Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Abstract
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences. We identify mucin utilizers and species inhibited by amino acids and short-chain fatty acids. Our analysis also uncovers media for in vitro studies wherein growth capacity correlates well with in vivo abundance. Further value of the underlying resource is demonstrated by correcting pathway gaps in available genome-scale metabolic models of gut microorganisms. Together, the media resource and the extracted knowledge on growth abilities widen experimental and computational access to the gut microbiota.
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Each gut commensal strain has its own nutrient utilization ability and preference, and competition is high between bacteria with overlapping nutrient utilization abilities.
“Each gut commensal strain has its own nutrient utilization ability and preference, and competition is high between bacteria with overlapping nutrient utilization abilities [64, 65].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [64]
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- Authors
- Tramontano, M., Andrejev, S., Pruteanu, M., Klünemann, M., Kuhn, M., Galardini, M., Jouhten, P., Zelezniak, A., Zeller, G., Bork, P., Typas, A., & Patil, K. R.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Humboldt-Universität zu Berlin (DE)
- European Bioinformatics Institute (GB)
- Corresponding author
- Typas, Athanasios
- Patil, Kiran Raosaheb
- ORCID
- Venue
- Nature Microbiology
- Published
- 2018-03-19
- Volume
- 3
- Issue
- 4
- Pages
- 514-522
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W2791571994
- Cited by
- 295
- References
- 65
- Citations by year
- 2026: 22 · 2025: 35 · 2024: 39 · 2023: 41 · 2022: 41 · 2021: 40 · 2020: 35 · 2019: 25 · 2018: 16 · 2017: 1
- FWCI
- 11.56
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- Chalmers Research (Chalmers University of Technology) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
- Keywords
- gut microbiota, bacterial growth characteristics, nutritional preferences, chemically defined medium, mucin utilization, amino acid inhibition, short-chain fatty acids, host-microbiome interactions, genome-scale metabolic models, bacterial metabolism
- MeSH terms
- Gastrointestinal Microbiome, Amino Acids, Bacteria, Culture Media, Fatty Acids, Volatile, Humans, Mucins
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