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.
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 Halıcıoğlu Data Science Institute 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 900 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 35,000 times, including QIIME 2) and UniFrac (cited over 12,000 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
Administration
Peggy Castaneda
Executive Assistant to Prof. Rob Knight
Katharine Gilbert
Communications Specialist
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
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.
Kalan Tu
Research Administrative Assistant
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 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.
Post-Doctoral Research Associates
Alejandra Rios Hernandez
Post-doctoral Research Associate
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.
Jianshu Zhao
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.
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.
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
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.
Omar Din
POST-DOCTORAL RESEARCH ASSOCIATE
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
Simone Renwick
Post-doctoral Research Associate
Simone obtained her PhD in Molecular and Cellular Biology from the University of Guelph, ON, Canada in 2022. Throughout her doctoral studies, she employed in vitro models of the human colon to study interactions between human milk oligosaccharides (HMOs) and gut bacteria. Currently, Simone is affiliated with the UCSD Mother-Milk-Infant Center of Research Excellence (MOMI CORE) and is jointly advised by Dr. Knight, Dr. Lars Bode, Dr. Pieter Dorrestein, and Dr. Jack Gilbert. Her present research is dedicated to understanding the pivotal role of milk components, including HMOs and milk microbes, in shaping the infant gut microbiota, as well as exploring their potential therapeutic applications for adult health.
Professional Research Associates
Gail Ackermann
Research Analyst
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.
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.
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.
MacKenzie Bryant
Wet Lab Supervisor
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.
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.
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.
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.
Tara Boyer
Professional Research Associate
Tara graduated from UC Riverside with a B.S. in Biology with a minor in Education. She joined the Knight Lab in October 2022 as part of the wastewater SARs-CoV-2 detection project. Since then, Tara has transitioned to shotgun metagenomic and metatranscriptomic pipelines for microbiome sequencing analysis. She works on other various projects regarding development within the lab as well.
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.
Graduate Students
Caitlin Guccione
Graduate Student
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 Perry
Graduate Student
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.
Joycelyn Yiu
Graduate Student
Joycelyn holds a background in the life sciences, with a strong foundation in molecular biology, metaproteomics, and bioinformatics. As a graduate student, she has had the opportunity to work on various research projects, gaining valuable experience in data analysis and interpretation. She is highly motivated by her passion for advancing our understanding of the human gut microbiome and its impact on health and disease.
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.
Rodolfo Antonio Salido Benítez
Graduate Student
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 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.
Caitriona Brennan
Graduate Student
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.
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.
Kalen Cantrell
Graduate Student
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 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.
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.
Stephany Flores-Ramos
Graduate Student
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.
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.
Visiting Scholars
Britta De Pessemier
Visiting Scholar
Britta is a PhD student at Ghent University, Belgium, visiting the Knight Lab with the support of an FWO grant. Her research focuses on studying the role of the skin microbiome in skin disorders, as well as exploring the impact of lifestyle and environmental factors on the skin microbiome. During her stay at the Knight Lab, she will concentrate on exploring various bioinformatic tools to process metagenomics and metabolomics datasets, and perform multi-omics data analyses to obtain a better understanding of the skin microbiome.
