培养组学：让更多肠道微生物可培养

Title：
Culture of previously uncultured members of the human gut microbiota by culturomics

DOI：
10.1038/NMICROBIOL.2016.203

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 studies3,4,5. 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.

All 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,Jeremy 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

First Authors：
Jean-Christophe Lagier

Correspondence：
Didier Raoult

内容要点：

1、在近年来，随着宏基因组技术的发展，对原核生物的纯培养逐渐被忽视，但纯培养对于阐明这些微生物的功能是必需的；

2、本研究介绍了一种微生物培养组学（culturomics），综合利用多重培养条件、MALDI–TOF及16s rRNA测序；

3、通过这种方法，鉴定出1057个原核生物物种，其中531种属于人体肠道菌群；

4、利用培养组学，至少被分离一次的肠道物种增加了一倍。

*罗宁生物扩增子测序（基于16S rRNA基因高通量测序分析）可为您提供更多微生物培养基信息。