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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
medicine
Microbial culturomics: Paradigm shift in the human gut microbiome study
Clinical Microbiology and Infection, Volume 18, No. 12, Year 2012
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Description
Comprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. Metagenomic analysis of the human gut microbiota detects mostly uncultured bacteria. We studied stools from two lean Africans and one obese European, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16S rRNA amplification and sequencing. In parallel, we analysed the same three samples by pyrosequencing 16S rRNA amplicons targeting the V6 region. The 32500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla (Deinococcus-Thermus and Synergistetes, five fungi, and a giant virus (Senegalvirus). The microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10000 new unknown genes (ORFans), which will help in future molecular studies. Among these, the new species Microvirga massiliensis has the largest bacterial genome so far obtained from a human, and Senegalvirus is the largest virus reported in the human gut. Concurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. Thus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches. © 2012 The Authors. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.
Authors & Co-Authors
Lagier, Jean Christophe
France, Marseille
Aix Marseille Université
Armougom, Fabrice
France, Marseille
Aix Marseille Université
Million, Matthieu
France, Marseille
Aix Marseille Université
Hugon, Perrine
France, Marseille
Aix Marseille Université
Pagnier, Isabelle
France, Marseille
Aix Marseille Université
Robert, Catherine
France, Marseille
Aix Marseille Université
Bittar, Fadi
France, Marseille
Aix Marseille Université
Fournous, Ghislain
France, Marseille
Aix Marseille Université
Gimenez, G.
France, Marseille
Aix Marseille Université
Maraninchi, Marie
France, Marseille
Hopital la Timone
Trape, Jean François
Senegal, Dakar
Institut de Recherche Pour le Développement Dakar
Koonin, Eugene V.
United States, Bethesda
National Library of Medicine Nlm
La Scola, Bernard
France, Marseille
Aix Marseille Université
Raoult, Didier A.
France, Marseille
Aix Marseille Université
Statistics
Citations: 930
Authors: 14
Affiliations: 4
Identifiers
Doi:
10.1111/1469-0691.12023
ISSN:
1198743X
e-ISSN:
14690691