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

ABSTRACT: 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.

SUBMITTER: Starke S

PROVIDER: S-EPMC10689445 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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

Starke Svenja S Harris Danielle M M DMM Zimmermann Johannes J Schuchardt Sven S Oumari Mhmd M Frank Derk D Bang Corinna C Rosenstiel Philip P Schreiber Stefan S Frey Norbert N Franke Andre A Aden Konrad K Waschina Silvio S

The ISME journal 20231027 12

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 ...[more]

PMID: 37891427

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Project description:BackgroundFew population-based studies have evaluated the influence of long-term diet on the gut microbiome, and data among Asian populations are lacking.ObjectiveWe examined the association of long-term diet quality, comprising 8 food groups (fruit, vegetables, dairy, fish/seafood, nuts/legumes, refined grains, red meat, and processed meat), with gut microbiome among Chinese adults.MethodsIncluded were 1920 men and women, enrolled in 2 prospective cohorts (baseline 1996-2006), who remained free of cardiovascular diseases, diabetes, and cancer at stool collection (2015-2018) and had no diarrhea or antibiotic use in the last 7 d before stool collection. Microbiome was profiled by 16S rRNA sequencing. Long-term diet was assessed by repeated surveys at baseline and follow-ups (1996-2011), with intervals of 5.2 to 20.5 y between dietary surveys and stool collection. Associations of dietary variables with microbiome diversity and composition were evaluated by linear or negative binomial hurdle models, adjusting for potential confounders. False discovery rate (FDR) <0.1 was considered significant.ResultsThe mean ± SD age at stool collection was 68 ± 1.5 y. Diet quality was positively associated with microbiome α-diversity (P = 0.03) and abundance of Firmicutes, Actinobacteria, Tenericutes, and genera/species within these phyla, including Coprococcus, Faecalibacterium/Faecalibacterium prausnitzii, Bifidobacterium / Bifidobacterium adolescentis, and order RF39 (all FDRs <0.1). Significant associations were also observed for intakes of dairy, fish/seafood, nuts/legumes, refined grains, and processed meat, including a positive association of dairy with Bifidobacterium and inverse associations of processed meat with Roseburia /Roseburia faecis. Most associations were similar, with or without adjustment for BMI and hypertension status or excluding participants with antibiotic use in the past 6 mo.ConclusionAmong apparently healthy Chinese adults, long-term diet quality is positively associated with fecal microbiome diversity and abundance of fiber-fermenting bacteria, although magnitudes are generally small. Future studies are needed to examine if these bacteria may mediate or modify diet-disease relations.

Dataset Information

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

Publications

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

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