Culture of previously uncultured members of the human gut microbiota by culturomics View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-12

AUTHORS

Jean-Christophe Lagier, Saber Khelaifia, Maryam Tidjani Alou, Sokhna Ndongo, Niokhor Dione, Perrine Hugon, Aurelia Caputo, Frédéric Cadoret, Sory Ibrahima Traore, El Hadji Seck, Gregory Dubourg, Guillaume Durand, Gaël Mourembou, Elodie Guilhot, Amadou Togo, Sara Bellali, Dipankar Bachar, Nadim Cassir, Fadi Bittar, Jérémy Delerce, Morgane Mailhe, Davide Ricaboni, Melhem Bilen, Nicole Prisca Makaya Dangui Nieko, Ndeye Mery Dia Badiane, Camille Valles, Donia Mouelhi, Khoudia Diop, Matthieu Million, Didier Musso, Jônatas Abrahão, Esam Ibraheem Azhar, Fehmida Bibi, Muhammad Yasir, Aldiouma Diallo, Cheikh Sokhna, Felix Djossou, Véronique Vitton, Catherine Robert, Jean Marc Rolain, Bernard La Scola, Pierre-Edouard Fournier, Anthony Levasseur, Didier Raoult

ABSTRACT

Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism1. The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms2. We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization-time of flight and 16S rRNA for identification2. Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies3-5. We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut. More... »

PAGES

nmicrobiol2016203

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmicrobiol.2016.203

DOI

http://dx.doi.org/10.1038/nmicrobiol.2016.203

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1044832209

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27819657


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