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Applied and Environmental Microbiology, November 1999, p. 4799-4807, Vol. 65, No. 11
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

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

Antonia Suau,1,2,* Régis Bonnet,2 Malène Sutren,1 Jean-Jacques Godon,3 Glenn R. Gibson,2 Matthew D. Collins,2 and Joel Doré1

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, Institut National de la Recherche Agronomique, 11100 Narbonne,3 France, and Department of Food Science and Technology, University of Reading, Whiteknights, Reading, RG6 6AP United Kingdom2

Received 12 April 1999/Accepted 31 August 1999

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.

* Corresponding author. Mailing address: UEPSD, bat. 405, INRA, Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France. Phone: 33 (0) 1 34 65 27 09. Fax: 33 (0) 1 34 65 24 92. E-mail: suau{at}biotec.jouy.inra.fr.

Applied and Environmental Microbiology, November 1999, p. 4799-4807, Vol. 65, No. 11
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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