Sonnenburg Lab

🌱 Introducing the Stanford Food Fermentation Conference! Join us September 4–5, 2025 at Stanford University for two days of talks, discussion, and discovery at the frontier of fermentation science. We’ll explore: • How do fermentation communities assemble? • What is the shared evolutionary history between microbes and humans? • How do fermented foods interact with the gut microbiome? • What can we learn from the global, understudied fermented food landscape? • And what is the future of fermentation and health? Space is limited — apply by May 15! 🔗 Link in bio 💸 Travel grants available Organized by Elisa Caffrey, David Zilber, and Justin Sonnenburg Hosted by the Stanford School of Medicine, Department of Microbiology & Immunology #fermentationconference #microbiome #fermentedfoods #guthealth #microbialecology #foodscience #stanford #sustainability #futureoffood

The Fermentation Series is back! We are kicking off the speaker series with a conversation with Sevgi Mutlu Sirakova, Veronica Sinotte on their trip with David Zilber to Nova Mahala, Bulgaria. With the help of Sevgi’s family and insight from the rest of the community, the research group explored how rituals around yogurt making impacts the microbial community and final flavor of yogurt. One of the most well recognized microbes in food fermentation is Lactobacillus delbrueckii subsp. bulgaricus, used to produce most yogurts today. Originally named Bacillus bulgarian, the name plays homage to Bulgaria where it was first isolated in 1905. But before we isolated this microbe and cultured it to use as a starter, how was yogurt made? And what can relearning of these yogurt making practices teach us about microbial ecology? Veronica is a Postdoctoral Researcher at the University of Copenhagen’s Center for Evolutionary Hologenomics, and works in the Labs of Prof. Rob Dunn and Associate Prof. Sandra Andersen, and Sevgi is a PhD Candidate at the Ludwig-Maximilians-University Rachel Carson Center (Munich). Podcast link in bio.

Embark on a journey to a healthier gut and a happier you. Dive into the world of gut health with @david_zilber , @emeranmayer , and Erica & Justin from @sonnenburglab . Episode 1 is streaming now. Link in bio.

Excited to see our new resource article out in print in Cell Press today: "Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes." Congrats Matt Carter, @mattman0249 , and Bryan Merrill (Link in bio) This article presents a deep dive into the impact of industrialization on the gut microbiome. We discovered many incredible results with this dataset (read for yourself to see what I mean), but there is still much more to learn. These data are an invaluable reference for future studies to understand the global impacts of industrialization on the gut microbiome. Beyond uploading the data to public repositories, we also worked with Zenodo to make the data especially easy to access. See link in paper step-by-step instructions on how to download the reads, assemblies, genomes, and other key data. This work is reliant on the de-identified Hadza individuals who contributed to this academic pursuit. Please keep in mind that the Hadza are a modern people facing many challenges who deserve the same rights to self-determination as peoples in the post-industrialized west. A translated infographic of the results of this study was sent to the Hadza last year, but the presenting anthropologist got COVID after landing in Africa. Efforts are on-going to present the results back to the Hadza this year.

Join us Tuesday for our last discussion of this season! We will be joined by Dr. Rob Dunn (@your_wildlife ), an evolutionary biology professor holding joint appointments in the Department of Applied Ecology at North Carolina State University and the Center for Evolutionary Hologenomics at the University of Copenhagen. Together, we will explore our shared microbial history and what traditions of fermentation practice can teach us about microbiology. If you have any questions you want to see addressed, please submit them in the link in bio. And don’t forget to register!

Join us next Tuesday, June 6th, for a discussion with Dr. Maya Hey on “What are the social, rhetorical, and philosophical dimensions to studying ferments and (gut) microbiomes?” Bringing her 15 years of research in fermentation and health, @heymayahey will present on the need for health researchers to break down disciplinary silos and consult, collaborate, and coordinate with social sciences, humanities, and practitioners who all have partial perspectives on how fermentation/health come to be. We encourage you to ask questions ahead of time. Question submission and registration link in bio. ⤴️

Congrats Dr. Gellman! 🎉 On May 19th, Rebecca gave a fantastic thesis presentation on “Differential carbohydrate metabolism shapes colonization by intestinal Bacteroidetes” We are excited for your next adventure @uchicago in Dr. Laurie Comstock’s lab 🧫 Check out Rebecca’s work in the link in bio!

How has fermentation practice changed in the past 25 years? Where is regulation and public perceptions of food fermentation heading? How can fermentation impact community health? Alex Hozven has been fermenting and innovating at @culturedpickleshop in Berkeley with her husband, Kevin Farley. Over the past 25 years, they have observed plenty of changes in the fermentation landscape, and have much to share about the future of fermentation. Join us next Tuesday, April 18th, for a discussion with Alex around the past, present, and future of fermentation. Registration link and question submission in bio!

What is the connection between fermentation, flavor innovation, and biodiversity? And how does it relate to health? Our third talk in the Fermentation and Health Speaker Series will be presented by Dr. Joshua Evans (@jovidean ), on Tuesday, March 28th at 9am PST/6pm CET. Dr. Evans is Senior Researcher and Leader of the Sustainable Food Innovation Group at the Center for Biosustainability at the Technical University of Denmark. His multidisciplinary group uses culinary research & development to make flavorful, sustainable, often fermented foods, scientific methods to study their flavour, ecology and evolution, and social science and artistic practice to understand and experiment with how they might fit into food culture. In his talk, Dr. Evans will share some of his work on how the pursuit of new flavors through fermentation can lead to novel microbial ecologies and evolutionary histories, and how bringing together art, science, and cooking through fermentation can invite closer relationships to our bodies and to the planet. If you have questions for Dr. Evans, please submit them! Link in bio to register and submit questions. The talk will be recorded, so make sure to sign up for the mailing list to get the link. See you Tuesday!

Our new paper by @hcwastyk is out in Gut Microbes. In this randomized, placebo controlled study, we investigated the impact of probiotic supplements on individuals with metabolic syndrome. It helped some people improve their triglycerides and diastolic blood pressure, but made others slightly worse by increasing their blood glucose and insulin. Diet is one of the factors that distinguished these groups. To read more, see the paper link in bio ⇧

Join us for the second talk in our Fermentation and Health Speaker Series on Tuesday, February 28th at 9am PST/6pm CET with Dr. Suzanne Devkota (@suzannedevkota ). Dr. Devkota is an Associate Professor at the Cedars-Sinai Division of Gastroenterology and Director Microbiome Research at the F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute. Her research on the impact of diet and the gut microbiome on inflammatory and metabolic disease provides valuable insight into the current role and limitations of fermented foods in clinical applications. We want to encourage you to submit questions and topics you are interested in hearing her address! Link in bio to register and submit questions. The talk will be recorded, so make sure to sign up for the mailing list to get the link. See you next Tuesday!

What do we really know about fermented foods and health? We are excited to present the new Fermentation and Health Speaker Series! Led by David Zilber (@david_zilber ), Elisa Caffrey (@undefinedaesthetic ), and Dr. Justin Sonnenburg, (@sonnenburglab ) we will explore what is known and what we still need to understand about the relationship between fermented foods and human health. Starting January 24th at 09:00 PST/18:00 CET David Zilber will be our first presenter, discussing a framework through which to consider fermented foods and health. We will have an exciting new speaker every month, from Dr. Suzanne Devkota (@suzannedevkota ) from Cedars-Sinai discussing clinical relevance of fermented foods, Joshua Evans (@jovidean ) from the Novo Nordisk Foundation Center for Biosustainability speaking to the role of fermentation in the world of fine dining, Alex Hozven and Kevin Farley from the Cultured Pickle Shop (@culturedpickleshop ) discussing the needs and understandings of at-home and commercial fermentation practices, Maya Hey (@heymayahey ) from Colorado State University presenting her work on the public understanding and commercialization of fermented foods and health, and Rob Dunn (@your_wildlife ) from NC State, who will dive into the shared history of humans and their fermentation practices. Each presentation will be followed by a moderated discussion, with time for audience q&a. For updated, sign up using the link our bio!