ArticleNature2023
Profiling the human intestinal environment under physiological conditions.
Registry-linked trialOpen access · hybridAbstract read
In one paragraph
Article in Nature, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06903806 (Determination of Microbiome Diversity and Inflammation Throughout the GI Tract During Endurance Exercise), which is not on this map. Cited by 268 papers.
0numbers the graph read from it
0cells of the map it votes in
268citing papers in PubMed
64.8field-weighted citation impact, top 1% of its field
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.
Determination of Microbiome Diversity and Inflammation Throughout the GI Tract During Endurance Exercise
Who cites it
268 citing papers in PubMed, 419 citations in OpenAlex.
- Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial.Nature communications · 2026Trial
- Prebiotic Administration to Chronic Kidney Disease Patients Modifies Their Fecal Microbiome and Host Metabolism.Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation · 2026Trial
- Untargeted and semi-targeted metabolomics approach for profiling small intestinal and fecal metabolome using high-resolution mass spectrometry.Metabolomics : Official journal of the Metabolomic Society · 2025Trial
- Neonatal administration ofmSphere · 2025Trial
- The Impact of Milk on Gut Permeability, Fecal 16S rRNA Gene Microbiota Profiling, and Fecal Metabolomics in Children with Moderate Malnutrition in Sierra Leone: A Double-Blind, Randomized Controlled Trial.The American journal of clinical nutrition · 2024Trial
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Why probiotics fail: gut niche tension as the missing variable?Gut microbes · 2026Review
- Minimally invasive capsule-string device enables spatially resolved microbiome profiling across the upper gastrointestinal tract.Gut microbes · 2026Article
- Microbiota-bile acid-host axis dysregulation drives enteropathogenesis inThe veterinary quarterly · 2026Article
- Fermented food microbiome: influence on oral and gut microbiota, and human health.Nature reviews. Microbiology · 2026Review
- Pleiotropic roles of microbial bile acid metabolism in intestinal health and diseases.Cell host & microbe · 2026Review
- Extensive genomic diversity in Desulfovibrio reveals species-specific functional traits associated with disease.Nature communications · 2026Article
- Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions.Nature immunology · 2026Article
- Regional organization of nutrient absorption across the small intestine.Nature reviews. Gastroenterology & hepatology · 2026Review
- Expanding bile acid diversityNatural product reports · 2026Review
- From Diet to Dysbiosis: The Microbiome's Relationship to Eosinophilic Esophagitis.Current gastroenterology reports · 2026Review
- Ecological Engineering of the Human Gut Microbiome: A Narrative Review and Framework for Next-Generation Therapeutics.Microorganisms · 2026Review
- Tumor Topography Remodels TME Signalling via Compartment-Specific Host-Microbiome-Tumor Crosstalk in Hepatoblastoma.Cancers · 2026Article
- A roadmap to create FAIR collections of microbial strains.Nature microbiology · 2026Review
- Use of Fecal Sampling for Assessing Probiotic Effects on the Gut Microbiome: A Focused Narrative Review.Cureus · 2026Review
208 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
21 authors at 6 institutions in 2 countries.
Dari Shalon *Envivo Bio, Inc., San Francisco, CA, USA.ORCID 0000-0003-2646-6215
Rebecca Neal Culver *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. rculver@stanford.edu.ORCID 0000-0002-3963-193X
Jessica A Grembi *Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0001-6142-4913
Jacob Folz *West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA.
Peter V TreitDepartment of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.
Handuo ShiDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-1688-6905
Florian A RosenbergerDepartment of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.ORCID 0000-0003-4604-6170
Les DethlefsenDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Xiandong MengChan Zuckerberg Biohub, San Francisco, CA, USA.
Eitan YaffeDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Andrés Aranda-DíazDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Philipp E GeyerDepartment of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.
Johannes B Mueller-ReifDepartment of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.
Sean SpencerDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-7328-5399
Andrew D PattersonDepartment of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA.ORCID 0000-0003-2073-0070
George TriadafilopoulosDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-4233-3773
Susan P HolmesDepartment of Statistics, Stanford University, Stanford, CA, USA.
Matthias MannDepartment of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.ORCID 0000-0003-1292-4799
Oliver FiehnWest Coast Metabolomics Center, University of California, Davis, Davis, CA, USA. ofiehn@ucdavis.edu.ORCID 0000-0002-6261-8928
David A Relman *Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. relman@stanford.edu.ORCID 0000-0001-8331-1354
Kerwyn Casey Huang *Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. kchuang@stanford.edu.ORCID 0000-0002-8043-8138
Stanford University · USMax Planck Institute of Biochemistry · DEChan Zuckerberg Initiative (United States) · USUniversity of California, Davis · USPennsylvania State University · USVA Palo Alto Health Care System · US
Funding
A universal pipeline for functional characterization of the human microbiota at a massive scaleRM1GM135102 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BUIE, CULLEN RICHARD, DEUTSCHBAUER, ADAM M · 2020 to 2024
$7.6MTRAINING GRANT IN ACADEMIC GASTROENTEROLOGYT32DK007056 · NIDDK · STANFORD UNIVERSITY · PI Natalie J. Torok · 1986 to 2026
$6.5MAntimicrobial Resistance and Horizontal Gene Transfer in the Human Gut Microbiome in Response to an AntibioticR01AI147023 · NIAID · PALO ALTO VETERANS INSTIT FOR RESEARCH · PI RELMAN, DAVID A. · 2020 to 2024
$3.5MNIAID NIH HHS R01 AI147023NIDDK NIH HHS T32 DK007056NIGMS NIH HHS RM1 GM135102
Abstract
The spatiotemporal structure of the human microbiome
Indexed as
Bile Acids and SaltsGastrointestinal MicrobiomeIntestinesMetabolomeProteomeBacteriaBacteriophagesDigestionFecesHumansBile Acids and SaltsProteome
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
NCT06903806ClinicalTrials.gov
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.