Fermentation Speaker Series Elisa Caffrey, David Zilber, and Justin Sonnenburg

Dr. Chantle Swichkow, a postdoc in Leonid Kruglyak’s lab at UCLA, has been exploring the role of yeast in these symbiotic interactions. By applying her background in mouse genetics to yeast, she studies how yeast strain diversity impacts microbial community composition and the final organoleptic properties of wine, bread, and kombucha.

Join our conversation on the history of Saccharomyces, strain diversity in fermented food production, blue Takis, and the power of Reddit.

One way to characterize fermented foods is based on where the fermentation microbes come from: either spontaneously acquired from the environment (also known as wild fermentation), from a previous ferment (back-slopping), or from a commercial starter community. But how do we identify which microbes are involved in this process in the first place?

Paul Cotter, an Adjunct Professor at University College Cork and Head of Food Biosciences, as well as a Senior Principal Research Officer at Teagasc Food Research Centre, has spent his career addressing this question through tool development, collaborating with a global team of scientists, and exploring the diversity of the fermented food landscape.

Join our conversation on mapping fermented food metagenomes, personalized fermented foods, and lab kefir.

The microbiome of fermented foods, like any microbiome, is a multi-species microbial community and can include a rich mixture of bacteria, fungi, and yeast all in the same fermented food. The presence of a specific microbe cannot always predict the final quality, safety, or flavor of a fermented food, but studying their interactions gives a richer understanding of these community dynamics.

Ben Wolfe, an Associate Professor in the Department of Biology at Tufts University has been exploring these microbial ecologies. Using models such as cheese rinds, sterile baby cabbages, and kombucha, his lab investigates the origins of these fermentation community members, how they interact with each other, and how these communities can evolve and diversify over time.

Join our conversation on microbial onramps, phage resistance, and purple cheese…

Along with bacteria and yeast, fungi play an important role in fermentation. We primarily think of Aspergillus oryzae and Rhizopus oryzae, but there are a number of other fungi that are used in food production, including Aspergillus sojae, Monascus purpureus. We wanted to talk to Dr. Vayu Hill-Maini, postdoctoral Fellow at the Joint Bioengineering Institute at University of California Berkeley, working in the lab of Jay Keasling, who has been approaching research into filamentous fungi in two ways.

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?
With the help of Sevgi’s family and insight from the rest of the community, Sevgi, Veronica and David traveled to Nova Mahala, Bulgaria to explored how rituals around yogurt making impacts the microbial community and final flavor of yogurt.

Dr. Rob Dunn is an an evolutionary biologist, currently a professor at both the Center for Evolutionary Hologenomics at the University of Copenhagen and in the Department of Applied Ecology at North Carolina State University, where he holds the title of Senior Vice Provost for University Interdisciplinary Programs. He discusses the evolution of flavor and fermentation practice.