ArticleThe ISME journal2023
Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability.
Article in The ISME journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 60 citations in OpenAlex.
- Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure.Nature communications · 2025Trial
- The Impact of Fermented Milk Products ContainingNutrients · 2024Trial
- The phenotypic landscape of the model firmicuteProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Low Levels of Amino Acid Auxotrophy Among Environmental Pseudomonas Isolates.Environmental microbiology · 2026Article
- Bifidobacteria: biogeography, host adaptation and ecological functions.Nature reviews. Microbiology · 2026Review
- Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease.Scientific reports · 2026Article
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- Machine Learning Reveals Quantitative Amino Acid Preferences in Bifidobacterium longum Growth.Microbial biotechnology · 2026Article
- Comparative metabolomic assessment of bioconverted traditional and black wheat via the in vitro piglet digestion model.Scientific reports · 2026Article
- Limits to the evolution of metabolic dependency in spatially structured microbial communities.iScience · 2026Article
- Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.bioRxiv : the preprint server for biology · 2026Article
- pH regulates gut bacterial tryptophan metabolism.NPJ biofilms and microbiomes · 2026Article
- Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.The ISME journal · 2026Article
- Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function.Nature ecology & evolution · 2026Article
- BileActome reveals community-assembled bile acid metabolism in the rumen microbiome.ISME communications · 2026Article
- Cross-species engraftment biases and metabolic divergence in gnotobiotic mice humanized with ulcerative colitis microbiota.Gut microbes · 2025Article
- Microbial metabolites as engines of behavioral variation across animals.Gut microbes · 2025Review
- ComparingGut microbes · 2025Article
- Gut microbiota-mediated modulation of host amino acid availability and metabolism.Gut microbes · 2025Review
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.