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Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
Open accessAbstract
Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures or synthetic assemblies. Here, we show how kefir, a natural milk-fermenting community of prokaryotes (predominantly lactic and acetic acid bacteria) and yeasts (family Saccharomycetaceae), realizes stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microorganisms) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open the niche for the followers by making available metabolites such as amino acids and lactate. Through metabolomics, transcriptomics and large-scale mapping of inter-species interactions, we show how microorganisms poorly suited for milk survive in-and even dominate-the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.
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“L. kefiranofaciens and Lentilactobacillus kefiri 93,94 co-occurred in milk kefir,”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [93]
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Metadata
- Authors
- Blasche, S., Kim, Y., Mars, R. A. T., Machado, D., Maansson, M., Kafkia, E., Milanese, A., Zeller, G., Teusink, B., Nielsen, J., Benes, V., Neves, R., Sauer, U., & Patil, K. R.
- Affiliations
- European Molecular Biology Laboratory (DE)
- ETH Zurich (CH)
- Chr. Hansen (Denmark) (DK)
- University of Cambridge (GB)
- Vrije Universiteit Amsterdam (NL)
- Chalmers University of Technology (SE)
- Corresponding author
- Patil, Kiran Raosaheb
- ORCID
- Venue
- Nature Microbiology
- Published
- 2021-01-04
- Volume
- 6
- Issue
- 2
- Pages
- 196-208
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC7610452
- OpenAlex
- W3120785972
- Cited by
- 328
- References
- 73
- Citations by year
- 2026: 73 · 2025: 59 · 2024: 65 · 2023: 55 · 2022: 46 · 2021: 30
- FWCI
- 29.58
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- VU Research Portal (publishedVersion)
- PubMed Central (acceptedVersion)
- Chalmers Research (Chalmers University of Technology) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Apollo
- Funders
- Bundesministerium für Bildung und Forschung (031A601B)
- Innovationsfonden (6150-00033A)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Fermentation and Sensory Analysis
- Keywords
- kefir, microbial coexistence, metabolic cooperation, resource partitioning, kefir grains, lactic acid bacteria, acetic acid bacteria, Saccharomycetaceae, dairy fermentation, interspecies interactions, metabolite dynamics, species co-occurrence
- MeSH terms
- Kefir, Bacteria, Saccharomycetales, Fermentation, Phylogeny, Acetic Acid, Lactic Acid, Metabolomics, Microbial Interactions, Microbiota
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