ArticleFrontiers in microbiology2019
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture.
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 278 citations in OpenAlex.
- Effects of Black Soldier Fly (Plant-environment interactions (Hoboken, N.J.) · 2026Article
- Comparative analysis of metabolite and microbial community dynamics during spontaneous fermentation ofFood chemistry: X · 2025Article
- Optimization of process conditions and kinetic microbial growth for milk fermentation using domestic kefir grains from Costa Rica.Italian journal of food safety · 2025Article
- Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.BMC genomics · 2025Article
- The Production of Water Kefir Drink with the Addition of Dried Figs in the Horizontal Rotating Tubular Bioreactor.Foods (Basel, Switzerland) · 2024Article
- Microbial interactions shape cheese flavour formation.Nature communications · 2023Article
- Article
- Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors.Foods (Basel, Switzerland) · 2022Article
- Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities.Genes · 2021Article
- High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.Communications biology · 2021Article
- Structured environments foster competitor coexistence by manipulating interspecies interfaces.PLoS computational biology · 2021Article
- New Insights Into Cinnamoyl Esterase Activity ofFrontiers in microbiology · 2019Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that
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