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.
Andrea joined the Knight Lab in 2020. She has a background in trauma data management and research compliance. She will be assisting the admin team with a variety of responsibilities and support. In her free time she enjoys traveling, theme parks, coffee and spending time with family. She is a huge basketball fan!
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
Justin is a a plant and microbial ecologist with a strong background in mycology. He obtained his Ph.D. from the University of Arizona in 2017, and began working as a postdoc with the Knight lab in 2018. His research is focused on elucidating how dynamics in microbial communities contribute to emergent ecosystem function or host fitness. In particular, Justin wants to know how temporally early factors, such as priority effects and assembly rules, influence such outcomes. He focuses on host-associated microbes, and also considers the influence of their endosymbionts. Interactions with this level of cellular hierarchy are difficult to elucidate using common techniques such as high-throughput, shotgun sequencing of total DNA extracted from host tissues. Therefore, he is interested in using and developing tools, such as Hi-C and extensions, to assist in predicting which microbes may live inside of others. He is also involved in science education, and seek to improve education in biology through fostering inclusive environments, and by using active learning methods.
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.
Carlos got his Ph.D in 2020 from Stanford University, with a focus on elucidating host-gut microbe interactions using mass-spectrometry. In the Knight lab, he hopes to use a multiomic approach to help extend our knowledge of how microbes influence the nervous system, including psychiatric conditions such as depression and anxiety. Carlos is co-mentored by Drs. Rob Knight and David Gonzalez.
Smruthi obtained her PhD in Environmental Engineering from Georgia Institute of Technology in Dec 2019, mainly specializing in environmental microbial genomics, working at the interface of microbial ecology, computational biology and engineering. As a part of her PhD thesis, Smruthi worked on developing integrated wet-lab and computational biology based approaches to model, predict and forecast ecosystem recovery patterns in benthic ecosystems affected by the 2010 Deepwater Horizon oil spill. Smruthi joined the Knight lab in March 2020 and is interested in using multi-omics approaches to provide a holistic view of environmental systems.
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.
Tara joined the Knight Lab in 2015, and she works in the wet lab, assisting our talented team in preparing samples for NGS applications. Tara received her M.S. in Biology from San Diego State University, and her B.S. from Saint Mary’s College of California. She is most interested in human-microbe interactions, especially in regard to the gut-brain axis. Tara is particularly excited about the potential that microbiome research and innovation has in addressing aspects of generally treatment resistant psychiatric conditions such as PTSD, schizophrenia, certain depression and anxiety disorders, and a whole host of other maladies.
I joined the Knight Lab in 2021 as part of the Return to Learn (RTL) initiative and help screen the campus wastewater for SARS-CoV-2. I look forward to bringing our Tritons safely back to campus and hope to increase my understanding of viral ecology in the process. I graduated from UCSD in 2018 with a B.S. in Molecular Biology and have worked on a variety of research projects ranging from digital pathology, to plant genetics, clinical biophotonics, and dolphin cognition.
Lauren graduated from UC Santa Cruz in 2020 with a B.S. in Neuroscience. After graduating, she worked at a biotech company processing clinical samples for the detection of COVID-19. Lauren joined the Knight lab in 2022 to help screen samples for the presence of SARS-CoV-2. She is excited to learn more about the microbiome and its association with overall health and mental wellness
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.
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.
Karenina joined the Knight lab because of her interest in the current and future projects, and also to gain experience in preparation for grad school. Kara's background is in Decision Science and Physiology, but she is excited to learn more about the connection between microbiota and the mind/mental health. Karenina currently works in the wet lab, assisting with sample processing.
Martín Jesus Casas-Maya recently graduated from UCSD in 2022 with a B.S. in General Biology and a minor in Educational Studies. Throughout his undergraduate studies, Martín participated in the Knight Lab through UCSD’s Genentech Summer Research program, the PATHS Research Internship, and the STARS program. Additionally, Martín also volunteered as part of the Return to Learn (RTL) initiative and helped monitor the campus wastewater for SARS-CoV-2. As a DACA recipient from Mexico City who was raised in City Heights, Martín has faced many struggles that have inspired him to be a positive influence for other students from disadvantaged backgrounds who aspire to a career in science. Martín joined the Knight lab in October of 2022. He primarily extracts, purifies, and analyzes DNA and RNA for Next Gen Sequencing, but also works on different parts of the 16S pipeline and is learning some aspects of the shotgun metagenomics pipeline. Martín looks forward to spending his time within the Knight Lab to build his identity as a researcher in preparation for Graduate School.
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 excited to learn more about the microbiome and continue building her research experience. Outside of work, Tara can be found enjoying the outdoors, playing Breath of the Wild, reading, and spending time friends, family, and pets.
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.
Caitlin graduated with her B.S from UC San Diego in 2020 and joined the Knight Lab in 2021. She hopes to learn more about various omic approaches with her time in the wet lab. The interests that led her here include microbial ecology, particularly in extreme environments, and environmental biotechnology. Previous projects she has worked on range from fisheries conservation genetics, to supporting natural product drug discovery. During college she spent her free time rowing with the UCSD Rowing team, and volunteering on deep-sea research vessels.
Clare graduated from the University of Arizona in 2021 with a B.S. in Nutritional Sciences. While at UA, she worked on a research project involving LC/MS analysis of endocannabinoids. After graduating, Clare accepted a contract position at a pharmaceutical company in San Diego where she analyzed drug development compounds via HPLC and GC analyses. Clare joined the Knight Lab in May 2022 as part of the wastewater SARS-CoV-2 detection project. She is passionate about research and is excited to have the opportunity to learn more about the microbiome and its integral relationship with physical and mental wellness.
Maddy graduated from UC Riverside with her B.S. in Biology in December of 2021. While she was an undergrad at UC Riverside she was involved in a plant physiological ecology lab that primarily focused its research on plant hydraulics and plant survival under drought conditions. She joined the Knight Lab in March of 2022 to become a part of the Return to Learn wastewater program to track SARS-CoV-2
Rebecca is an undergraduate student pursuing a major in Human Biology and a minor in Human Developmental Sciences with a Specialization in Equity and Diversity. She is highly interested in scientific research and eager to expand both her knowledge and skillset.
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.
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.
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.
Kelly is a PhD Student in the Biomedical Sciences Program, co-advised by Dr. Amir Zarrinpar. She aims to study the role of the gut microbiome on the development and progression of metabolic syndrome and associated diseases. In particular, Kelly is interested in investigating the role of the gut microbiome and bile acid metabolism in NASH-associated HCC.
I am PhD student in the Biomedical Sciences Program, co-advised by Dr. Amir Zarrinpar. I am a former small animal veterinarian, who aims to study how the microbiome influences zoonotic disease transmission in order to help both animals and people. Other interests include modeling biological networks and 3D printing.
I am a PhD student in the Bioinformatics & Systems Biology department. I aim to advance longitudinal multi-omics investigation — to explore the vast microbial space for host-microbe interactions of value. By leveraging experimental and computational -biology in conjunction, I hope to gain a systems-level understanding of how these complex host-microbe systems are formed and perpetuated. More details can be found in the website below.
I am an MD/PhD candidate in the Bioengineering Department who is working to bring together two fields that do not frequently communicate: oncology and microbiology. My passion for the subject originates from losing my grandmother, who over the course of 4 weeks in 2013, went from a sudden diagnosis of pancreatic cancer to passing despite targeted chemotherapy. This catalyzed my research in cancer genomics at Duke-NUS (Singapore) and, through mentors, eventually broadened to include infectious disease genomics upon my return to Duke University (USA). When the first major cancer microbiome paper (9/2017) showed chemo-degrading bacteria living in more than half of pancreatic cancer patients, the message hit close to home and my research focus was decided. My strategies of study extend from bioinformatics and machine learning to histopathology and technology development in order to characterize, predict, and treat the cancer microbiome. Outside of work, I enjoy doing triathlons (up to HIM distances so far), volunteering at my local church, and traveling the Asia-Pacific region.
I'm a PhD student in the Bioengineering program, co-advised by Soumita Das. My goal is to develop ex vivo systems to explore the interactions between microbiota and the host tissue environment. I'm also passionate about making education accessible to students from underserved and underrepresented communities.
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.
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.
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.
After graduating from UCSD with a Bachelor of Science in Microbiology and a minor in Computer Science, Jeffrey joined the Knight lab in early 2020 as a master’s student. Jeffrey is broadly interested in how (or if) host-associated gut microbiomes influence the evolution of host species across the animal kingdom. Currently, Jeffrey is examining the patterns of bacterial strain diversification in vertebrates for signals of strain phylosymbiosis. When not staring at his computer screen, he most enjoys exploring the outdoors.
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.
I am a PhD student in the Bioinformatics and Systems Biology program at UCSD. My primary interest is computationally studying how the microbiome can affect the development and progression of cancer. In particular, I aim to investigate the interactions between the microbiome and immune response in cancer in the hopes of furthering development of precision medicine applications.
Dan is a bioinformatics PhD student, focused on Multiple Sclerosis and the microbiome. In his past life, he was a software engineer, and he keep his skills fresh through tool development.
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.
Khadijeh Sudqi is a Masters student in Bioengineering, co-mentored by Dr. David Gonzalez. She is interested in studying inflammatory biomarkers present in biopsy and stool samples in IBD patients.
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
Joseph (Joe) Madison is an NSF Postdoctoral Research Fellow visiting from the University of Massachusetts Boston. His research program is broadly interested in microbial evolutionary ecology in the context of microbe-metazoan systems. This includes conceptual and empirical investigations into the mechanisms of evolutionary novelties, innovations, and constraints in the context of microbe-metazoan diversity, speciation, and extinction. Joe also does overlapping work in the history and philosophy of biology.
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)
Sonia Rodriguez Ruano (2014)
Merete Eggesbo (2013)
Fred Delsuc (2012)
Juanma Peralta (2012)
Hongwei Zhou (2012)
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)