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Applied and Environmental Microbiology
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General Microbial Ecology

Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut

Antonia Suau, Régis Bonnet, Malène Sutren, Jean-Jacques Godon, Glenn R. Gibson, Matthew D. Collins, Joel Doré
Antonia Suau
Laboratoire d’Ecologie et Physiologie du Système Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, and
Department of Food Science and Technology, University of Reading, Whiteknights, Reading, RG6 6AP United Kingdom
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Régis Bonnet
Department of Food Science and Technology, University of Reading, Whiteknights, Reading, RG6 6AP United Kingdom
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Malène Sutren
Laboratoire d’Ecologie et Physiologie du Système Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, and
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Jean-Jacques Godon
Laboratoire de Biotechnologie de l’Environnement, Institut National de la Recherche Agronomique, 11100 Narbonne, France, and
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Glenn R. Gibson
Department of Food Science and Technology, University of Reading, Whiteknights, Reading, RG6 6AP United Kingdom
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Matthew D. Collins
Department of Food Science and Technology, University of Reading, Whiteknights, Reading, RG6 6AP United Kingdom
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Joel Doré
Laboratoire d’Ecologie et Physiologie du Système Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, and
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DOI: 10.1128/AEM.65.11.4799-4807.1999
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ABSTRACT

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: theBacteroides group, the Clostridium coccoidesgroup, 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.

  • Copyright © 1999 American Society for Microbiology
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Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut
Antonia Suau, Régis Bonnet, Malène Sutren, Jean-Jacques Godon, Glenn R. Gibson, Matthew D. Collins, Joel Doré
Applied and Environmental Microbiology Nov 1999, 65 (11) 4799-4807; DOI: 10.1128/AEM.65.11.4799-4807.1999

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Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut
Antonia Suau, Régis Bonnet, Malène Sutren, Jean-Jacques Godon, Glenn R. Gibson, Matthew D. Collins, Joel Doré
Applied and Environmental Microbiology Nov 1999, 65 (11) 4799-4807; DOI: 10.1128/AEM.65.11.4799-4807.1999
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KEYWORDS

Bacteroides
Clostridium
feces
Fusobacterium
phylogeny
RNA, Bacterial
RNA, Ribosomal, 16S

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