J. Debelius, J. A. Gilbert and R. KnightMicrob Ecol Health Dis 262015
Ribosomal RNA, the lens into lifeD. McDonald, Z. Xu, E. R. Hyde and R. KnightRna 21, (4) 692-6942015
Microbiome Studies of Carrion DecompositionJ. L. Metcalf, D. O. Carter and R. KnightCarrion Ecology, Evolution, and Their Applications 4212015
Exercise is more effective at altering gut microbial composition and producing stable changes in lean mass in juvenile versus adult male F344 ratsA. Mika, W. Van Treuren, A. González, J. J. Herrera, R. Knight and M. FleshnerPLoS One 10, (5)2015
Microbial endocrinology: the interplay between the microbiota and the endocrine systemH. Neuman, J. W. Debelius, R. Knight and O. KorenFEMS Microbiol Rev2015
Subsistence strategies in traditional societies distinguish gut microbiomesA. J. Obregon-Tito, R. Y. Tito, J. Metcalf, K. Sankaranarayanan, J. C. Clemente, L. K. Ursell, Z. Z. Xu, W. Van Treuren, R. Knight and P. M. GaffneyNature Communications 62015
Genetic and environmental control of host-gut microbiota interactionsE. Org, B. W. Parks, J. W. J. Joo, B. Emert, W. Schwartzman, E. Y. Kang, M. Mehrabian, C. Pan, R. Knight and R. GunsalusGenome Res 25, (10) 1558-15692015
The gut microbiota in human energy homeostasis and obesityM. Rosenbaum, R. Knight and R. L. LeibelTrends in Endocrinology & Metabolism 26, (9) 493-5012015
The MS Microbiome Consortium (MSMC): an academic multi-disciplinary collaborative effort to elucidate the role of the gut microbiota in MS (P2. 205)I. K. Sand, S. Baranzini, R. Knight, R. S. Farber, Y. Bencosme, R. Kanner, R. Gomez, S. Mazmanian, P. Casaccia and B. CreeNeurology 84, (14 Supplement) P2. 2052015
The microbiome quality control project: baseline study design and future directionsR. Sinha, C. C. Abnet, O. White, R. Knight and C. HuttenhowerGenome Biol 16, (1) 1-62015
Collecting Fecal Samples for Microbiome Analyses in Epidemiology StudiesR. Sinha, J. Chen, A. Amir, E. Vogtmann, K. S. Inman, R. Flores-Munguia, J. N. Sampson, R. Knight and N. ChiaCancer Epidemiology Biomarkers & Prevention2015
Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiotaC. C. Smith, L. K. Snowberg, J. G. Caporaso, R. Knight and D. I. BolnickIsme Journal2015
Faecal transplantsT. Spector and R. Knight2015
Authors' reply to Mawer and Wilcox and Mullish and WilliamsT. Spector and R. KnightBmj 3512015
Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral MicrobiotaF. Teng, F. Yang, S. Huang, C. Bo, Z. Z. Xu, A. Amir, R. Knight, J. Ling and J. XuCell Host Microbe 18, (3) 296-3062015
Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and SexW. Van Treuren, L. Ponnusamy, R. J. Brinkerhoff, A. Gonzalez, C. M. Parobek, J. J. Juliano, T. G. Andreadis, R. C. Falco, L. B. Ziegler, N. Hathaway, C. Keeler, M. Emch, J. A. Bailey, R. M. Roe, C. S. Apperson, R. Knight and S. R. MeshnickAppl Environ Microbiol 81, (18) 6200-92015
Can Your Microbiome Tell You What to Eat?J. K. Vanamala, R. Knight and T. D. SpectorCell Metab 22, (6) 960-12015
Dynamic changes in short-and long-term bacterial composition following fecal microbiota transplantation for recurrent infectionA. Weingarden, A. González, Y. Vázquez-Baeza, S. Weiss, G. Humphry, D. Berg-Lyons, D. Knights, T. Unno, A. Bobr and J. KangMicrobiome 3, (1) 12015
Dietary effects on human gut microbiome diversityZ. Xu and R. KnightBritish Journal of Nutrition 113, S1-S52015
Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversityD. I. Bolnick, L. K. Snowberg, J. G. Caporaso, C. Lauber, R. Knight and W. E. StutzMol Ecol 23, (19) 4831-452014
Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)D. I. Bolnick, L. K. Snowberg, P. E. Hirsch, C. L. Lauber, R. Knight, J. G. Caporaso and R. SvanbäckEcol Lett 17, (8) 979-9872014
Individual diet has sex-dependent effects on vertebrate gut microbiotaD. I. Bolnick, L. K. Snowberg, P. E. Hirsch, C. L. Lauber, E. Org, B. Parks, A. J. Lusis, R. Knight, J. G. Caporaso and R. SvanbäckNature Communications 52014
The human microbiome: getting personalK. Califf, A. Gonzalez, R. Knight and J. G. CaporasoMicrobe 9, 410-4152014
The founding charter of the Genomic Observatories NetworkN. Davies, D. Field, L. Amaral-Zettler, M. S. Clark, J. Deck, A. Drummond, D. P. Faith, J. Geller, J. Gilbert, F. O. Glockner, P. R. Hirsch, J. A. Leong, C. Meyer, M. Obst, S. Planes, C. Scholin, A. P. Vogler, R. D. Gates, R. Toonen, V. Berteaux-Lecellier, M. Barbier, K. Barker, S. Bertilsson, M. Bicak, M. J. Bietz, J. Bobe, L. Bodrossy, A. Borja, J. Coddington, J. Fuhrman, G. Gerdts, R. Gillespie, K. Goodwin, P. C. Hanson, J. M. Hero, D. Hoekman, J. Jansson, C. Jeanthon, R. Kao, A. Klindworth, R. Knight, R. Kottmann, M. S. Koo, G. Kotoulas, A. J. Lowe, V. T. Marteinsson, F. Meyer, N. Morrison, D. D. Myrold, E. Pafilis, S. Parker, J. J. Parnell, P. N. Polymenakou, S. Ratnasingham, G. K. Roderick, N. Rodriguez-Ezpeleta, K. Schonrogge, N. Simon, N. J. Valette-Silver, Y. P. Springer, G. N. Stone, S. Stones-Havas, S. A. Sansone, K. M. Thibault, P. Wecker, A. Wichels, J. C. Wooley, T. Yahara, A. Zingone and G. O. COS2014
Convergence of gut microbiomes in myrmecophagous mammalsF. Delsuc, J. L. Metcalf, L. Wegener Parfrey, S. J. Song, A. González and R. KnightMol Ecol 23, (6) 1301-13172014
Finding the missing links among metabolites, microbes, and the hostP. C. Dorrestein, S. K. Mazmanian and R. KnightImmunity 40, (6) 824-322014
From microbiomess to metabolomes to function during host-microbial interactionsP. C. Dorrestein, S. K. Mazmanian and R. KnightImmunity 40, (6) 8242014
Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptationsO. Eilam, R. Zarecki, M. Oberhardt, L. K. Ursell, M. Kupiec, R. Knight, U. Gophna and E. RuppinMBio 5, (4)2014
pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soilsY. Feng, P. Grogan, J. G. Caporaso, H. Zhang, X. Lin, R. Knight and H. ChuSoil Biology and Biochemistry 74, 193-2002014
Temporal variability is a personalized feature of the human microbiomeG. E. Flores, J. G. Caporaso, J. B. Henley, J. R. Rideout, D. Domogala, J. Chase, J. W. Leff, Y. Vazquez-Baeza, A. Gonzalez, R. Knight, R. R. Dunn and N. FiererGenome Biol 15, (12) 5312014
Bacterial phylogeny structures soil resistomes across habitatsK. J. Forsberg, S. Patel, M. K. Gibson, C. L. Lauber, R. Knight, N. Fierer and G. DantasNature 509, (7502) 612-62014
The treatment-naive microbiome in new-onset Crohn's diseaseD. Gevers, S. Kugathasan, L. A. Denson, Y. Vazquez-Baeza, W. Van Treuren, B. Ren, E. Schwager, D. Knights, S. J. Song, M. Yassour, X. C. Morgan, A. D. Kostic, C. Luo, A. Gonzalez, D. McDonald, Y. Haberman, T. Walters, S. Baker, J. Rosh, M. Stephens, M. Heyman, J. Markowitz, R. Baldassano, A. Griffiths, F. Sylvester, D. Mack, S. Kim, W. Crandall, J. Hyams, C. Huttenhower, R. Knight and R. J. XavierCell Host Microbe 15, (3) 382-922014
The Earth Microbiome project: successes and aspirationsJ. A. Gilbert, J. K. Jansson and R. KnightBMC Biol 12, 692014
SnapShot: the human microbiomeA. Gonzalez, Y. Vazquez-Baeza and R. KnightCell 158, (3) 690-690.e12014
Conducting a microbiome studyJ. K. Goodrich, S. C. Di Rienzi, A. C. Poole, O. Koren, W. A. Walters, J. G. Caporaso, R. Knight and R. E. LeyCell 158, (2) 250-622014
Human genetics shape the gut microbiomeJ. K. Goodrich, J. L. Waters, A. C. Poole, J. L. Sutter, O. Koren, R. Blekhman, M. Beaumont, W. Van Treuren, R. Knight, J. T. Bell, T. D. Spector, A. G. Clark and R. E. LeyCell 159, (4) 789-992014
Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samplesH. C. Green, R. A. Haugland, M. Varma, H. T. Millen, M. A. Borchardt, K. G. Field, W. A. Walters, R. Knight, M. Sivaganesan and C. A. KeltyAppl Environ Microbiol 80, (10) 3086-30942014
Predictive modeling of gingivitis severity and susceptibility via oral microbiotaS. Huang, R. Li, X. Zeng, T. He, H. Zhao, A. Chang, C. Bo, J. Chen, F. Yang, R. Knight, J. Liu, C. Davis and J. XuIsme j 8, (9) 1768-802014
Advancing the microbiome research communityC. Huttenhower, R. Knight, C. T. Brown, J. G. Caporaso, J. C. Clemente, D. Gevers, E. A. Franzosa, S. T. Kelley, D. Knights, R. E. Ley, A. Mahurkar, J. Ravel and O. WhiteCell 159, (2) 227-302014
Rethinking “Enterotypes”D. Knights, T. L. Ward, C. E. McKinlay, H. Miller, A. Gonzalez, D. McDonald and R. KnightCell Host Microbe 16, (4) 433-4372014
The amphibian skin‐associated microbiome across species, space and life history stagesJ. G. Kueneman, L. W. Parfrey, D. C. Woodhams, H. M. Archer, R. Knight and V. J. McKenzieMol Ecol 23, (6) 1238-12502014
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strainsN. C. Kyrpides, P. Hugenholtz, J. A. Eisen, T. Woyke, M. Goker, C. T. Parker, R. Amann, B. J. Beck, P. S. Chain, J. Chun, R. R. Colwell, A. Danchin, P. Dawyndt, T. Dedeurwaerdere, E. F. DeLong, J. C. Detter, P. De Vos, T. J. Donohue, X. Z. Dong, D. S. Ehrlich, C. Fraser, R. Gibbs, J. Gilbert, P. Gilna, F. O. Glockner, J. K. Jansson, J. D. Keasling, R. Knight, D. Labeda, A. Lapidus, J. S. Lee, W. J. Li, J. Ma, V. Markowitz, E. R. Moore, M. Morrison, F. Meyer, K. E. Nelson, M. Ohkuma, C. A. Ouzounis, N. Pace, J. Parkhill, N. Qin, R. Rossello-Mora, J. Sikorski, D. Smith, M. Sogin, R. Stevens, U. Stingl, K. Suzuki, D. Taylor, J. M. Tiedje, B. Tindall, M. Wagner, G. Weinstock, J. Weissenbach, O. White, J. Wang, L. Zhang, Y. G. Zhou, D. Field, W. B. Whitman, G. M. Garrity and H. P. KlenkPLoS Biol 12, (8)2014
Vertebrate decomposition is accelerated by soil microbesC. L. Lauber, J. L. Metcalf, K. Keepers, G. Ackermann, D. O. Carter and R. KnightAppl Environ Microbiol 80, (16) 4920-49292014
Longitudinal analysis of microbial interaction between humans and the indoor environmentS. Lax, D. P. Smith, J. Hampton-Marcell, S. M. Owens, K. M. Handley, N. M. Scott, S. M. Gibbons, P. Larsen, B. D. Shogan, S. Weiss, J. L. Metcalf, L. K. Ursell, Y. Vazquez-Baeza, W. Van Treuren, N. A. Hasan, M. K. Gibson, R. Colwell, G. Dantas, R. Knight and J. A. GilbertScience 345, (6200) 1048-522014
HLA-B27 and human beta2-microglobulin affect the gut microbiota of transgenic ratsP. Lin, M. Bach, M. Asquith, A. Y. Lee, L. Akileswaran, P. Stauffer, S. Davin, Y. Pan, E. D. Cambronne, M. Dorris, J. W. Debelius, C. L. Lauber, G. Ackermann, Y. V. Baeza, T. Gill, R. Knight, R. A. Colbert, J. D. Taurog, R. N. Van Gelder and J. T. RosenbaumPLoS One 9, (8) e1056842014
Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)A. H. Loudon, D. C. Woodhams, L. W. Parfrey, H. Archer, R. Knight, V. McKenzie and R. N. HarrisIsme j 8, (4) 830-8402014
Anal gas evacuation and colonic microbiota in patients with flatulence: effect of dietC. Manichanh, A. Eck, E. Varela, J. Roca, J. C. Clemente, A. González, D. Knights, R. Knight, S. Estrella and C. HernandezGut 63, (3) 401-4082014
Gut Microbes and the Brain: Paradigm Shift in NeuroscienceE. A. Mayer, R. Knight, S. K. Mazmanian, J. F. Cryan and K. TillischThe Journal of Neuroscience 34, (46) 15490-154962014
Ancient human oral plaque preserves a wealth of biological dataJ. L. Metcalf, L. K. Ursell and R. KnightNat Genet 46, (4)2014
Multilevel research strategies and biological systemsM. A. O’Malley, I. Brigandt, A. C. Love, J. W. Crawford, J. A. Gilbert, R. Knight, S. D. Mitchell and F. RohwerPhilosophy of Science 81, (5) 811-8282014
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversityL. W. Parfrey, W. A. Walters, C. L. Lauber, J. C. Clemente, D. Berg-Lyons, C. Teiling, C. Kodira, M. Mohiuddin, J. Brunelle, M. Driscoll, N. Fierer, J. A. Gilbert and R. KnightFront Microbiol 5, 2982014
Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow NestsJ. M. Peralta-Sánchez, J. J. Soler, A. M. Martín-Platero, R. Knight, M. Martínez-Bueno and A. P. MøllerMicrobial ecology 67, (2) 480-4872014
The promise of the microbiome: Function and dysfunction in humans and beyondD. A. Relman, J. A. Gilbert and R. KnightScience 345, (6193) 226-2262014
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequencesJ. R. Rideout, Y. He, J. A. Navas-Molina, W. A. Walters, L. K. Ursell, S. M. Gibbons, J. Chase, D. McDonald, A. Gonzalez, A. Robbins-Pianka, J. C. Clemente, J. A. Gilbert, S. M. Huse, H. W. Zhou, R. Knight and J. G. CaporasoPeerJ 2, e5452014
Bacteria from diverse habitats colonize and compete in the mouse gutH. Seedorf, N. W. Griffin, V. K. Ridaura, A. Reyes, J. Cheng, F. E. Rey, M. I. Smith, G. M. Simon, R. H. Scheffrahn, D. Woebken, A. M. Spormann, W. Van Treuren, L. K. Ursell, M. Pirrung, A. Robbins-Pianka, B. L. Cantarel, V. Lombard, B. Henrissat, R. Knight and J. I. GordonCell 159, (2) 253-662014
Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial DiversityA. Shade, S. E. Jones, J. G. Caporaso, J. Handelsman, R. Knight, N. Fierer and J. A. GilbertMBio 5, (4)2014
Specialized Metabolites from the Microbiome in Health and DiseaseG. Sharon, N. Garg, J. Debelius, R. Knight, P. C. Dorrestein and S. K. MazmanianCell Metab 20, (5) 719-7302014
Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forestN. Tas, E. Prestat, J. W. McFarland, K. P. Wickland, R. Knight, A. A. Berhe, T. Jorgenson, M. P. Waldrop and J. K. JanssonIsme j 8, (9) 1904-192014
Structural basis for diversity in the SAM clan of riboswitchesJ. J. Trausch, Z. Xu, A. L. Edwards, F. E. Reyes, P. E. Ross, R. Knight and R. T. BateyProceedings of the National Academy of Sciences 111, (18) 6624-66292014
The Intestinal Metabolome: An Intersection Between Microbiota and HostL. K. Ursell, H. J. Haiser, W. Van Treuren, N. Garg, L. Reddivari, J. Vanamala, P. C. Dorrestein, P. J. Turnbaugh and R. KnightGastroenterology 146, (6) 1470-14762014
Meta-analyses of human gut microbes associated with obesity and IBDW. A. Walters, Z. Xu and R. KnightFEBS Lett 588, (22) 4223-42332014
Tracking down the sources of experimental contamination in microbiome studiesS. Weiss, A. Amir, E. R. Hyde, J. L. Metcalf, S. J. Song and R. KnightGenome Biol 15, (12) 1-32014
Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectivenessD. C. Woodhams, H. Brandt, S. Baumgartner, J. Kielgast, E. Kupfer, U. Tobler, L. R. Davis, B. R. Schmidt, C. Bel, S. Hodel, R. Knight and V. McKenziePLoS One 9, (4)2014
Which is more important for classifying microbial communities: who’s there or what they can doZ. Xu, D. Malmer, M. G. Langille, S. F. Way and R. KnightIsme j 8, (12) 2357-23592014
Toward Effective Probiotics for Autism and Other Neurodevelopmental DisordersJ. A. Gilbert, R. Krajmalnik-Brown, D. L. Porazinska, S. J. Weiss and R. KnightCell 155, (7) 1446-14482013
Supplementary Material Cross-biome comparison of microbial association networksK. Faust, G. Lima-Mendez, J.-S. Lerat, J. Fah, R. K. Sathirapongsasuti, C. Huttenhower, T. Lenaerts and J. Raes
Microbiota Restoration: Natural and Supplemented Recovery of Human Microbial CommunitiesH. C. Younes, G. B. Gloor, R. Knight and H. J. Busscher
Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal ringsLK Ursell, M Gunawardana, S Chang, M Mullen, JA Moss, BC Herold, ...Antiviral research 102, 87-942014
What Is the Value of a Food and Drug Administration Investigational New Drug Application for Fecal Microbiota Transplantation to Treat Clostridium difficile Infection?GA Hecht, MJ Blaser, J Gordon, LM Kaplan, R Knight, L Laine, R Peek, ...Clinical gastroenterology and hepatology: the official clinical practice ...2014
Genomic Standards Consortium ProjectsD Field, P Sterk, R Kottmann, W De Smet, L Amaral-Zettler, G Cochrane, ...Standards in Genomic Sciences 9 (3)2014
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spillOU Mason, NM Scott, A Gonzalez, A Robbins-Pianka, J Bælum, J Kimbrel, ...The ISME Journal2014
Technology and Techniques for Microbial Ecology via DNA SequencingWA Walters, R KnightAnnals of the American Thoracic Society 11 (Supplement 1), S16-S202014
Diversity of Rickettsiales in the Microbiome of the Lone Star Tick, Amblyomma americanumL Ponnusamy, A Gonzalez, W Van Treuren, S Weiss, CM Parobek, ...Applied and environmental microbiology 80 (1), 354-3592014
Toward Effective Probiotics for Autism and Other Neurodevelopmental DisordersJA Gilbert, R Krajmalnik-Brown, DL Porazinska, SJ Weiss, R KnightCell 155 (7), 1446-14482013
Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)AH Loudon, DC Woodhams, LW Parfrey, H Archer, R Knight, V McKenzie, ...The ISME Journal2013
EMPeror: a tool for visualizing high-throughput microbial community dataY Vázquez-Baeza, M Pirrung, A Gonzalez, R KnightGigaScience 2 (1), 1-42013
A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel DiseaseM Tong, X Li, LW Parfrey, B Roth, A Ippoliti, B Wei, J Borneman, ...PLOS ONE 8 (11)2013
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United StatesN Fierer, J Ladau, JC Clemente, JW Leff, SM Owens, KS Pollard, R Knight, ...Science 342 (6158), 621-6242013
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environmentEM Glass, Y Dribinsky, P Yilmaz, H Levin, R Van Pelt, D Wendel, A Wilke, ...The ISME Journal2013
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiotaPC Kashyap, A Marcobal, LK Ursell, SA Smits, ED Sonnenburg, ...Proceedings of the National Academy of Sciences 110 (42), 17059-170642013
A microbial clock provides an accurate estimate of the postmortem interval in a mouse model systemJL Metcalf, L Wegener Parfrey, A Gonzalez, CL Lauber, D Knights, ...eLife 22013
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiotaPC Kashyap, A Marcobal, LK Ursell, SA Smits, ED Sonnenburg, ...Proceedings of the National Academy of Sciences 110 (42), 17059-170642013
The amphibian skin‐associated microbiome across species, space and life history stagesJG Kueneman, LW Parfrey, DC Woodhams, HM Archer, R Knight, ...Molecular Ecology2013
Meta-analyses of studies of the human microbiotaCA Lozupone, J Stombaugh, A Gonzalez, G Ackermann, D Wendel, ...Genome research 23 (10), 1704-17142013
Alterations in the Gut Microbiota Associated with HIV-1 InfectionCA Lozupone, M Li, TB Campbell, SC Flores, D Linderman, MJ Gebert, ...Cell Host & Microbe 14 (3), 329-3392013
Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato PhyllosphereAR Ottesen, A Gonzalez, R Bell, C Arce, S Rideout, M Allard, P Evans, ...PLOS ONE 8 (9)2013
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in MiceVK Ridaura, JJ Faith, FE Rey, J Cheng, AE Duncan, AL Kau, NW Griffin, ...Science 341 (6150)2013
Replenishing our defensive microbesLK Ursell, WV Treuren, JL Metcalf, M Pirrung, A Gewirtz, R KnightBioEssays 35 (9), 810-8172013
Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and ColonAA Devine, A Gonzalez, KE Speck, R Knight, M Helmrath, PK Lund, ...PLOS ONE 8 (8)2013
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequencesMGI Langille, J Zaneveld, JG Caporaso, D McDonald, D Knights, ...Nature biotechnology 31 (9), 814-8212013
Convergence of gut microbiomes in myrmecophagous mammalsF Delsuc, JL Metcalf, L Wegener Parfrey, SJ Song, A González, R KnightMolecular Ecology2013
The Long-Term Stability of the Human Gut MicrobiotaJJ Faith, JL Guruge, M Charbonneau, S Subramanian, H Seedorf, ...Science 341 (6141)2013
The Ecology of Microbial Communities Associated with Macrocystis pyriferaVK Michelou, JG Caporaso, R Knight, SR PalumbiPLOS ONE 8 (6)2013
Anal gas evacuation and colonic microbiota in patients with flatulence: effect of dietC Manichanh, A Eck, E Varela, J Roca, JC Clemente, A González, ...Gut2013
Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized micePC Kashyap, A Marcobal, LK Ursell, M Larauche, H Duboc, KA Earle, ...Gastroenterology 144 (5), 967-9772013
Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitchCD Stoddard, J Widmann, JJ Trausch, JG Marcano-Velázquez, R Knight, ...Journal of molecular biology 425 (10), 1596-16112013
Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)AR Ottesen, AG Peña, JR White, JB Pettengill, C Li, S Allard, S Rideout, ...BMC Microbiology 13 (1), 1142013
Widespread Colonization of the Lung by Tropheryma whipplei in HIV InfectionC Lozupone, A Cota-Gomez, BE Palmer, DJ Linderman, ES Charlson, ...American journal of respiratory and critical care medicine 187 (10), 1110-11172013
The 15th Genomic Standards Consortium meetingL Schriml, I Mizrachi, P Sterl, D Field, L Hirschman, T Tatusova, ...Standards in Genomic Sciences 8 (1)2013
Cohabiting family members share microbiota with one another and with their dogsSJ Song, C Lauber, EK Costello, CA Lozupone, G Humphrey, ...eLife 22013
Meeting Report: Fungal ITS Workshop (October 2012)ST Bates, S Ahrendt, HM Bik, TD Bruns, JG Caporaso, J Cole, M Dwan, ...Standards in genomic sciences 8 (1), 1182013
The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012D Smith, J Alverdy, G An, M Coleman, S Garcia-Houchins, J Green, ...Standards in genomic sciences 8 (1), 1122013
A meta-analysis of changes in bacterial and archaeal communities with timeA Shade, JG Caporaso, J Handelsman, R Knight, N FiererThe ISME journal2013
Translating the human microbiomeJ Brown, WM de Vos, PS DiStefano, J Doré, C Huttenhower, R Knight, ...Nature biotechnology 31 (4), 304-82013
Biphasic assembly of the murine intestinal microbiota during early developmentIG Pantoja-Feliciano, JC Clemente, EK Costello, ME Perez, MJ Blaser, ...The ISME journal 7 (6), 1112-11152013
Evidence for a persistent microbial seed bank throughout the global oceanSM Gibbons, JG Caporaso, M Pirrung, D Field, R Knight, JA GilbertProceedings of the National Academy of Sciences 110 (12), 4651-46552013
Xenobiotics and the Human Gut Microbiome: Metatranscriptomics Reveal the Active PlayersLK Ursell, R KnightCell Metabolism 17 (3), 317-3182013
How delivery mode and feeding can shape the bacterial community in the infant gut.SJ Song, MG Dominguez-Bello, R KnightCMAJ: Canadian Medical Association journal= journal de l'Association ...2013
Global biogeography of highly diverse protistan communities in soilST Bates, JC Clemente, GE Flores, WA Walters, LW Parfrey, R Knight, ...The ISME journal 7 (3), 652-6592013
Collaborative cloud-enabled tools allow rapid, reproducible biological insightsB Ragan-Kelley, WA Walters, D McDonald, J Riley, BE Granger, ...The ISME journal 7 (3), 4612013
From molecules to dynamic biological communitiesD McDonald, Y Vázquez-Baeza, WA Walters, JG Caporaso, R KnightBiology & philosophy 28 (2), 241-2592013
Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial CommunitiesS Kittelmann, H Seedorf, WA Walters, JC Clemente, R Knight, JI Gordon, ...PloS one 8 (2), e478792013
The microbiome explored: recent insights and future challengesM Blaser, P Bork, C Fraser, R Knight, J WangNature Reviews Microbiology 11 (3), 213-2172013
Diversity, distribution and sources of bacteria in residential kitchensGE Flores, ST Bates, JG Caporaso, CL Lauber, JW Leff, R Knight, N FiererEnvironmental microbiology 15 (2), 588-5962013
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor.MI Smith, T Yatsunenko, MJ Manary, I Trehan, R Mkakosya, J Cheng, ...Science (New York, NY) 339 (6119), 548-5542013
Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)KM Hewitt, FL Mannino, A Gonzalez, JH Chase, JG Caporaso, R Knight, ...PloS one 8 (1)2013
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome DatasetsO Koren, D Knights, A Gonzalez, L Waldron, N Segata, R Knight, ...PLoS computational biology 9 (1)2013
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in miceBW Parks, E Nam, E Kostem, F Norheim, ST Hui, C Pan, M Civelek, ...Cell metabolism 17 (1), 141-1522013
What's the Value of an FDA IND for Fecal Microbiota Transplantation in Clostridium difficile Infection?GA Hecht, MJ Blaser, J Gordon, LM Kaplan, R Knight, L Laine, R Peek, ...Clinical gastroenterology and hepatology: the official clinical practice ...2013
Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow NestsJM Peralta-Sánchez, JJ Soler, AM Martín-Platero, R Knight, ...Microbial Ecology, 1-82013
Advancing Our Understanding of the Human Microbiome Using QIIMEJA Navas-Molina, JM Peralta-Sánchez, A González, PJ McMurdie, ...Methods in enzymology 531, 371-4442013
Mathematical Approaches for Describing Microbial Populations: Practice and Theory for Extrapolation of Rich EnvironmentsME Lladser, R KnightThe Human Microbiota: How Microbial Communities Affect Health and Disease ...2013
Correction: Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1T Maslanik, K Tannura, L Mahaffey, AB Loughridge, L Benninson, L Ursell, ...PloS one 8 (8)2013
Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycleHV Carey, WA Walters, R KnightAmerican Journal of Physiology-Regulatory, Integrative and Comparative ...2013
Crystal ball–2013T Curtis, JM Daran, JT Pronk, J Frey, JK Jansson, A Robbins‐Pianka, ...Microbial Biotechnology 6 (1), 3-162013
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residentsMJ Blaser, MG Dominguez-Bello, M Contreras, M Magris, G Hidalgo, ...The ISME journal 7 (1), 85-952013
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencingNA Bokulich, S Subramanian, JJ Faith, D Gevers, JI Gordon, R Knight, ...Nature methods 10 (1), 57-592013
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial matJK Harris, JG Caporaso, JJ Walker, JR Spear, NJ Gold, CE Robertson, ...The ISME journal 7 (1), 50-602013
Insights from characterizing extinct human gut microbiomesRY Tito, D Knights, J Metcalf, AJ Obregon-Tito, L Cleeland, F Najar, B Roe, ...PloS one 7 (12), e511462012
Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1T Maslanik, K Tannura, L Mahaffey, AB Loughridge, L Benninson, L Ursell, ...PloS one 7 (12), e506362012
Colitis in TLR5‐deficiency Mice: Role of the Microbiota: P‐259 YIF Carvalho, O Koren, B Chassaing, A Darfeuille-Michaud, R Knight, R Ley, ...Inflammatory Bowel Diseases 18, S113-S1142012
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial CommunitiesJ Kuczynski, J Stombaugh, WA Walters, A González, JG Caporaso, ...Current protocols in microbiology, 1E. 5.1-1E. 5.202012
Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthoodSS Stahringer, JC Clemente, RP Corley, J Hewitt, D Knights, WA Walters, ...Genome research 22 (11), 2146-21522012
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbiontsC Lozupone, K Faust, J Raes, JJ Faith, DN Frank, J Zaneveld, JI Gordon, ...Genome research 22 (10), 1974-19842012
Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the ZebrafishI Semova, JD Carten, J Stombaugh, LC Mackey, R Knight, SA Farber, ...Cell Host & Microbe 12 (3), 277-2882012
Diversity, stability and resilience of the human gut microbiotaCA Lozupone, JI Stombaugh, JI Gordon, JK Jansson, R KnightNature 489 (7415), 220-2302012
Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan PlateauJ Xiong, Y Liu, X Lin, H Zhang, J Zeng, J Hou, Y Yang, T Yao, R Knight, ...Environmental microbiology 14 (9), 2457-24662012
Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient miceFA Carvalho, O Koren, JK Goodrich, MEV Johansson, I Nalbantoglu, ...Cell host & microbe 12 (2), 139-1522012
Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic SyndromeML Zupancic, BL Cantarel, Z Liu, EF Drabek, KA Ryan, S Cirimotich, ...PloS one 7 (8), e430522012
The Human Microbiome Project: A Community Resource for the Healthy Human MicrobiomeD Gevers, R Knight, JF Petrosino, K Huang, AL McGuire, BW Birren, ...PLoS biology 10 (8), e10013772012
Host Remodeling of the Gut Microbiome and Metabolic Changes during PregnancyO Koren, JK Goodrich, TC Cullender, A Spor, K Laitinen, H Kling Bäckhed, ...Cell 150 (3), 470-4802012
Defining the human microbiomeLK Ursell, JL Metcalf, LW Parfrey, R KnightNutrition Reviews 70 (s1), S38-S442012
Discussion from the 24th Marabou Symposium: Nutrition and the human microbiomeD Ehrlich, R Knight, R Ley, J Nielsen, G Hansson, W de Vos, J Nielsen, ...NUTRITION REVIEWS 70, S57-S862012
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-omeD McDonald, JC Clemente, J Kuczynski, JR Rideout, J Stombaugh, ...GigaScience 1 (1), 72012
RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAsJ Widmann, J Stombaugh, D McDonald, J Chocholousova, P Gardner, ...RNA 18 (7), 1319-13272012
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequencesX Wang, Y Cai, Y Sun, R Knight, V MaiThe ISME journal 6 (7), 12772012
Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysisKE Sullam, SD Essinger, CA Lozupone, MP O’CONNOR, GL Rosen, ...Molecular Ecology 21 (13), 3363-33782012
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveysJJ Werner, D Zhou, JG Caporaso, R Knight, LT AngenentThe ISME journal 6 (7), 1273-12762012
Characterizing microbial communities through space and timeA Gonzalez, A King, MS Robeson II, S Song, A Shade, JL Metcalf, ...Current opinion in biotechnology 23 (3), 431-4362012
Lake microbial communities are resilient after a whole-ecosystem disturbanceA Shade, JS Read, ND Youngblut, N Fierer, R Knight, TK Kratz, NR Lottig, ...The ISME journal 6 (12), 2153-21672012
A framework for human microbiome researchHuman Microbiome Project ConsortiumNature 486 (7402), 215-2212012
Structure, function and diversity of the healthy human microbiomeHuman Microbiome Project ConsortiumNature 486 (7402), 207-2142012
Unlocking the potential of metagenomics through replicated experimental designR Knight, J Jansson, D Field, N Fierer, N Desai, JA Fuhrman, ...Nature biotechnology 30 (6), 513-5202012
The identification of environmental parameters which could influence soil bacterial community composition on the Antarctic Peninsula-a statistical approachCW Chong, DA Pearce, P Convey, IKP TanAntarctic Science 24 (03), 249-2582012
Human Immunodeficiency Virus nef Signature Sequences Are Associated with Pulmonary HypertensionS Almodovar, R Knight, AA Allshouse, S Roemer, C Lozupone, ...AIDS Research and Human Retroviruses 28 (6), 607-6182012
The Western English Channel contains a persistent microbial seed bankJG Caporaso, K Paszkiewicz, D Field, R Knight, JA GilbertThe ISME journal 6 (6), 1089-10932012
Su1926 Defining a Mosaic of Functional Microbial Communities at the Human Mucosal Surface, and Their Association With IBDM Tong, XX Li, LW Parfrey, A Ippoliti, B Wei, DP McGovern, D Frank, E Li, ...Gastroenterology 142 (5), S-5382012
Su1991 Diet-Induced Change in Gastrointestinal Transit Significantly Alters Distal Gut Microbial CommunitiesPC Kashyap, S Higginbottom, L Ursell, PJ Pasricha, R Knight, G Farrugia, ...Gastroenterology 142 (5), S-554-S-5552012
Spatial and temporal variability of the human microbiotaLW Parfrey, R KnightClinical Microbiology and Infection 18 (s4), 8-112012
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sitesLK Ursell, JC Clemente, JR Rideout, D Gevers, JG Caporaso, R KnightJournal of Allergy and Clinical Immunology 129 (5), 1204-12082012
Human gut microbiome viewed across age and geographyT Yatsunenko, FE Rey, MJ Manary, I Trehan, MG Dominguez-Bello, ...Nature 486 (7402), 222-2272012
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradientsN Fierer, CL Lauber, KS Ramirez, J Zaneveld, MA Bradford, R KnightThe ISME journal 6 (5), 1007-10172012
Sequencing our way towards understanding global eukaryotic biodiversityHM Bik, DL Porazinska, S Creer, JG Caporaso, R Knight, WK ThomasTrends in ecology & evolution 27 (4), 233-2432012
Hibernation alters the gut microbial community in ground squirrelsHV Carey, WA Walters, R KnightFASEB JOURNAL 262012
Broad patterns in the diversity of eukaryotic microbesWL Parfrey, R KnightINTEGRATIVE AND COMPARATIVE BIOLOGY 52, E188-E1882012
Responses of gut microbiota to diet composition and weight loss in lean and obese miceY Ravussin, O Koren, A Spor, C LeDuc, R Gutman, J Stombaugh, ...Obesity 20 (4), 738-7472012
Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquiferX Lin, J McKinley, CT Resch, R Kaluzny, CL Lauber, J Fredrickson, ...The ISME Journal 6 (9), 1665-16762012
Conceptualizing a Genomics Software Institute (GSI)JA Gilbert, C Catlett, N Desai, R Knight, O White, R Robbins, R Sankaran, ...Standards in Genomic Sciences 6 (1)2012
The impact of the gut microbiota on human health: an integrative viewJC Clemente, LK Ursell, LW Parfrey, R KnightCell 148 (6), 1258-12702012
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsJG Caporaso, CL Lauber, WA Walters, D Berg-Lyons, J Huntley, N Fierer, ...The ISME journal 6 (8), 1621-16242012
Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitisFA Carvalho, I Nalbantoglu, S Ortega-Fernandez, JD Aitken, Y Su, ...Gut 61 (3), 373-3842012
Co-habiting amphibian species harbor unique skin bacterial communities in wild populationsVJ McKenzie, RM Bowers, N Fierer, R Knight, CL LauberThe ISME journal 6 (3), 588-5962012
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaeaD McDonald, MN Price, J Goodrich, EP Nawrocki, TZ DeSantis, A Probst, ...The ISME journal 6 (3), 610-6182012
Advancing analytical algorithms and pipelines for billions of microbial sequencesA Gonzalez, R KnightCurrent opinion in biotechnology 23 (1), 64-712012
SitePainter: a tool for exploring biogeographical patternsA Gonzalez, J Stombaugh, CL Lauber, N Fierer, R KnightBioinformatics 28 (3), 436-4382012
Defining seasonal marine microbial community dynamicsJA Gilbert, JA Steele, JG Caporaso, L Steinbrück, J Reeder, B Temperton, ...The ISME journal 6 (2), 298-3082012
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequencesDAW Soergel, N Dey, R Knight, SE BrennerThe ISME journal 6 (7), 1440-14442012
List of participants from the 24th Marabou Symposium: Nutrition and the Human MicrobiomeB Angelin, A Berstad, R Black, P Brandtzaeg, F Bäckhed, W de Vos, ...Nutrition Reviews 70 (1), S952012
Evidence for a persistent microbial community in the Western English ChannelJG Caporaso, D Field, K Paszkiewicz, R Knight, J GilbertISME Journal 6 (ANL/CLS/JA-69610)2012
Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetrasporaJR Grant, DJG Lahr, FE Rey, JG Burleigh, JI Gordon, R Knight, ...Protist Genomics 1, 3-182012
Community Page-The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome-e1001377D Gevers, R Knight, JF Petrosino, K Huang, AL McGuire, BW Birren, ...PLoS-Biology 10 (8), 14822012
A preliminary survey of lichen associated eukaryotes using pyrosequencingST Bates, D Berg-Lyons, CL Lauber, WA Walters, R Knight, N FiererThe Lichenologist 44 (01), 137-1462012
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysisY Sun, Y Cai, SM Huse, R Knight, WG Farmerie, X Wang, V MaiBriefings in bioinformatics 13 (1), 107-1212012
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveysJJ Werner, O Koren, P Hugenholtz, TZ DeSantis, WA Walters, ...The ISME journal 6 (1), 94-1032012
Composition of human skin microbiota affects attractiveness to malaria mosquitoesNO Verhulst, YT Qiu, H Beijleveld, C Maliepaard, D Knights, S Schulz, ...PloS one 6 (12), e289912011
Experimental and analytical tools for studying the human microbiomeJ Kuczynski, CL Lauber, WA Walters, LW Parfrey, JC Clemente, D Gevers, ...Nature Reviews Genetics 13 (1), 47-582011
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial CommunitiesJ Kuczynski, J Stombaugh, WA Walters, A González, JG Caporaso, ...Current Protocols in Bioinformatics, 10.7. 1-10.7. 202011
The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011JA Gilbert, M Bailey, D Field, N Fierer, JA Fuhrman, B Hu, J Jansson, ...Standards in Genomic Sciences 5 (2), 2432011
Microbial biogeography of public restroom surfacesGE Flores, ST Bates, D Knights, CL Lauber, J Stombaugh, R Knight, ...PLoS One 6 (11), e281322011
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences: Supplementary MaterialsDAW Soergel, N Dey, R Knight, SE Brenner2011
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadataM Pirrung, R Kennedy, JG Caporaso, J Stombaugh, D Wendel, R KnightBioinformatics 27 (21), 3067-30692011
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptationJRR Zaneveld, LW Parfrey, W Van Treuren, C Lozupone, JC Clemente, ...Trends in microbiology 19 (10), 472-4822011
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twinsNP McNulty, T Yatsunenko, A Hsiao, JJ Faith, BD Muegge, AL Goodman, ...Science translational medicine 3 (106)2011
Linking long-term dietary patterns with gut microbial enterotypesGD Wu, J Chen, C Hoffmann, K Bittinger, YY Chen, SA Keilbaugh, ...Science 334 (6052), 105-1082011
Human-Associated Microbial Signatures: Examining Their Predictive ValueD Knights, LW Parfrey, J Zaneveld, C Lozupone, R KnightCell host & microbe 10 (4), 292-2962011
The genomic standards consortium: bringing standards to life for microbial ecologyP Yilmaz, JA Gilbert, R Knight, L Amaral-Zettler, I Karsch-Mizrachi, ...The ISME journal 5 (10), 15652011
Sources of bacteria in outdoor air across cities in the midwestern United StatesRM Bowers, AP Sullivan, EK Costello, JL Collett, R Knight, N FiererApplied and environmental microbiology 77 (18), 6350-63562011
ANALYSIS OF TRANSCRIPTOMES FROM THREE MICROBIAL EUKARYOTESJR Grant, DJ Lahr, F Rey, R Knight, LA Katz, J GordonJOURNAL OF PHYCOLOGY 47, S74-S752011
UCHIME improves sensitivity and speed of chimera detectionRC Edgar, BJ Haas, JC Clemente, C Quince, R KnightBioinformatics 27 (16), 2194-22002011
The under-recognized dominance of< i> Verrucomicrobia</i> in soil bacterial communitiesGT Bergmann, ST Bates, KG Eilers, CL Lauber, JG Caporaso, WA Walters, ...Soil Biology and Biochemistry 43 (7), 1450-14552011
Bayesian community-wide culture-independent microbial source trackingD Knights, J Kuczynski, ES Charlson, J Zaneveld, MC Mozer, RG Collman, ...nature methods 8 (9), 761-7632011
Our microbial selves: what ecology can teach usA Gonzalez, JC Clemente, A Shade, JL Metcalf, S Song, B Prithiviraj, ...EMBO reports 12 (8), 775-7842011
Sharing and archiving nucleic acid structure mapping dataP Rocca-Serra, S Bellaousov, A Birmingham, C Chen, P Cordero, R Das, ...RNA 17 (7), 1204-12122011
Boulder ALignment Editor (ALE): a web-based RNA alignment toolJ Stombaugh, J Widmann, D McDonald, R KnightBioinformatics 27 (12), 1706-17072011
The genomic standards consortiumD Field, L Amaral-Zettler, G Cochrane, JR Cole, P Dawyndt, GM Garrity, ...PLoS biology 9 (6)2011
Controlled Feeding Experiments Demonstrate the Impact of Diet on the Composition of the Human Gut MicrobiomeGD Wu, M Bewtra, C Hoffmann, YY Chen, SA Keilbaugh, K Bittinger, ...Gastroenterology 140 (5), S-472011
Development of the human gastrointestinal microbiota and insights from high-throughput sequencingMG Dominguez-Bello, MJ Blaser, RE Ley, R KnightGastroenterology 140 (6), 1713-17192011
Moving pictures of the human microbiomeJG Caporaso, CL Lauber, EK Costello, D Berg-Lyons, A Gonzalez, ...Genome Biol 12 (5), R502011
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humansBD Muegge, J Kuczynski, D Knights, JC Clemente, A González, ...Science 332 (6032), 970-9742011
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specificationsP Yilmaz, R Kottmann, D Field, R Knight, JR Cole, L Amaral-Zettler, ...Nature biotechnology 29 (5), 415-4202011
Examining the global distribution of dominant archaeal populations in soilST Bates, D Berg-Lyons, JG Caporaso, WA Walters, R Knight, N FiererThe ISME journal 5 (5), 908-9172011
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primersWA Walters, JG Caporaso, CL Lauber, D Berg-Lyons, N Fierer, R KnightBioinformatics 27 (8), 1159-11612011
New Insight into the Diversity of Life's Building Blocks: Evenness, Not VarianceJG Caporaso, R KnightAstrobiology 11 (3), 197-1982011
Meeting report of the RNA Ontology Consortium January 8-9, 2011A Birmingham, JC Clemente, N Desai, J Gilbert, A Gonzalez, N Kyrpides, ...Standards in genomic sciences 4 (2), 252-2562011
Supervised classification of microbiota mitigates mislabeling errorsD Knights, J Kuczynski, O Koren, RE Ley, D Field, R Knight, TZ DeSantis, ...The ISME journal 5 (4), 5702011
Microbes do not follow the elevational diversity patterns of plants and animalsN Fierer, CM McCain, P Meir, M Zimmermann, JM Rapp, MR Silman, ...Ecology 92 (4), 797-8042011
Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environmentsRM Bowers, S McLetchie, R Knight, N FiererThe ISME journal 5 (4), 601-6122011
Spatially and Temporally Resolved Studies of the Human Microbiome (2011 JGI User Meeting)R KnightDOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National ...2011
Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twinsEE Hansen, CA Lozupone, FE Rey, M Wu, JL Guruge, A Narra, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4599-46062011
Human oral, gut, and plaque microbiota in patients with atherosclerosisO Koren, A Spor, J Felin, F Fåk, J Stombaugh, V Tremaroli, CJ Behre, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4592-45982011
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sampleJG Caporaso, CL Lauber, WA Walters, D Berg-Lyons, CA Lozupone, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4516-45222011
Succession of microbial consortia in the developing infant gut microbiomeJE Koenig, A Spor, N Scalfone, AD Fricker, J Stombaugh, R Knight, ...Proceedings of the National Academy of Sciences 108 (Supplement 1), 4578-45852011
Bacterial community structures are unique and resilient in full-scale bioenergy systemsJJ Werner, D Knights, ML Garcia, NB Scalfone, S Smith, K Yarasheski, ...Proceedings of the National Academy of Sciences 108 (10), 4158-41632011
The mind-body-microbial continuumA Gonzalez, J Stombaugh, C Lozupone, PJ Turnbaugh, JI Gordon, ...Dialogues in clinical neuroscience 13 (1), 552011
Supervised classification of human microbiotaD Knights, EK Costello, R KnightFEMS microbiology reviews 35 (2), 343-3592011
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR ampliconsBJ Haas, D Gevers, AM Earl, M Feldgarden, DV Ward, G Giannoukos, ...Genome research 21 (3), 494-5042011
Host-associated and free-living phage communities differ profoundly in phylogenetic compositionJG Caporaso, R Knight, ST KelleyPloS one 6 (2)2011
Bacterial communities associated with the lichen symbiosisST Bates, GWG Cropsey, JG Caporaso, R Knight, N FiererApplied and environmental microbiology 77 (4), 1309-13142011
UniFrac: an effective distance metric for microbial community comparisonC Lozupone, ME Lladser, D Knights, J Stombaugh, R KnightThe ISME journal 5 (2), 1692011
641: Depth of 16S rRNA sequencing required for characterization of microbial composition in the vaginal, oral, and rectal compartments in pregnancyO Cohavy, J Acuna, I Solt, J Reeder, M Kim, I Lebovics, B Paster, R Knight, ...American Journal of Obstetrics and Gynecology 204 (1), S2542011
257: Preliminary observations on the microbial phylogeny of the oral, vaginal, and rectal microbiome in gestational diabetes and healthy pregnanciesJ Acuna, O Cohavy, I Solt, J Reeder, M Kim, I Lebovics, B Paster, R Knight, ...American Journal of Obstetrics and Gynecology 204 (1), S109-S1102011
Closure of the NCBI SRA and implications for the long-term future of genomics data storageGBE TeamGenome biology 12 (3), 4022011
Community Page-The Genomic Standards ConsortiumD Field, L Amaral-Zettler, G Cochrane, JR Cole, P Dawyndt, GM Garrity, ...PLoS-Biology 9 (6), 11892011
Analytic Strategies for Understanding Host-Associated Microbial CommunitiesJ Kuczynski, R KnightMicrobe 6 (9), 3892011
Microbial eukaryotes in the human microbiome: ecology, evolution, and future directionsLW Parfrey, WA Walters, R KnightFrontiers in microbiology 22011
The RNA Ontology (RNAO): an ontology for integrating RNA sequence and structure dataR Hoehndorf, C Batchelor, T Bittner, M Dumontier, K Eilbeck, R Knight, ...Applied Ontology 6 (1), 53-892011
Global patterns in the biogeography of bacterial taxaDR Nemergut, EK Costello, M Hamady, C Lozupone, L Jiang, SK Schmidt, ...Environmental microbiology 13 (1), 135-1442011
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010JA Gilbert, F Meyer, R Knight, D Field, N Kyrpides, P Yilmaz, J WooleyStandards in genomic sciences 3 (3), 2352010
The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.JA Gilbert, F Meyer, J Jansson, J Gordon, N Pace, J Tiedje, R Ley, ...Standards in genomic sciences 3 (3), 2492010
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome projectJ Gilbert, F Meyer, DA Antonopoulos, P Balaji, CT Brown, CT Brown, ...Standards in genomic sciences 3 (3), 243-2482010
Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systemsKS Ramirez, CL Lauber, R Knight, MA Bradford, N FiererEcology 91 (12), 3463-34702010
Microbiota restoration: natural and supplemented recovery of human microbial communitiesG Reid, JA Younes, HC Van der Mei, GB Gloor, R Knight, HJ BusscherNature Reviews Microbiology 9 (1), 27-382010
The “Minimum Information about an ENvironmental Sequence”(MIENS) specificationP Yilmaz, R Kottmann, D Field, R Knight, JR Cole, L Amaral-Zettler, ...Nature Publishing Group2010
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leavesAJ Redford, RM Bowers, R Knight, Y Linhart, N FiererEnvironmental microbiology 12 (11), 2885-28932010
Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomesH Chu, N Fierer, CL Lauber, JG Caporaso, R Knight, P GroganEnvironmental Microbiology 12 (11), 2998-30062010
The bacterial microbiota in the oral mucosa of rural AmerindiansM Contreras, EK Costello, G Hidalgo, M Magris, R Knight, ...Microbiology 156 (11), 3282-32872010
Changes through time: integrating microorganisms into the study of successionN Fierer, D Nemergut, R Knight, JM CraineResearch in microbiology 161 (8), 635-6422010
Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newbornMG Dominguez-Bello, EK Costello, R KnightProceedings of the National Academy of Sciences 107 (42), E160-E1602010
A data analysis and coordination center for the human microbiome projectJ Wortman, M Giglio, H Creasy, A Chen, K Liolios, K Chu, N Davidovics, ...Genome Biology 11 (Suppl 1), O132010
Translational medicine and the human microbiomeR KnightGenome Biology 11 (Suppl 1), I152010
Loss of toll-like receptor-5 changes gut microbiota and results in metabolic syndromeM Vijay-Kumar, J Aitken, F Carvalho, T Cullendar, S Mwangi, S Srinivasan, ...DIABETES OBESITY & METABOLISM 12, 44-442010
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNAI Majerfeld, J Chocholousova, V Malaiya, J Widmann, D McDonald, ...RNA 16 (10), 1915-19242010
Reshaping the gut microbiome with bacterial transplantation and antibiotic intakeC Manichanh, J Reeder, P Gibert, E Varela, M Llopis, M Antolin, R Guigo, ...Genome research 20 (10), 1411-14192010
Estimate of the abundance of cardiomyopathic mutations in the β-myosin geneM Hamady, M Buvoli, LA Leinwand, R KnightInternational journal of cardiology 144 (1), 124-1262010
Microbial community resemblance methods differ in their ability to detect biologically relevant patternsJ Kuczynski, Z Liu, C Lozupone, D McDonald, N Fierer, R KnightNature methods 7 (10), 813-8192010
Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distributionJ Reeder, R KnightNature methods 7 (9), 6682010
Biogeography and habitat modelling of high-alpine bacteriaAJ King, KR Freeman, KF McCormick, RC Lynch, C Lozupone, R Knight, ...Nature Communications 1, 532010
OOS 31-5: Using phylogenetic β diversity measures to understand the factors structuring microbial diversity over large and fine scalesC Lozupone, R KnightThe 95th ESA Annual Meeting2010
OOS 31-9: Soil bacterial diversity in the Arctic is not fundamentally different from other biomesH Chu, N Fierer, C Lauber, JG Caporaso, R Knight, P GroganThe 95th ESA Annual Meeting2010
Stable tRNA-based phylogenies using only 76 nucleotidesJ Widmann, JK Harris, C Lozupone, A Wolfson, R KnightRNA 16 (8), 1469-14772010
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tagsGD Wu, JD Lewis, C Hoffmann, YY Chen, R Knight, K Bittinger, J Hwang, ...BMC microbiology 10 (1), 2062010
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relativesJR Zaneveld, C Lozupone, JI Gordon, R KnightNucleic acids research 38 (12), 3869-38792010
Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soilKG Eilers, CL Lauber, R Knight, N FiererSoil Biology and Biochemistry 42 (6), 896-9032010
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newbornsMG Dominguez-Bello, EK Costello, M Contreras, M Magris, G Hidalgo, ...Proceedings of the National Academy of Sciences 107 (26), 11971-119752010
Postprandial remodeling of the gut microbiota in Burmese pythonsEK Costello, JI Gordon, SM Secor, R KnightThe ISME journal 4 (11), 1375-13852010
279 Altered Gut Microbiota in Toll-Like Receptor-5 (TLR5) Deficient Mice Results in Metabolic SyndromeM Vijay-Kumar, JD Aitken, FA Carvalho, TC Cullender, SM Mwangi, ...Gastroenterology 138 (5), S-522010
Soil bacterial and fungal communities across a pH gradient in an arable soilJ Rousk, E Bååth, PC Brookes, CL Lauber, C Lozupone, JG Caporaso, ...The ISME journal 4 (10), 1340-13512010
Direct sequencing of the human microbiome readily reveals community differencesJ Kuczynski, EK Costello, DR Nemergut, J Zaneveld, CL Lauber, ...Genome Biol 11 (5), 2102010
Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutations (vol 18, pg 141, 2008)M Buvoli, M Hamady, LA Leinwand, R KnightTRENDS IN CARDIOVASCULAR MEDICINE 20 (4), 141-1412010
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twinsPJ Turnbaugh, C Quince, JJ Faith, AC McHardy, T Yatsunenko, F Niazi, ...Proceedings of the National Academy of Sciences 107 (16), 7503-75082010
QIIME allows analysis of high-throughput community sequencing dataJG Caporaso, J Kuczynski, J Stombaugh, K Bittinger, FD Bushman, ...Nature methods 7 (5), 335-3362010
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5M Vijay-Kumar, JD Aitken, FA Carvalho, TC Cullender, S Mwangi, ...Science 328 (5975), 228-2312010
Forensic identification using skin bacterial communitiesN Fierer, CL Lauber, N Zhou, D McDonald, EK Costello, R KnightProceedings of the National Academy of Sciences 107 (14), 6477-64812010
Simple, recurring RNA binding sites for L-arginineT Janas, JJ Widmann, R Knight, M YarusRNA 16 (4), 805-8162010
Effect of storage conditions on the assessment of bacterial community structure in soil and human‐associated samplesCL Lauber, N Zhou, JI Gordon, R Knight, N FiererFEMS microbiology letters 307 (1), 80-862010
Natural and artificial RNAs occupy the same restricted region of sequence spaceR Kennedy, ME Lladser, Z Wu, C Zhang, M Yarus, H De Sterck, R KnightRNA 162010