Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono‐genomics description
Authors: Pierre E Fournier
Thi T Nguyen
Ziad Daoud
Didier Raoult
Melhem Bilen
Magali Richez
Maxime D Mbogning Fonkou
Frédéric Cadoret
Journal: MicrobiologyOpen (2019)
Discipline: MICROBIOLOGY
Keywords: Miniphocibacter massiliensis; culturomics; gut microbiota; new species; pygmy
Affiliations: Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 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:  With the aim of describing the human microbiota by the means of culture methods, culturomics was developed in order to target previously un-isolated bacterial species and describe it via the taxono-genomics approach. While performing a descriptive study of the human gut microbiota of the pygmy people, strain Marseille-P4678T has been isolated from a stool sample of a healthy 39-year-old pygmy male. Cells of this strain were Gram-positive cocci, spore-forming, non-motile, catalase-positive and oxidase-negative, and grow optimally at 37°C under anaerobic conditions. Its 16S rRNA gene sequence exhibited 89.69% of sequence similarity with Parvimonas micra strain 3119BT (NR 036934.1), its phylogenetically closest species with standing in nomenclature. The genome of strain Marseille-P4678T is 2,083,161 long with 28.26 mol% of G+C content. Based on its phenotypic, biochemical, genotypic and proteomic profile, this bacterium was classified as a new bacterial genus and species Miniphocibacter massiliensis gen. nov., sp. nov. with the type strain Marseille-P4678T . 

Retracted: No

PubPeer comments:
 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 39-year old pygmy male from Congo. The article offers few details, so I hope the authors could answer some questions here. * Surprisingly, the Methods start with a description of the stool sample, without mentioning the human donor at all. The age and country are mentioned in the final sentence of the main text, almost as an afterthought, but not in the Methods. * 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. That seems a bit researcher-centered. Why not name it after the human ethnic group who donated the sample (pygmy people) or their country (Congo)? * The study mentions *An approval under the number 09-022 was obtained from the Ethic Committee of the Institut Fu00e9du00e9ratif de Recherche 48 along with a signed consent from the sampleu2019s donor.* 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. In addition, the authors are from France, Saudi Arabia, and Lebanon, without any local researchers to contribute. Could the authors please explain how the research was being performed, and why local researchers were not given a chance to participate? How was this individual selected? , 
 In this article from 2018, the authors describe their materials and methods mentionning the  Culture Top company: ![file] The authors clearly state they have no conflict of interest, but in this article from 2021: https: doi.org 10.1371 journal.pntd.0009555 One of the authors mentions his competing interest with this company mentionned : ![file] This **competing interest should have also been mentionned** in this publication and this author should rectify this. ,