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Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample

  • A. Pfleiderer
  • J.-C. Lagier
  • F. Armougom
  • C. Robert
  • B. Vialettes
  • D. Raoult
Article

Abstract

The rebirth of bacterial culture has been highlighted successively by environmental microbiologists, the design of axenic culture for intracellular bacteria in clinical microbiology, and, more recently, by human gut microbiota studies. Indeed, microbial culturomics (large scale of culture conditions with the identification of colonies by MALDI-TOF or 16S rRNA) allowed to culture 32 new bacterial species from only four stool samples studied. We performed culturomics in comparison with pyrosequencing 16S rRNA targeting the V6 region on an anorexia nervosa stool sample because this clinical condition has never been explored before by culture, while its composition has been observed to be atypical by metagenomics. We tested 88 culture conditions generating 12,700 different colonies identifying 133 bacterial species, with 19 bacterial species never isolated from the human gut before, including 11 new bacterial species for which the genome has been sequenced. These 11 new bacterial species isolated from a single stool sample allow to extend more significantly the repertoire in comparison to the bacterial species validated by the rest of the world during the last 2 years. Pyrosequencing indicated a dramatic discrepancy with the culturomics results, with only 23 OTUs assigned to the species level overlapping (17 % of the culturomics results). Most of the sequences assigned to bacteria detected only by pyrosequencing belonged to Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae constituted by strictly anaerobic species, indicating the future route for culturomics. This study revealed new bacterial species participating significantly to the extension of the gut microbiota repertoire, which is the first step before being able to connect the bacterial composition with the geographic or clinical status.

Keywords

Anorexia Nervosa Bacterial Species Stool Sample Blood Culture Bottle Firmicutes Phylum 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We are very grateful to M. Maraninchi for the stool collection and B. Davoust for the rumen collection.

Funding source

This work was supported by Fondation Méditerranée Infection.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10096_2013_1900_MOESM1_ESM.doc (21 mb)
ESM 1 (DOC 21518 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • A. Pfleiderer
    • 1
  • J.-C. Lagier
    • 1
  • F. Armougom
    • 1
  • C. Robert
    • 1
  • B. Vialettes
    • 2
  • D. Raoult
    • 1
    • 3
  1. 1.Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095MarseilleFrance
  2. 2.Service de Nutrition, Maladies Métaboliques et EndocrinologieUMR-INRA U1260, CHU de la TimoneMarseilleFrance
  3. 3.Faculté de MédecineURMITE, UM63, CNRS 7278, IRD 198, INSERM 1095Marseille Cedex 5France

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