Culture of previously uncultured members of the human gut microbiota by culturomics
Authors: El Hadji Seck
Fehmida Bibi
Sokhna Ndongo
J√©r√©my Delerce
Catherine Robert
Davide Ricaboni
Fadi Bittar
Melhem Bilen
Ga√´l Mourembou
Camille Valles
Fr√©d√©ric Cadoret
Anthony Levasseur
Amadou Togo
Pierre-Edouard Fournier
Felix Djossou
J√¥natas Abrah√£o
Khoudia Diop
Jean Marc Rolain
Dipankar Bachar
Saber Khelaifia
Morgane Mailhe
Nicole Prisca Makaya Dangui Nieko
Niokhor Dione
Sory Ibrahima Traore
Guillaume Durand
Matthieu Million
Aldiouma Diallo
Jean-Christophe Lagier
Didier Musso
Esam Ibraheem Azhar
V√©ronique Vitton
Sara Bellali
Elodie Guilhot
Cheikh Sokhna
Donia Mouelhi
Gregory Dubourg
Maryam Tidjani Alou
Aurelia Caputo
Perrine Hugon
Muhammad Yasir
Didier Raoult
Nadim Cassir
Ndeye Mery Dia Badiane
Bernard La Scola
Journal: Nature Microbiology (2016)
Discipline: MICROBIOLOGY
Keywords: Metagenomics; Human microbiome; Health; Diseases; Prokaryotes
Affiliations: Aix Marseille Universit√© URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France., Institut Louis Malard√©, Papeete, Tahiti, Polyn√©sie Fran√ßaise., Departamento de Microbiologia Laboratorio de Virus, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil., Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia., Institut de Recherche pour le D√©veloppement, UMR 198 (URMITE), Campus International de Hann, IRD, BP 1386, CP, 18524 Dakar, S√©n√©gal., Department of Infectious and Tropical Diseases, Centre Hospitalier de Cayenne, Cayenne, French Guiana., Service de Gastroent√©rologie, H√¥pital Nord, Assistance Publique-H√¥pitaux de Marseille, 13915 Marseille, France.

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. 

Retracted: No

PubPeer comments:
 There is no statement about how the healthy children got selected or if her parent(s) gave consent. The paper mentions healthy children, healthy participants and other participants have been recruited in different part of the world to participate to this study : Brazil, Niger, Senegal, India... The study mentions *Consent was obtained from each patient, and the study was approved by the local Ethics Committee of the IFR48 (Marseille, France; agreement no. 09u2013022)*. There is no word about obtaining IRB approval e.g. on consent wording with the local authorities. The population included in this study is considered as vulnerable (children). A special care to the ethics committee approval and ethical condition needs to be considered. Furthermore, Ethics Committee of the IFR48 is not a certified IRB in France, able to deliver authorization to start a clinical study in humans. Could the authors please explain how and where the research was being performed, and why local ethics committee were not involved. Why the study didn t mention any ethics committee approvals in the countries where the study has been performed? Indeed, for example, in Brazil, the collection of biological material and studies on human and children require an Ethics Committee Approval in Brazil before to start the study. [Source: Brazilian guidelines for biorepositories and biobanks of human biological material] This is in line with the Helsinski Declaration. As you can see in this other study, from a different team, but with a similar design (fecal sample collected in Brazil), the research team get Ethics Committee approval from Brazilian Ethics Committee. https: journals.plos.org plosntds article?id=10.1371 journal.pntd.0003186 [source: Sources and Distribution of Surface Water Fecal Contamination and Prevalence of Schistosomiasis in a Brazilian Village] Why this team for this article in Nature Microbiology don t mention any ethics committee approval in Brazil like other teams performing similar study in the same country ? And for the other countries of the study? Performing a study in children without the proper ethics committee approval is a serious breach to Helsinki Declaration. It is in the public interest to clarify why the authors did not mention any approvals from local Ethics committee in each country where the study has been performed. , 
 In this article from 2016, the authors declare they have no competing interest:  But on the institutionnal website of Culture Top, founded in 2015 by some of the authors, this article is cited (reference 1) as allowing to  cultivate bacterial species not detected by molecular techniques : http: www.eurobio.fr produits-culture-top-xsl-269_828.html  This could mean that **the authors should clarify their competing interest**. ,