Peggy joined the Knight Lab in 2022. She has a background in Communications and is a graduate of UCSD. She provides administrative support, scheduling and documentation as needed. She enjoys spending time with her family and exploring San Diego.
Principal InvestigatorRob Knight, Principal Investigator
Rob Knight is the founding Director of the Center for Microbiome Innovation and Professor of Pediatrics, Bioengineering, and Computer Science & Engineering at UC San Diego. He is the Wolfe Family Endowed Chair in Microbiome Research at Rady Children’s. He is a Fellow of the American Association for the Advancement of Science and of the American Academy of Microbiology. He was honored with the 2019 NIH Director’s Pioneer Award for his microbiome research and received the 2017 Massry Prize, often considered a predictor of the Nobel. He is the author of “Follow Your Gut: The Enormous Impact of Tiny Microbes” (Simon & Schuster, 2015), coauthor of “Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System (St. Martin’s Press, 2017), and written over 700 scientific articles. He spoke at TED in 2014 which is viewed over 2 million times. His lab has produced many of the software tools and laboratory techniques that enabled high-throughput microbiome science, including the QIIME pipeline (cited over 30,000 times, including QIIME 2) and UniFrac (cited over 10,000 times including its web interface). He is co-founder of the Earth Microbiome Project, the American Gut Project, and the company Biota, Inc., which uses DNA from microbes in the subsurface to guide oilfield decisions. His work has linked microbes to a range of health conditions including obesity and inflammatory bowel disease, has enhanced our understanding of microbes in environments ranging from the oceans to the tundra, and made high-throughput sequencing techniques accessible to thousands of researchers around the world. Dr. Knight can be followed on Twitter (@knightlabnews) or on his web site http://knightlab.ucsd.edu/. Read more about Rob & his research efforts
Katharine joined the Knight Lab in 2019 as their Communications Specialist focused on developing The Microsetta Initiative and its connecting projects. She has an extensive background in Arts & Business Development and will be paying particular attention to content creation, and how it can support and engage communities in the realm of public health.
Jerry Kennedy has been with the Knight lab since ~2009 and has been known to wrangle legal issues and financial matters in the Knight lab. He is indispensable.
Kalan joined the Knight Lab in 2023, and has a background in Public Health. At the Knight Lab, he attends to clerical duties related to the lab's administrative operation. Ensuring the lab's general functions, he is usually overseeing organizational tasks like facilitating meetings, implementing system's policy, and solving broad departmental issues. Ask him about his rambunctious cat, Penelope.
Yna joined the Knight Lab in 2019, and has a background in Anthropology. At the Knight Lab, she provides administrative support, such as coordinating schedules, document preparation, and overall making the lab members' lives just a little bit easier. In her free time, she is caring for her plants.
Post-Doctoral Research Associates
Alejandra obtained her PhD in Food Science and Nutrition from the University of Barcelona. She has experience conducting clinical trials in the field of Pediatrics in countries such as Mexico, Spain, and New Zealand. Her main research areas investigate the interrelationship between children’s diet and sleep and their health and development. Alejandra joined the Knight lab in 2021 and her research activities involve the correspondence of dietary instruments, and their relation to microbiome composition. Alejandra is passionate about child wellbeing and translating research to make a difference in the health of children and future adults.
Celeste is a veterinarian and received her DVM from Colorado State University in 2014. She was in clinical practice for several years before returning to do research. Celeste received her PhD in 2022 from UC San Diego, with a focus on temporal microbiome dynamics. She plans to use a multi-omic approach to learn more about how microbes influence central biological processes across the web of life. She has a particular interest in bile acid signaling.
Mohammad is a physician who obtained his MD from the Mashhad University of Medical Sciences. In 2022, he started his postdoctoral fellowship at UC San Diego, where he conducted research on neurological complications in people with HIV. In 2023, he joined the Knight Lab and focused his research on investigating the effects of cannabidiol and tetrahydrocannabinol on microbiome composition, endocannabinoids and neuroinflammation in people with HIV, using novel metagenomic techniques such as shotgun metagenomic sequencing
Omar's background is in the fields of synthetic and quantitative biology. Previously, he worked on engineering microbes with novel genetic circuits for the development of microbial drug delivery vehicles, synthetic ecologies, and bacteria-electrode interfaces for biosensing. He is interested in studying the physiology of bacteria in vivo and how this understanding might inform future engineering approaches. He is currently focused on investigating the evolution and expression of bacteria in the microbiota through the application of novel tools, such as spatial transcriptomic technologies, among others
Professional Research Associates
Gail moved to Rob's lab in 2011, where she has accepted responsibility for many things. This includes IRB, IBC and IACUC protocols. Gail assists with metadata curation and upload of projects to the database.
Lauren graduated from UC Santa Cruz in 2020 with a B.S. in Neuroscience and after graduation worked at a biotech company to detect COVID-19 in clinical samples. Lauren joined the Knight lab in 2022 to help screen surface samples for SARS-CoV-2 as a part of the SASEA program. She now mainly works on the Knight lab’s metatranscriptomic and metagenomic pipelines for microbiome sequencing analysis. Lauren is also involved with the development and optimization of new methods for various projects within the lab. She is excited to learn more about the microbiome and continue building her career as a researcher.
Madison graduated from Michigan State University with a B.S. in Genomics and Molecular Genetics. As an undergrad, she was a part of a lab investigating metabolites from the mouse microbiome. After graduating, she moved to San Diego and worked at a biotech company optimizing and developing DNA sequencing technology. Madison is excited to take part in microbiome research that improves understanding of health and disease and to learn more about automating experiments. In her free time, she enjoys going to the beach and exploring San Diego
Cooper is a second-year undergraduate volunteer attending San Diego Miramar College as an Engineering Pre-Studies major. Next fall, he plans to transfer to UCSD as a Bioengineering student and hopes to study Biomaterials and Tissue Engineering. Cooper joined the Knight Lab as a volunteer in 2023 and is excited to continue learning more about lab work, procedures, and more!
MacKenzie graduated in April 2017 with my MS degree in Infectious Diseases and Microbiology from the University of Pittsburgh. MacKenzie's thesis was focused on the variability of the lung microbiome in macaques throughout the course of Mycobacterium tuberculosis infection. After she graduated, MacKenzie wanted to expand her knowledge about the microbiome and DNA sequencing. The Knight lab was a perfect fit for her interests! In the lab, MacKenzie works on different parts of the 16S pipeline and am learning some aspects of the shotgun metagenomics pipeline. In her free time, she enjoys photography, going to music festivals, hiking, and camping.
Maddy graduated from UC Riverside in 2021 with a B.S. in Biology. While she was an undergrad she was involved in a plant physiological ecology lab that focused on plant hydraulics and plant survival under drought conditions. Maddy joined the lab in March 2022 to join the Return to Learn program. Maddy currently works on the 16S amplicon and shotgun metagenomics pipelines.
Antonio's main interest is developing new computational methods to compare large numbers of microbial communities and to put these comparisons in a temporal and spatial context, with the ultimate goal of understanding and controlling microbial communities to improve health in different environments. Antonio has worked on many projects in environments from soils to the human body, leading to the development of novel analysis methods and software packages including QIIME, Qiita, SitePainter, Emperor, and Evident.
Jackson is an undergraduate student majoring in Neurobiology. During high school, Jackson worked in a neuroscience lab studying the links between REM sleep and memory formation. He joined the Knight Lab in September 2022 to help perform DNA extraction protocols and learn about metagenomic methods. He is excited to learn about the microbiome in the context of aging and age-linked diseases. In his free time, Jackson enjoys playing basketball and practicing classical guitar.
Daniel's research emphasis is on the development of computational methods that enable analysis of microbiome data at scale irrespective of the environment (although poop is fun). Daniel is a core developer on many of the software projects the lab is involved in, and has a strong interest in open source and open access processes. Daniel is the American Gut project manager, overseeing the effort including its expansion into the British Gut and an Australian aggregation site.
Tara graduated from UC Riverside with a B.S. in Biology with a minor in Education. During her undergrad years, Tara joined an entomology lab, and conducted her own experiment focused on Salvia (California Sage), pests, and pesticide use. She is passionate about research and joining a microbiome research lab is a great fit. Tara joined the Knight Lab in October 2022 as part of the wastewater SARs-CoV-2 detection project. She is currently working on the 16s amplicon and the shotgun metagenomic pipeline.
Gillian graduated from UC Riverside in 2020 with a B.S. in Microbiology and went on to complete her M.S. in Microbiology at UC Davis in 2023. Her thesis was focused on early-life perturbation of the microbiota, gut, and brain axis in a mouse model of pediatric inflammatory bowel disease. Gillian joined the Knight Lab in April 2023 with the goal of expanding her knowledge of next-generation sequencing methods. She currently works on the 16S and metagenomics pipelines. In her free time, Gillian enjoys reading, cooking, going to the zoo, and snuggling up with her pets at home.
Hazel is a PhD student in the Biomedical Sciences program. Hazel's research utilizes computational tools to elucidate connections between the gut microbiome and mental illness. She is particularly interested in how microbially-derived metabolites may influence the progression of mental illness.
Caitlin is a PhD student in the Bioinformatics and Systems Biology (BISB) program, co-advised by Dr. Kit Curtius. Caitlin's research is centered on the intersection between the human microbiome and cancer. She aims to build mathematical models to better understand why patients progress to cancer by combing mutations in human host DNA with changes in the microbiome.
Daniela is a PhD graduate student in the bioinformatics and systems biology (BISB) program. Her main roles are in software development, as she is primarily interested in how mathematical and deep learning techniques can be used to improve microbiome data analysis, especially in early child development cohorts. Elsewhere Daniela can be found in the mountains.
Kristina is a PhD Student in the Bioengineering program and graduated from UC Berkeley with a BS in Molecular Environmental Biology. She implements computational tools for microbiome analysis of female health/disease and is energized by its potential to support gender equality in science. Her work extends into wet lab protocol development for host DNA depletion via collaboration with CMI and Pfizer. In her free time, Kristina also loves rock climbing and watercolor painting.
Lora is a PhD student in the Neurosciences Graduate Program. She is interested in uncovering the connections between the microbiome and the brain. Her research focuses on using computational models to investigate how microbial cells in the body influence neurotransmitter regulation and neuroinflammation, and how this impacts mental health and neurodegenerative diseases.
I am a PhD student in the Bioengineering program. I joined the Knight Lab because I have a deep interest in lab automation and high throughput systems. I am a fan of robotics that constantly pursues replacing monotonous human labor with hands off experimentation.
Yang is a Ph.D. student in the Biomedical Sciences program, co-advised by Dr. Richard Gallo. Her research focuses on the role of the skin microbiome on dermatological diseases. Yang is particularly interested in microbiome-based therapeutics for skin disorders and building efficient and accessible bioinformatics tools for microbial research.
Anirudh is a Master's student in the Bioengineering Department. His research focuses on analyzing microbial patterns to investigate the progression of Alzheimer's disease. Other than research, Anirudh loves to run and hike various nature areas!
Caitriona is a PhD student in the Biological Sciences program, co-advised by Dr. Jeff Hasty. Caitriona’s interests consist of expanding our understanding of the complex microbial communities that surround and inhabit us. To do this she aims to use metagenomic approaches including long-read sequencing technologies to uncover novel microbial diversity, gene functions and host-microbe interactions.
Kalen is a PhD student in the Computer Science and Engineer program. His interests include developing and optimizing computational methods to analyze and visual large scale microbial data. Kalen is also interested in utilizing deep learning to help automate pipelines used in microbial research and assist researchers with their studies.
Lucas is an MD/PhD student in the Bioinformatics and Systems Biology program. He is interested in applying genomic techniques and imaging modalities towards precision medicine. His research focuses on decoding microbial interactions that influence neurological health. Lucas also builds and maintains computational tools and software packages for large-scale microbial analysis.
Renee is a PhD student in the Biomedical Sciences program, co-advised by Dr. Hiutung Chu. She focuses on the role of the gut microbiota in IBD and inflammation. Renee's research examines the association between disease scores/immune cell activation and the genomes of intestinal microbes. She hopes to work at the interface between computational biology and microbiology to make computational tools more accessible to biologists from a variety of backgrounds.
Stephany is a PhD student in the Biomedical Sciences program, co-advised by Dr. Rob Knight and Dr. Amir Zarrinpar. Stephany is interested in discovering new microbially derived metabolites and how they can influence various metabolic disorders such as a liver disease, diabetes, etc. Towards this aim, she is utilizing her classical statistical training and new methods developed by the Knight lab to find diurnal and circadian patterns in the metabolomic and microbiome profiles of mice and clinical subjects.
Sherlyn is a PhD student in the Bioinformatics & Systems Biology department, co-advised by Dr. Karsten Zengler. Her primary research interest is centered around the roles of the human microbiome in various diseases. On the side, she is also interested in exploring genome organization and community composition in the indoor environment.
Bertalan is a PhD Student at the University of Szeged, Hungary, visiting the Knight Lab on a Fulbright Scholarship. He is primarily interested in bioinformatic analysis of the human microbiome and utilizing machine learning models to predict diseases based on the composition of the microbial community.
Former Lab Members
Dorota Porazinska (2013-2015), University of Colorado Boulder
Douglas Woodhams (2012-2015), University of Massachussetts Boston
Christian Lauber (2008-2014), Nestle
Laura Parfrey (2011-2013), University of British Columbia
Jose Carlos Clemente Litran (2010-2013), Icahn School of Medicine at Mount Sinai
Catherine Lozupone (2007-2013), University of Colorado Denver
Jesse Stombaugh (2009-2012), Thermo Fisher Scientific
Bharath Prithiviraj (2011), CGCS
J Gregory Caporaso (2009-2011), Northern Arizona University
Jens Reeder (2008-2010), Genentech
Sara Nakielny (2009-2010), University of California San Fransisco
Elizabeth Costello (2008-2009), Stanford University
Zongzhi Liu (2006-2008), Yale
Jana Chocholousova (2006), Institute of Organic and Biochemistry, Czech Republic
Grant Gogul (2013-2015), ASCUS
Emily TerAvest (2013-2015) University of Colorado Boulder
Will van Treuren (2012-2014), Stanford University
Michael Oberg (2013-2014), University of Colorado Boulder
Elijah Lovelace (2014) STRIVE Preparatory School
Matthew Gebert (2011-2013), University of Colorado Denver
Donna Berg-Lyons (2008-2014)University of Colorado Boulder
Juanma Peralta (2013-2013), UGR
Doug Wendel (2009-2013), Archer
Daniel McDonald (2008-2011) University of California San Diego
Bill Shaffer (2009-2010)
Bob Larsen (2009-2010)
John Hayes (2009)
Dimitry Krementsov (2022)
Trine Zachariasen (2022)
Nancy Rehrer (2022)
Roberta Raffaeta (2021)
Sonia Rodriguez Ruano (2014)
Merete Eggesbo (2013)
Fred Delsuc (2012)
Juanma Peralta (2012)
Hongwei Zhou (2012)
Jeffrey Chiu (2021-2023) UC San Diego
Sophie Weiss (2013-2015), SomaLogic
Daniel McDonald (2011-2015), Institute of Systems Biology
Luke Ursell (2011-2015), Biota
Nigel Cook (2010-2011)
Meg Pirrung (2009-2013) Pacific Northwest National Lab
Tony Walters (2009-2014), Max Planck Institute
Antonio Gonzalez-Peña (2010-2012) University of Colorado, Boulder
Jeremy Widmann (2005-2007), Archer
Dan Knights (2009-2012), University of Minnesota
Justin Kuczynski (2008-2011), Second Genome
Jesse Zaneveld (2006-2011), Oregon State University
Micah Hamady (2004-2009), TwistBio
Sandra Smit (2004-2008), Wageningen
Shandy Wikmann (2004-2006)
Megan Lau (2015)
Cole Heale (2015-2017)
Zach Owyang (2015-2017)
Michael Leung (2015-2017)
Alec Bibat (2013-2014)
Matthew Malone (2014)
Genevieve Bennett (2014)
Tim Vigers (2013)
Kathy Holt (2013)
Elijah Lovelace (2013)
Catherine Nichols (2012-2013)
Kyle Keeper (2012-2013)
Kumar Thurimella (2012-2013)
Will van Treuren (2009-2012), Stanford University
Becky Paulson (2009-2010)
Greg Humphrey (2009-2010)
Reece Gesumaria (2009-2010)
Ryan Kennedy (2007-2009)
Julia Goodrich (2008-2010)
Daniel McDonald (2004-2008)
Anh Vu (2007-2009)
Jonathan Griego (2008)
Jason Forbes (2006-2007)
Hazel Ozuna (summer 2007)
Nick Zhou (summer 2007)
Vikas Malaiya (2005-2007)
Stephanie Wilson (2005-2007)
Matthew Iyer (2006-2007)
John Quinn (2005-2006)
Preston Galais (2006)
Ian Sharp (2006)
Johnross Ford (2005)
Ravi Kumar (2005)
Michael Eaton (2004)
Roberto Marquez (summer 2004)