ArticleProceedings of the National Academy of Sciences of the United States of America2009
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 349 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
349 citing papers in PubMed, 1 synthesis or guideline pooled it, 749 citations in OpenAlex.
- The Effects of Glucosamine and Chondroitin Sulfate on Gut Microbial Composition: A Systematic Review of Evidence from Animal and Human Studies.Nutrients · 2019Pooled it
- Gut microbiota composition in relation to the metabolic response to 12-week combined polyphenol supplementation in overweight men and women.European journal of clinical nutrition · 2017Trial
- Significant changes in the fecal bacteriobiota richness and diversity in patients with relapsing-remitting multiple sclerosis compared to healthy individuals.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Gut Microbiota, Immunity, and Metabolism in the Progression From Chronic Liver Disease to Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Gut health in broiler chickens fed a mixture of Hermetia illucens and Tenebrio molitor meals: does it have a key role in shaping bird performance?Poultry science · 2026Article
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- Self-actuated probiotic-nanozyme hybrid system with mucus penetration, biofilm eradication and microbiota regulation for Helicobacter pylori infection.Journal of nanobiotechnology · 2026Article
- Niche specialization and cross-feeding interactions shaping gut microbial fiber degradation in a model omnivore.bioRxiv : the preprint server for biology · 2026Article
- Limosilactobacillus reuteri fermentation enhances the anti-type 2 diabetic activity of Gastrodia elata polysaccharides.AMB Express · 2026Article
- Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities.Research square · 2026Article
- Metagenomic insights into effect of pulse cell wall integrity on gut microbiota, CAZyme gene responses and starch/protein metabolism during in vitro fecal fermentation.NPJ science of food · 2025Article
- The Combined Hypoglycemic Effect of Quercetagetin and Lutein from Marigold and Related Molecular Mechanisms in Mice.Foods (Basel, Switzerland) · 2025Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- Effects ofVeterinary sciences · 2025Article
- Sequential Galacto- and Xylo-Oligosaccharide Feeding Transiently Modulates Gut Microbiota and Upregulates Intestinal Alkaline Phosphatase in Weaning Piglets.Animals : an open access journal from MDPI · 2025Article
- Molecular Mechanisms of the Microbiota-Gut-Brain Axis in the Onset and Progression of Stroke.International journal of molecular sciences · 2025Review
- Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.Microbiome · 2025Article
- Unstable pathogen profile in spotted seal (Phoca largha) gut microbiota and limited turnover with habitat microbiome.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Modulation of oral vaccine efficacy by the gut microbiota.NPJ vaccines · 2025Review
- A combination of potential psychobiotics alleviates anxiety and depression behaviors induced by chronic unpredictable mild stress.NPJ biofilms and microbiomes · 2025Article
289 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors at 4 institutions in 2 countries.
Funding
Abstract
The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial-microbial and microbial-host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.
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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.