Metabolic dependencies drive species co-occurrence in diverse microbial communities
Open accessAbstract
Significance: Although metabolic interactions have long been implicated in the assembly of microbial communities, their general prevalence has remained largely unknown. In this study, we systematically survey, by using a metabolic modeling approach, the extent of resource competition and metabolic cross-feeding in over 800 microbial communities from diverse habitats. We show that interspecies metabolic exchanges are widespread in natural communities, and that such exchanges can provide group advantage under nutrient-poor conditions. Our results highlight metabolic dependencies as a major driver of species co-occurrence. The presented methodology and mechanistic insights have broad implications for understanding compositional variation in natural communities as well as for facilitating the design of synthetic microbial communities.
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Flux Balance Analysis models have been used to predict and understand the behavior of microbes given their environment.
“For instance, Flux Balance Analysis (FBA) models have been used to predict and understand the behavior of microbes given their environment (Orth et al., 2010;Thiele et al., 2013;Zelezniak et al., 2015).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Zelezniak et al., 2015
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- Authors
- Zelezniak, A., Andrejev, S., Ponomarova, O., Mende, D. R., Bork, P., & Patil, K. R.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2015-05-04
- Volume
- 112
- Issue
- 20
- Pages
- 6449-6454
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4443341
- OpenAlex
- W2102681753
- Cited by
- 930
- References
- 6
- Citations by year
- 2026: 116 · 2025: 117 · 2024: 109 · 2023: 102 · 2022: 105 · 2021: 81 · 2020: 74 · 2019: 52 · 2018: 62 · 2017: 48 · 2016: 50 · 2015: 13
- FWCI
- 25.05
- Type
- journal article
- Language
- en
- Update notices
- correction (2015-12-14)
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- microbial community assembly, species co-occurrence, metabolic dependencies, resource competition, metabolite exchange, genome-scale metabolic modeling, flux balance analysis, collaborative interaction, amino acid substitutions, nutrient limitation
- MeSH terms
- Models, Biological, Phylogeny, Species Specificity, Symbiosis, Statistics, Nonparametric, Metabolic Networks and Pathways, Microbial Interactions, Microbial Consortia
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