Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability
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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.
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Thank you for this great work! Your article will be very helpful for anyone interested in the ecological significance of amino acid metabolism by bacteria. You have done an outstanding job compiling information on biochemical pathways involved in the metabolism of the 20 canonical amino acids, as well as metabolic pathways for many other compounds (bile acids, carboxylic acids, etc.). Using your methodology, I was wondering if it would be possible to explore the prevalence of D-amino acid metabolism in human gut bacteria? I suspect there is a dearth of metabolic knowledge for most D-amino acids which may not allow running your pipeline. However it may be possible to use your experimental approach to look into the metabolism of well-studied D-amino acids such as D-alanine, D-glutamate, may be also D-serine. Thank you for your time!
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Thank you for this great work! Your article will be very helpful for anyone interested in the ecological significance of amino acid metabolism by bacteria. You have done an outstanding job compiling information on biochemical pathways involved in the metabolism of the 20 canonical amino acids, as well as metabolic pathways for many other compounds (bile acids, carboxylic acids, etc.). Using your methodology, I was wondering if it would be possible to explore the prevalence of D-amino acid metabolism in human gut bacteria? I suspect there is a dearth of metabolic knowledge for most D-amino acids which may not allow running your pipeline. However it may be possible to use your experimental approach to look into the metabolism of well-studied D-amino acids such as D-alanine, D-glutamate, may be also D-serine. Thank you for your time!
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