Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov
Authors: Maxime Descartes Mbogning Fonkou
Pierre-Edouard Fournier
Jérémy Delerce
Mamadou Beye
Nicholas Armstrong
Thi Tien Nguyen
Didier Raoult
Melhem Bilen
Ziad Daoud
Frédéric Cadoret
Saber Khelaifia
Journal: MicrobiologyOpen (2018)
Discipline: MICROBIOLOGY
Keywords: Collinsella bouchesdurhonensis; culturomics; genome; pygmy; taxonomy.
Affiliations: Aix-Marseille Université; URMITE; UM63, CNRS7278, IRD198; INSERM 1095; Assistance Publique-Hôpitaux de Marseille; Institut Hospitalo-Universitaire Méditerranée-Infection; Faculté de médecine; Marseille France, Clinical Microbiology Department; Faculty of Medicine and Medical sciences; University of Balamand; Amioun Lebanon, Special Infectious Agents Unit; King Fahd Medical Research Center; King Abdulaziz University; Jeddah Saudi Arabia

Abstract:  Using culturomics, a recently developed strategy based on diversified culture conditions for the isolation of previously uncultured bacteria, we isolated strain Marseille-P3296T from a fecal sample of a healthy pygmy female. A multiphasic approach, taxono-genomics, was used to describe the major characteristics of this anaerobic and gram-positive bacillus that is unable to sporulate and is not motile. The genome of this bacterium is 1,878,572 bp-long with a 57.94 mol% G + C content. On the basis of these characteristics and after comparison with its closest phylogenetic neighbors, we are confident that strain Marseille-P3296T (=CCUG 70328 = CSUR P3296) is the type strain of a novel species for which we propose the name Collinsella bouchesdurhonensis sp. nov. 

Retracted: No

PubPeer comments:
 Another concern is that this 2018 paper does not mention that this *newly isolated* strain (exact same Genbank ID) has been previously described by some of the same authors in a 2017 paper, i.e. Bilen M et al., New Microbes and New Infections (2017), DOI: 10.1016 j.nmni.2016.11.004 - https: pubpeer.com publications B9CE098B715177FECFAF92C0D04B53 That paper is cited in Table 1, but not in the main text. The paper appears to describe the strain for the first time, as suggested by wording such as *newly isolated*, *novel species*, and *new species*. Can the authors please comment why they did not cite the 2017 paper, e.g. in the introduction of this paper? , 
 This paper is part of a set of papers from the Aix-Marseille Universitu00e9 Institut Hospitalo-Universitaire Mu00e9diterranu00e9e-Infection in Marseille, France, that all describe novel bacterial strains isolated in African countries, but without mentioning ethical approval by local authorities, and without local authors. In this paper, a novel bacterial species is described, isolated from the stool of a healthy 50y old pygmy woman from Congo. The article offers few details, so I hope the authors could answer some questions here. * What was the approximate place of residence of the subject? The text says that the samples were collected in Congo. Do the authors mean ([Republic of the Congo](http: en.wikipedia.org wiki Republic_of_the_Congo) or neighboring [Democratic Republic of the Congo](http: https: en.wikipedia.org wiki Democratic_Republic_of_the_Congo)? * Are there any details known about e.g. diet, living conditions (rural vs urban, agricultural vs. hunter gatherer) of the study subject? There is only limited value to describe a novel human-associated bacterial species if those details about the human host are not given. * Although the first paragraph of the paper states that the samples were collected in Congo, the last paragraph of the paper says the strain was named after Marseille, where the strain was discovered. * The Genbank Entry LT623900 does not mention that the isolate came from a woman in Congo either. Rather it says that it was isolated in the hospital of Timone (Marseille). See: https: www.ncbi.nlm.nih.gov nuccore LT623900 * How did the authors manage to incubate the specimen in a blood culture bottle under anaerobic conditions? Some details appear to be missing. Was the sample transported from Congo back to France at some cold temperature, and then added stored in a freezer? When was the sample added to the blood culture bottle - was this done in France, or was the sample processed locally? Did local researchers or authorities participate? * The study mentions *The culturomics study was approved by the ethics committee of the Institut Fu00e9du00e9ratif de Recherche 48 under number 09u2013022* But that is a committee in France, not in one of the Congo republics. There is no word about obtaining IRB approval e.g. on consent wording with the local authorities or to perform a study on a small and unique ethnic group. In addition, the authors are from France, Lebanon, and Saudi Arabia, without any local researchers to contribute. ,