Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut
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The human intestinal tract harbors a complex microbial ecosystem which plays a key role in nutrition and health. Although this microbiota has been studied in great detail by culture techniques, microscopic counts on human feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. Using comparative analysis of cloned 16S rRNA gene (rDNA) sequences, we have investigated the bacterial diversity (both cultivated and noncultivated bacteria) within an adult-male fecal sample. The 284 clones obtained from 10-cycle PCR were classified into 82 molecular species (at least 98% similarity). Three phylogenetic groups contained 95% of the clones: the Bacteroides group, the Clostridium coccoides group, and the Clostridium leptum subgroup. The remaining clones were distributed among a variety of phylogenetic clusters. Only 24% of the molecular species recovered corresponded to described organisms (those whose sequences were available in public databases), and all of these were established members of the dominant human fecal flora (e.g., Bacteroides thetaiotaomicron, Fusobacterium prausnitzii, and Eubacterium rectale). However, the majority of generated rDNA sequences (76%) did not correspond to known organisms and clearly derived from hitherto unknown species within this human gut microflora.
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Detection and identification of translocated bacteria and characterisation of collapsing gut communities are no longer limited by insensitive culture-based techniques, which cannot detect most gut bacteria.
“The detection and identification of translocated bacteria and characterisation of collapsing gut communities are no longer limited by insensitive culture-based techniques, which cannot detect most gut bacteria.”
From The microbiome and critical illness (2016) · cites this paper as [108]
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PASSCLAIM1?Gut health and immunity
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The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
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Human gut microbiome aging clock based on taxonomic profiling and deep learning
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Gut microbiota and gastrointestinal health: current concepts and future directions
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Cultivable bacterial diversity from the human colon
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Self-citationCulture‐independent analysis of the gut microbiota in colorectal cancer and polyposis
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Dietary fibre and the gut microbiota
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Analysis of the Intestinal Lumen Microbiota in an Animal Model of Colorectal Cancer
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The Gut Microbiota Predispose to the Pathophysiology of Acute Postradiotherapy Diarrhea
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Unstable Composition of the Fecal Microbiota in Ulcerative Colitis During Clinical Remission
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Tumor microbiome links cellular programs and immunity in pancreatic cancer
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Metabolism of Maillard reaction products by the human gut microbiota – implications for health
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Human gut microbiota: Does diet matter?
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Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment
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The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis
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Microbes Are Associated with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis
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Microbiomic analysis of the bifidobacterial population in the human distal gut
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Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa
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The active human gut microbiota differs from the total microbiota
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Cultured microbes represent a substantial fraction of the human and mouse gut microbiota
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Molecular Nutrition Research—The Modern Way Of Performing Nutritional Science
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- Authors
- Suau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G. R., Collins, M. D., & Doré, J.
- Affiliations
- Institut National de la Recherche Agronomique (FR)
- <!--label omitted: 2-->Department of Food Science and Technology, University of Reading, Whiteknights, Reading, RG6 6AP United Kingdom2
- <!--label omitted: 1-->Laboratoire d’Ecologie et Physiologie du Système Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex,1 and
- Laboratoire de Biotechnologie de l'Environnement (FR)
- University of Reading (GB)
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 1999-11
- Volume
- 65
- Issue
- 11
- Pages
- 4799-4807
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- PMC
- PMC91647
- OpenAlex
- W2117130914
- Cited by
- 1,490
- References
- 37
- Citations by year
- 2026: 10 · 2025: 13 · 2024: 24 · 2023: 20 · 2022: 23 · 2021: 37 · 2020: 45 · 2019: 40 · 2018: 49 · 2017: 40 · 2016: 61 · 2015: 56 · 2014: 75 · 2013: 65 · 2012: 57
- FWCI
- 12.23
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Applied and Environmental Microbiology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- CentAUR (University of Reading) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- human gut microbiome, 16S rRNA gene, bacterial diversity, uncultured bacteria, molecular species, fecal bacteria, Bacteroides, Clostridium coccoides, Clostridium leptum, novel bacterial species, Bacteroides thetaiotaomicron, Eubacterium rectale, phylogenetic classification
- MeSH terms
- Bacteroides, Clostridium, Eubacterium, Feces, Fusobacterium, Genes, Bacterial, Humans, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S
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