Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability

Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and funct...

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Bibliographic Details
Published in:The ISME Journal 2023-12, Vol.17 (12), p.2370-2380
Main Authors: Starke, Svenja, Harris, Danielle M. M., Zimmermann, Johannes, Schuchardt, Sven, Oumari, Mhmd, Frank, Derk, Bang, Corinna, Rosenstiel, Philip, Schreiber, Stefan, Frey, Norbert, Franke, Andre, Aden, Konrad, Waschina, Silvio
Format: Article
Language:English
Subjects:
45/23
45/47
631/158/2451
631/326/2565/2134
631/45/320
Amino acids
Auxotrophs
Auxotrophy
Bacteria
Bile acids
Ecology
Evolutionary Biology
Genotypes
Intestinal microflora
Life Sciences
Metabolism
Metabolomics
Metagenomics
Microbial activity
Microbial Ecology
Microbial Genetics and Genomics
Microbiology
Microbiomes
Microorganisms
Stability
Syntrophism
Trimethylamine
Tryptophan
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Summary:Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and function of the human gut microbiome remain poorly understood. This study performed the first systematic analysis of the distribution of amino acid auxotrophies in the human gut microbiome using a combined metabolomic, metagenomic, and metabolic modeling approach. Results showed that amino acid auxotrophies are ubiquitous in the colon microbiome, with tryptophan auxotrophy being the most common. Auxotrophy frequencies were higher for those amino acids that are also essential to the human host. Moreover, a higher overall abundance of auxotrophies was associated with greater microbiome diversity and stability, and the distribution of auxotrophs was found to be related to the human host’s metabolome, including trimethylamine oxide, small aromatic acids, and secondary bile acids. Thus, our results suggest that amino acid auxotrophies are important factors contributing to microbiome ecology and host-microbiome metabolic interactions.
ISSN:1751-7362
1751-7370
DOI:10.1038/s41396-023-01537-3