ArticleBMC microbiology2018
Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.
Article in BMC microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It has been retracted, and should not be counted. Cited by 46 papers, 1 of them a synthesis that pooled it.
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
46 citing papers in PubMed, 1 synthesis or guideline pooled it, 75 citations in OpenAlex.
- Predicting Personalized Diets Based on Microbial Characteristics between Patients with Superficial Gastritis and Atrophic Gastritis.Nutrients · 2023Pooled it
- Alterations in the Duodenal Fluid Microbiome of Patients With Pancreatic Cancer.Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association · 2022Trial
- Infant Acid-Suppressant Medication, C. difficile Colonisation, and Childhood Body Mass Index in a Canadian Cohort.Acta paediatrica (Oslo, Norway : 1992) · 2025Article
- New perspectives on gastric disorders: the relationship between innate lymphoid cells and microbes in the stomach.Cellular and molecular life sciences : CMLS · 2025Review
- Exploring the serotonin-probiotics-gut health axis: A review of current evidence and potential mechanisms.Food science & nutrition · 2024Review
- Relationships among bacterial cell size, diversity, and taxonomy in rumen.Frontiers in microbiology · 2024Article
- Tissue adaptation of CD4 T lymphocytes in homeostasis and cancer.Frontiers in immunology · 2024Article
- Intestinal barrier permeability: the influence of gut microbiota, nutrition, and exercise.Frontiers in physiology · 2024Review
- Commensal Fecal Microbiota Profiles Associated with Initial Stages of Intestinal Mucosa Damage: A Pilot Study.Cancers · 2023Article
- Host Transcriptional Regulatory Genes and Microbiome Networks Crosstalk through Immune Receptors Establishing Normal and Tumor Multiomics Metafirm of the Oral-Gut-Lung Axis.International journal of molecular sciences · 2023Review
- Spontaneous and Microbiota-Driven Degradation of Anthocyanins in an In Vitro Human Colon Model.Molecular nutrition & food research · 2023Article
- Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants.BMC microbiology · 2023Article
- Maliibacterium massiliense gen. nov. sp. nov., Isolated from Human Feces and Proposal of Maliibacteriaceae fam. nov.Current microbiology · 2023Article
- Isolation and Cultivation of Human Gut Microorganisms: A Review.Microorganisms · 2023Review
- The Influence ofAntibiotics (Basel, Switzerland) · 2023Review
- Microbiota as key factors in inflammatory bowel disease.Frontiers in microbiology · 2023Review
- Gut microbiota short-chain fatty acids and their impact on the host thyroid function and diseases.Frontiers in endocrinology · 2023Review
- Review
- The human microbiome: A promising target for lung cancer treatment.Frontiers in immunology · 2023Review
- Effect of a Proton Pump Inhibitor on the Duodenum Microbiome of Gastric Ulcer Patients.Life (Basel, Switzerland) · 2022Article
Corrections and comments
- Retraction · 2024-01-03Lack of IRB/IACUC Approval and/or Compliance · Objections by Author(s) · · See also: https://pubpeer.com/publications/22CD1DE1EFAF7016CAFEC3BB502D6E
- Retracted
Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMost studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.
resultsUsing culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02). Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).
conclusionSignificant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.
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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.