Caffrey, Elisa B., Matthew R. Olm, Caroline I. Kothe, Hannah C. Wastyk, Joshua D. Evans, and Justin L. Sonnenburg. "MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics." Msystems (2025): e00141-25.
- This study presents MiFoDB, a scalable workflow and database for alignment-based metagenomic analysis of fermented foods that enables strain-level resolution of microbial community dynamics.
- It demonstrates how MiFoDB can be used to track microbial succession, identify novel fermentation-associated species, and standardize data across food microbiome studies.
Caffrey, Elisa B., Dalia Perelman, Catherine P. Ward, Erica D. Sonnenburg, Christopher D. Gardner, and Justin L. Sonnenburg. "Unpacking food fermentation: Clinically relevant tools for fermented food identification and consumption." Advances in Nutrition (2025): 100412.
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This paper outlines a framework for defining, identifying, and quantifying fermented foods in clinical and epidemiological research.
- It provides practical tools and classification criteria to improve reproducibility and facilitate comparisons across human diet–microbiome studies.
- Positions prebiotics, probiotics, and postbiotics within the broader context of fermented foods to clarify their overlapping yet distinct roles in human health.
Caffrey, Elisa B., Justin L. Sonnenburg, and Suzanne Devkota. "Our extended microbiome: The human-relevant metabolites and biology of fermented foods." Cell metabolism 36, no. 4 (2024): 684-701.
- This review reframes fermented foods as an extension of the human microbiome, emphasizing the metabolites and microbial interactions they contribute to host biology.
- It integrates evidence from microbiology, metabolomics, and nutrition to highlight how fermented food metabolites influence immunity, metabolism, and gut–brain communication.
Gerrick, E.R., Zlitni, S., West, P.T., Carter, M.M., Mechler, C.M., Olm, M.R., Caffrey, E.B., Li, J.A., Higginbottom, S.K., Severyn, C.J. and Kracke, F., 2024. Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition. Cell, 187(1), pp.62-78.
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This paper reveals that commensal protists exhibit remarkable metabolic diversity that shapes intestinal immune responses and mediates competition across kingdoms of life.
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Using integrative multi-omics and gnotobiotic models, the study uncovers specific protist-derived metabolites that modulate host–microbe and microbe–microbe interactions in the gut.