ArticlePloS one2009
More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
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.
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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
70 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Investigating the Effect of Ginger-Derived Nanovesicles on the Growth and Metabolic Activity ofJournal of extracellular biology · 2026Article
- The Gut-Lung Microbiome Crosstalk and Pulmonary Disease.Biomolecules · 2026Review
- 'Smart', microbiome-sparing antibacterial therapy with a focus on the novel Lolamicin: an overview.Infection · 2025Review
- Gut microbiota's role in heart failure.Heart failure reviews · 2025Review
- Gut Microbiota Alterations in Heart Failure Patients: Insights from a Systematic Review.Journal of clinical medicine · 2025Review
- The Microbiome and Metabolic Dysfunction-Associated Steatotic Liver Disease.International journal of molecular sciences · 2025Review
- Article
- Gut microbiota changes associated with low-carbohydrate diet intervention for obesity.Open life sciences · 2024Article
- Impact of gut microbiota and associated mechanisms on postprandial glucose levels in patients with diabetes.Journal of translational internal medicine · 2023Article
- Impact of Microbiome-Brain Communication on Neuroinflammation and Neurodegeneration.International journal of molecular sciences · 2023Review
- Intratumor microbiome: selective colonization in the tumor microenvironment and a vital regulator of tumor biology.MedComm · 2023Review
- Growth Stages and Inter-Species Gut Microbiota Composition and Function in Captive Red Deer (Animals : an open access journal from MDPI · 2023Article
- Changes in the gut microbiota of NOD mice in response to an oral Salmonella-based vaccine against type 1 diabetes.PloS one · 2023Article
- Functionality of immune cells in COVID-19 infection: development of cell-based therapeutics.BioImpacts : BI · 2023Review
- Role of the duodenal microbiota in functional dyspepsia.Neurogastroenterology and motility · 2022Review
- Enterococci-Involvement in Pathogenesis and Therapeutic Potential in Cancer Treatment: A Mini-Review.Pathogens (Basel, Switzerland) · 2022Review
- An Advanced Bioreactor Simulating Dynamic Physiological Conditions in the Human Ascending Colon: MimiColPharmaceutics · 2022Article
- Uric acid extrarenal excretion: the gut microbiome as an evident yet understated factor in gout development.Rheumatology international · 2022Review
- Intermittent fasting positively modulates human gut microbial diversity and ameliorates blood lipid profile.Frontiers in microbiology · 2022Article
10 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEstimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism. PRINCIPAL
findingsWe presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged.
conclusionBy combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.
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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.