ArticleMicrobiome2021
Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 2 of them syntheses that pooled it.
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Who cites it
45 citing papers in PubMed, 2 syntheses or guidelines pooled it, 87 citations in OpenAlex.
- Manifestations of the oral mucosa and salivary glands in irritable bowel syndrome and microscopic colitis - A systematic review.Acta odontologica Scandinavica · 2025Pooled it
- Symptomatic Response to Antibiotics in Patients With Small Intestinal Bacterial Overgrowth: A Systematic Review and Meta-analysis.Journal of neurogastroenterology and motility · 2024Pooled it
- The duodenal microbiota is compartmentalized and clinically stable yet rapidly responsive to nutrient exposure.Gut microbes · 2026Article
- Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?Current gastroenterology reports · 2026Review
- Article
- Critical Review: The Past, Present, and Future of Small Intestinal Bacterial Overgrowth (SIBO).JGH open : an open access journal of gastroenterology and hepatology · 2026Review
- Article
- Small intestinal microbiome, the underrated maestro of SIMO disease.FEMS microbiology reviews · 2026Review
- Ileostoma as a promising tool in pathophysiological study and clinical intervention: a review from bench to beside.Frontiers in immunology · 2026Review
- Crossroads of well-being: oral health, neurology, neuronutrition and healthy aging.Open medicine (Warsaw, Poland) · 2026Review
- Duodenal Fluid Microbiome Diversity and Pancreatic Cyst Status Among Patients Undergoing Pancreatic Surveillance.Gastro hep advances · 2026Article
- Contamination-controlled upper gastrointestinal microbiota profiling reveals salivary-duodenal community types linked to opportunistic pathogen carriage and inflammation.Gut microbes · 2025Article
- An Effective Oral Drug Delivery Route for Pharmacokinetic Complications: Spirulina Lipid Nanotechnology System.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Hydrogen Sulfide and Methane on Breath Test Correlate with Human Small Intestinal Hydrogen Sulfide Producers and Methanogens.Digestive diseases and sciences · 2025Article
- Alterations in Gut Microbiota After Upper Gastrointestinal Resections: Should We Implement Screening to Prevent Complications?Medicina (Kaunas, Lithuania) · 2025Observational
- Inducible, but not constitutive, pancreatic REG/Reg isoforms are regulated by intestinal microbiota and pancreatic diseases.Mucosal immunology · 2025Article
- Review
- Role of microbiota in pain: From bench to bedside.iMetaOmics · 2025Review
- Microbiome-centered therapies for the management of metabolic dysfunction-associated steatotic liver disease.Clinical and molecular hepatology · 2025Review
- Soy-based purified ingredient diet affects mouse gut permeability and the microbiome in fragile X mice.Frontiers in molecular neuroscience · 2025Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundUpper gastrointestinal (GI) disorders and abdominal pain afflict between 12 and 30% of the worldwide population and research suggests these conditions are linked to the gut microbiome. Although large-intestine microbiota have been linked to several GI diseases, the microbiota of the human small intestine and its relation to human disease has been understudied. The small intestine is the major site for immune surveillance in the gut, and compared with the large intestine, it has greater than 100 times the surface area and a thinner and more permeable mucus layer.
resultsUsing quantitative sequencing, we evaluated total and taxon-specific absolute microbial loads from 250 duodenal-aspirate samples and 21 paired duodenum-saliva samples from participants in the REIMAGINE study. Log-transformed total microbial loads spanned 5 logs and were normally distributed. Paired saliva-duodenum samples suggested potential transmission of oral microbes to the duodenum, including organisms from the HACEK group. Several taxa, including Klebsiella, Escherichia, Enterococcus, and Clostridium, seemed to displace strict anaerobes common in the duodenum, so we refer to these taxa as disruptors. Disruptor taxa were enriched in samples with high total microbial loads and in individuals with small intestinal bacterial overgrowth (SIBO). Absolute loads of disruptors were associated with more severe GI symptoms, highlighting the value of absolute taxon quantification when studying small-intestine health and function.
conclusionThis study provides the largest dataset of the absolute abundance of microbiota from the human duodenum to date. The results reveal a clear relationship between the oral microbiota and the duodenal microbiota and suggest an association between the absolute abundance of disruptor taxa, SIBO, and the prevalence of severe GI symptoms. Video Abstract.
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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.