Jan joined the Knight lab in 2025 but has been part of UCSD since 2017 as a Research Coordinator for the Winzeler, Lewis, Rana, Aceves, and Siva labs. She is a media and communications professional with a Bachelor of Science degree from San Diego State University. She loves her cat, family, the beach, and travel (yes, she is married to Einstein).
Rob Knight
Principal Investigator
Rob Knight, Principal InvestigatorRob Knight is the founding Director of the Center for Microbiome Innovation, and Professor of Pediatrics, Bioengineering, Computer Science & Engineering and Data Science at UC San Diego. He is the Wolfe Family Endowed Chair in Microbiome Research at Rady Children's, and a Visiting Fellow at the Hong Kong Jockey Club Institute of Advanced Science at Hong Kong University of Science and Technology. He was elected to the National Academy of Engineering in 2024, and is a Fellow of the American Association for the Advancement of Science (AAAS), the American Academy of Microbiology (AAM), and the American Institute for Medical and Biological Engineering (AIMBE). He received the 2019 NIH Director’s Pioneer Award and the 2017 Massry Prize. 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 has coauthored over 1000 scientific articles. His talk at TED in 2014 has been viewed over 2 million times. His lab has produced many of the software tools and laboratory techniques that enabled high-throughput microbiome science, including QIIME and UniFrac, and his work has been cited over half a million times. He is co-founder of the Earth Microbiome Project, the American Gut Project, and the companies Biota, Inc., and Micronoma, Inc. He is also Vice President of the Microbiota Vault. His work has linked microbes to a range of health conditions ranging from obesity to Alzheimer’s, has enhanced our understanding of microbes in environments ranging from oceans to deserts, and made high-throughput sequencing techniques accessible to thousands of researchers around the world. Read more about Rob & his research efforts
Administration
Jan M Economy
Research Coordinator
Jerry Kennedy
Academic Program Manager
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.
Traeson Salcido
Administrative Assistant
Traeson joined the Knight Lab in 2025 and is a 4th year undergraduate at UCSD majoring in Public Health with a concentration in Epidemiology. He provides administrative support around the Knight Lab as needed. He enjoys collecting vinyl records and watching baseball.
April Tang
Administrative Assistant
April joined the Knight Lab in 2026 and is a 3rd year undergraduate student at UCSD majoring in Business Economics. She provides administrative support and documentation around the Knight Lab as needed. Outside of work, she enjoys scrapbooking and baking.
Yna Villanueva
Project Coordinator
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.
Lindsey Rogers
Research Project Manager
Lindsey joined the Knight Lab in 2026 as a Research Project Manager. She ensures the award for the project stays on track by aligning work plans with project goals, coordinating across teams, and overseeing progress and spending. Outside of work, she enjoys hiking, teaching yoga, and riding her motorcycle.
Aileen Chung
Research Data Analyst
Aileen joined the Knight Lab in 2025 as an undergrad and now graduated from UCSD in 2026 with a B.S. in Applied Mathematics. She supports handling financial matters in the Knight Lab.
Kaitlyn Phan
Administrative Assistant
Kaitlyn joined the Knight Lab in 2026 and is a 2nd year undergraduate at UCSD majoring in Political Science with a concentration in International Relations. She provides administrative support around the Knight Lab as needed. She enjoys playing basketball and snowboarding.
Post-Doctoral Research Associates
Jianshu Zhao
POST-DOCTORAL RESEARCH ASSOCIATE
Jianshu obtained his Ph.D. in bioinformatics from the Georgia Institute of Technology. He has experience in both software development and algorithm design. Specifically, he is very interested in developing high-performance computational tools for microbial genomics, metagenomics, metatranscriptomics, and so on. He is also interested in the field of environmental microbiology and is obsessed with the enormous diversity of various environments such as soil, the deep sea, and the gut. He was also trained as a community ecologist/microbial ecologist before going into bioinformatics.
Mohammadsobhan Andalibi
POST-DOCTORAL RESEARCH ASSOCIATE
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
Celeste Allaband
Post-doctoral Research Associate
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.
Sam Degregori
POST-DOCTORAL RESEARCH ASSOCIATE
Sam is largely interested in building large-scale comparative microbiome datasets to answer ecological and evolutionary questions concerning host-associated microbiomes from across the tree of life. He is also interested in applying this approach to humans, looking at how our microbiomes interact with geography, lifestyle, and disease on a global scale. Sam completed his PhD at UCLA with Dr. Paul Barber in 2022 and was previously co-advised by Katherine Amato and Rob at Northwestern before officially joining the Knight Lab in 2024. On his free time Sam enjoys surfing and playing chess.
Britta De Pessemier
POST-DOCTORAL RESEARCH ASSOCIATE
Britta obtained her PhD in Bioscience Engineering from Ghent University (Belgium) in December 2025, where her research focused on the role of the skin microbiome in health and disease using multi-omics approaches. She was a visiting scholar in the Knight Lab during her PhD and has since continued as a postdoctoral researcher supported by a B.A.E.F. Fellowship.
Her current research focuses on integrative analysis of metagenomic and metabolomic data to study the skin microbiome across diverse populations, including Indigenous communities, with an emphasis on how lifestyle and environmental factors shape microbial and functional diversity.
Professional Research Associates
Jennifer Cao
Wet Lab Manager
Jennifer has a background in Biology, minoring in Psychology at UC San Diego. She carries with her an industry background of working in microbiology, specifically with the animal microbiome, where she worked in Wet Labs for a number of years before her transition into lab management. She looks forward to understanding more about the microbiome and different analytical methods, as well as supporting and learning alongside our Wet Lab team. In her free time, Jennifer enjoys music and cooking.
Omar Din
Assistant Project Scientist
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
Lauren Hansen
Professional Research Associate
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.
Isabelle Shepherd
Professional Research Associate
Izzy graduated from UC San Diego in 2023 with a B.S in Biochemistry and is on track to finalize a M.S in Chemistry from UC San Diego. During undergrad Izzy worked in a microbiology lab where she studied novel bacteriophage proteins associated with the phage nucleus. Izzy joined the Knight Lab in July 2024, and she is excited to gain experience with next-generation sequencing techniques. In her free time, Izzy enjoys running and listening to music.
Daniel McDonald
Scientific Director
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.
Madison Ambre
Professional Research Associate
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.
Rachel Bock
Professional Research Associate
Rachel has industry experience working with animal gut microbes. As she brings in knowledge surrounding animal microbiomes from her previous place of work, she is enthusiastic to be part of the Knight Lab advancing knowledge of human microbiomes. In her free time, she likes to take her dog to the beach. She looks forward to learning & developing knowledge of the microbiome, as well as developing wetlab methods and various sequencing techniques.
Meika Tomita
Student Research Assistant
Meika is an undergraduate at UC San Diego, pursuing a B.S. in Human Biology. In the Knight Lab, she works with Caitriona Brennan to improve low-biomass sequencing. She is also interested in the connection between the gut and brain, and how microbes play a role in human health and disease. After graduation, Meika hopes to pursue a career that bridges research and healthcare. In her free time, she enjoys playing volleyball and trying new ice cream flavors!
Antonio González Peña
Programmer Analyst
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.
Gillian Wright
Professional Research Associate
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.
Sophia Alonso
Professional Research Associate
Sophia graduated from UC San Diego in 2023 with a B.S. in Bioengineering, with a specialization in Biotechnology. She previously served as a Quality Control Team Lead at Native Microbials, where she managed a team and led process improvements. Sophia joined the Knight Lab in July 2025, eager to expand her knowledge of next-generation sequencing methods and learn more about the link between the human microbiome and health. In her free time, she enjoys reading and baking new desserts.
Graduate Students
Jonathan Kirkland
Graduate Student
Jonathan is a PhD student in the Bioinformatics and Systems Biology program. Previously working in early-stage drug discovery, his focus is on applying computational methods such as deep learning to better understand the relationship between microbial interactions and cancer. Jonathan also works on exploring better visualization techniques for large datasets and generalizable disease models based on microbial research.
Lucas Patel
Graduate Student
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.
Yang Chen
Graduate Student
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.
Michael Iter
Graduate Student
Michael is a PhD student in the Bioinformatics and Systems Biology program. He is interested in incorporating large-scale microbiome analyses with Electronic Health Records to further precision medicine initiatives, especially in the realms of nutrition and metabolic disorders. He has extensive experience with metagenomics and metatranscriptomics. In his free time, you can usually find him on the tennis or basketball court.
Swan Van
Graduate Student
Swan is a PhD student in the Biochemistry and Molecular Biophysics program, co-advised by Dr. David Gonzalez. Her research focuses on integrating metagenomics and metaproteomics to discover and characterize the microbial dark proteome across health and diseases. She also has a broad interest in method development for multi-omics analyses and in applying these approaches to diverse biological systems.
Lora Khatib
Graduate Student
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.
Renee Oles
Graduate Student
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.
Yuhan Sherlyn Weng
Graduate Student
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.
Tanya Kumar
Graduate Student
Tanya is an MD/PhD student in the Bioengineering department, co-advised by Dr. Erika Cyphert. She is interested in studying and engineering polymicrobial biofilms both in health-related and environmental contexts. Outside of lab, she can be found outdoors or spending time with her senior dog, Scroodle.
