Resource competition predicts assembly of gut bacterial communities in vitro.

Autor: Ho PY; Department of Bioengineering, Stanford University, Stanford, CA, USA. poyiho@westlake.edu.cn.; School of Engineering, Westlake University, Hangzhou, China. poyiho@westlake.edu.cn., Nguyen TH; Department of Bioengineering, Stanford University, Stanford, CA, USA., Sanchez JM; Chan Zuckerberg Biohub, San Francisco, CA, USA., DeFelice BC; Chan Zuckerberg Biohub, San Francisco, CA, USA., Huang KC; Department of Bioengineering, Stanford University, Stanford, CA, USA. kchuang@stanford.edu.; Chan Zuckerberg Biohub, San Francisco, CA, USA. kchuang@stanford.edu.; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. kchuang@stanford.edu.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2024 Apr; Vol. 9 (4), pp. 1036-1048. Date of Electronic Publication: 2024 Mar 14.
DOI: 10.1038/s41564-024-01625-w
Abstrakt: Microbial community dynamics arise through interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms to community structure are challenging to untangle. Here we develop a framework to estimate multispecies niche overlaps by combining metabolomics data of individual species, growth measurements in spent media and mathematical models. We applied our framework to an in vitro model system comprising 15 human gut commensals in complex media and showed that a simple model of resource competition accounted for most pairwise interactions. Next, we built a coarse-grained consumer-resource model by grouping metabolomic features depleted by the same set of species and showed that this model predicted the composition of 2-member to 15-member communities with reasonable accuracy. Furthermore, we found that incorporation of cross-feeding and pH-mediated interactions improved model predictions of species coexistence. Our theoretical model and experimental framework can be applied to characterize interspecies interactions in bacterial communities in vitro.
(© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
Databáze: MEDLINE
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