ArticleCell2022
Gut bacterial nutrient preferences quantified in vivo.
Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
What it found
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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.
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Who cites it
127 citing papers in PubMed.
- Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial.Nature communications · 2023Trial
- Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.Gut microbes · 2026Article
- An engineered bacterial symbiont maps micron-scale sugar gradients in the honeybee gut.PLoS biology · 2026Article
- Fecal metabolomic profiles by LDL-C target achievement status in statin-treated patients: a cross-sectional study.Journal of lipid research · 2026Article
- Anaerobic riboflavin degradation by human gutJournal of bacteriology · 2026Article
- Probiotics unveiled: bridging general health benefits to the era of precision medicine.World journal of microbiology & biotechnology · 2026Review
- Differential effects of dietary protein sources on nitrogen metabolism and ileal microbiota in pigs correlated with amino acid release rates.Journal of animal science and biotechnology · 2026Article
- Host metabolism can produce many indoles and phenols independently of the microbiome.Nature metabolism · 2026Article
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism.bioRxiv : the preprint server for biology · 2026Article
- Premature transcription termination modulates stochastic gene expression in bacteria.Science advances · 2026Article
- Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.FEMS microbiology ecology · 2026Article
- Advances and opportunities in measuring dietary intake: from omics to AI.Nature metabolism · 2026Review
- A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice.Nature microbiology · 2026Article
- Catabolism of serine enantiomers represses enterohemorrhagicProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Gut microbiota and Parkinson's disease: exploring pathogenesis and potential therapeutic strategies from a gut-brain axis perspective.iScience · 2026Review
- Anaerobic riboflavin degradation by human gutbioRxiv : the preprint server for biology · 2026Article
- Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.Scientific reports · 2026Article
- Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.Applied microbiology and biotechnology · 2026Article
- Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.The ISME journal · 2026Article
67 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
Abstract
Great progress has been made in understanding gut microbiomes' products and their effects on health and disease. Less attention, however, has been given to the inputs that gut bacteria consume. Here, we quantitatively examine inputs and outputs of the mouse gut microbiome, using isotope tracing. The main input to microbial carbohydrate fermentation is dietary fiber and to branched-chain fatty acids and aromatic metabolites is dietary protein. In addition, circulating host lactate, 3-hydroxybutyrate, and urea (but not glucose or amino acids) feed the gut microbiome. To determine the nutrient preferences across bacteria, we traced into genus-specific bacterial protein sequences. We found systematic differences in nutrient use: most genera in the phylum Firmicutes prefer dietary protein, Bacteroides dietary fiber, and Akkermansia circulating host lactate. Such preferences correlate with microbiome composition changes in response to dietary modifications. Thus, diet shapes the microbiome by promoting the growth of bacteria that preferentially use the ingested nutrients.
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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.