ArticleMicroorganisms2022
Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome.
Article in Microorganisms, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 36 citations in OpenAlex.
- A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.Science translational medicine · 2024Trial
- Phocaeicola vulgatus promote growth rate via tryptophan metabolism pathway mediated gut sIgA production in Taihe Silky fowl.Journal of advanced research · 2026Article
- Phytochemicals remodel antitumor immunity via the "microbiota-metabolite-receptor" axis: focus on colorectal cancer and immunotherapy.Medical oncology (Northwood, London, England) · 2026Review
- Host-Microbiota Interactions in the Regulation of Intestinal Health in Weaned Piglets: Molecular Mechanisms and Nutritional Intervention Strategies.Animals : an open access journal from MDPI · 2026Review
- Spatial ecology of theMicrobiology spectrum · 2026Article
- Temperature Elevation Alters the Gut Antibiotic Resistome and Carbohydrate-Active Enzymes in the Desert LizardMicroorganisms · 2026Article
- Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.The ISME journal · 2026Article
- Effects of intergenerational transmission of small intestinal bacteria cultured from stunted Bangladeshi children with enteropathy.bioRxiv : the preprint server for biology · 2025Article
- Mechanistic insights into microbiome-dependent and personalized responses to dietary fibre in a randomized controlled trial.medRxiv : the preprint server for health sciences · 2025Article
- Review
- Intestinal microbiome changes in response to amino acid and micronutrient supplementation: secondary analysis of the AMAZE trial.Gut microbiome (Cambridge, England) · 2025Article
- Interactive tools for functional annotation of bacterial genomes.Database : the journal of biological databases and curation · 2024Article
- Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage.FEMS microbiology ecology · 2024Article
- Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition.Nature microbiology · 2024Article
- Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability.The ISME journal · 2023Article
- Taxonomic and environmental distribution of bacterial amino acid auxotrophies.Nature communications · 2023Article
- Dietary L-Tryptophan consumption determines the number of colonic regulatory T cells and susceptibility to colitis via GPR15.Nature communications · 2023Article
- AgingReG: a curated database of aging regulatory relationships in humans.Database : the journal of biological databases and curation · 2023Article
- Pesticide exposure and the microbiota-gut-brain axis.The ISME journal · 2023Review
- Personalized Response of Parkinson's Disease Gut Microbiota to Nootropic Medicinal Herbs In Vitro: A Proof of Concept.Microorganisms · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
The human gut microbiota (HGM) have an impact on host health and disease. Amino acids are building blocks of proteins and peptides, also serving as precursors of many essential metabolites including nucleotides, cofactors, etc. Many HGM community members are unable to synthesize some amino acids (auxotrophs), while other members possess complete biosynthetic pathways for these nutrients (prototrophs). Metabolite exchange between auxotrophs and prototrophs affects microbial community structure. Previous studies of amino acid biosynthetic phenotypes were limited to model species or narrow taxonomic groups of bacteria. We analyzed over 2800 genomes representing 823 cultured HGM species with the aim to reconstruct biosynthetic pathways for proteinogenic amino acids. The genome context analysis of incomplete pathway variants allowed us to identify new potential enzyme variants in amino acid biosynthetic pathways. We further classified the studied organisms with respect to their pathway variants and inferred their prototrophic vs. auxotrophic phenotypes. A cross-species comparison was applied to assess the extent of conservation of the assigned phenotypes at distinct taxonomic levels. The obtained reference collection of binary metabolic phenotypes was used for predictive metabolic profiling of HGM samples from several large metagenomic datasets. The established approach for metabolic phenotype profiling will be useful for prediction of overall metabolic properties, interactions, and responses of HGM microbiomes as a function of dietary variations, dysbiosis and other perturbations.
Indexed as
Identifiers
What OpenQuestion holds
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.