Fermented foods seminar by Elisa Caffery

TITLE: A targeted exploration of the fermented food multi-omics landscape: Microbe-food-metabolite dynamics and implications for human health

SPEAKER: Elisa Caffery, PhD fellow, Stanford University, Department of Microbiology and Immunology, Sonnenburg Lab

FERMENTS: kombucha and water kefir to be served

ABSTRACT: Fermented foods, traditionally prepared for preservation and flavor, recently have been implicated in promoting human health through reduced circulating inflammatory markers and increased intestinal microbiota diversity in interventional human studies (Wastyk et al, Cell, 2021). A key next question is whether these benefits are due to metabolites (chemical compounds produced during the microbial fermentation process) or the microbes themselves. While fermented food metabolomics has been a growing area of research, time-course studies are needed to compare how metabolites and microbial strains change over time during fermentation. In addition, understanding which aspects of a fermented food’s metabolite signature is shared with a broad category of ferments versus unique is informative to a broad array of topics ranging from hypothesis generation to guiding future health recommendations. Focusing on lactic acid fermented foods, we used our mass spectrometry (LC-MS) pipeline (Han et al., Nature 2021) to perform time-course metabolomics. Computational analysis allowed for the identification of over 100 microbial metabolites that change over fermentation, including compounds implicated in human health and flavor. To identify and characterize microbes involved in the changes in metabolite landscape, a novel fermented food focused metagenomics reference database was constructed using the computational tools dRep and inStrain (Olm et al., Journal, 2017; Olm et al., Journal, 2021) to identify microbes involved in the fermentation process. Defining the broad spectrum of metabolites that are produced, as well as characterizing novel microbes involved in fermentation sets the stage for mechanistic interrogation of fermentation. Current work is focused on gaining insight into food safety, flavor development, food adulteration, and how metabolites present in fermented foods affect human health.