Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481 , a moderate halophilic bacterium isolated from the human gut microflora
Authors: El Hadji Seck
Caroline Blanc-Tailleur
Didier Raoult
Pierre-Edouard Fournier
Gregory Dubourg
Awa Diop
Nicholas Armstrong
Journal: MicrobiologyOpen (2019)
Discipline: MICROBIOLOGY
Keywords: Gracilibacillus timonensis; halophilic; human gut flora; microbial culturomics; taxonogenomics.
Affiliations: URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France., URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095Aix‐Marseille UniversitéInstitut hospitalo‐universitaire Mediterranee‐infection Marseille France, Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.

Abstract:  Microbial culturomics represents an ongoing revolution in the characterization of the human gut microbiota. By using three culture media containing high salt concentrations (10, 15, and 20% [w/v] NaCl), we attempted an exhaustive exploration of the halophilic microbial diversity of the human gut and isolated strain Marseille-P2481 (= CSUR P2481 = DSM 103076), a new moderately halophilic bacterium. This bacterium is a Gram-positive, strictly aerobic, spore-forming rod that is motile by use of a flagellum and exhibits catalase, but not oxidase activity. Strain Marseille-P2481 was cultivated in media containing up to 20% (w/v) NaCl, with optimal growth being obtained at 37°C, pH 7.0-8.0, and 7.5% [w/v] NaCl). The major fatty acids were 12-methyl-tetradecanoic acid and hexadecanoic acid. Its draft genome is 4,548,390 bp long, composed of 11 scaffolds, with a G+C content of 39.8%. It contains 4,335 predicted genes (4,266 protein coding including 89 pseudogenes and 69 RNA genes). Strain Marseille-P2481 showed 96.57% 16S rRNA sequence similarity with Gracilibacillus alcaliphilus strain SG103T , the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille-P2481T was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed. 

Retracted: No

PubPeer comments:
 Figure 4: *Gram staining of Gracilibacillus timonensis strain Marseille-P2481T* This photo of the proposed new species of a salt-loving bacterium looks remarkably similar to that of Figure 4 in another paper by several of the same authors (shown with red boxes). That paper is: EH Seck et al., New Microbe and New Infect 2018; 23: 28u201338 DOI: 10.1016 j.nmni.2017.12.006 - https: pubpeer.com publications 974B19C32CBE7BDD5A3D93C941CF73 The photos appear to represent different bacterial species. * In the EH Seck 2018 paper: Bacillus salis strain ES3-T from table salt * In the Diop 2019 paper: Gracilibacillus timonensis strain Marseille-P2481-T from stool from a 10y old boy living in Senegal. ![file] Pointed out on Twitter. https: twitter.com Monox5 status 1375873070792073221 Could the authors check with of the photos is which bacterium, please? , 
 I am also a bit uncomfortable with researchers from France (Aix-Marseille Universitu00e9) and Saudi Arabia (King Abdulaziz University) publishing data obtained from a 10 year old boy from Senegal. Although there was approval by the National Ethics Committee of Senegal, and one can argue that a stool sample is not an invasive procedure, it is strange that there is no author from Senegal on this paper. Could the authors please give some background on how this study was performed? Was this part of a larger study, or did the authors just sample this one child? , 
 In another article * [High Prevalence of Mansonella perstans Filariasis in Rural Senegal] * , same authors mention that: * The national ethics committee of Senegal approved the project (program of identification of emergent pathogensu2014No. 00.87 MSP DS CNERS, June 2, 2010 ) * We can note that the Senegalese Ethics approval number No. 00.87 MSP DS CNERS is used for both papers. In the article * [Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseilleu2010P2481T, a moderate halophilic bacterium isolated from the human gut microflora]  *, the author * attempted an exhaustive exploration of the halophilic microbial diversity. * This objective seems to be far from the objective of the protocol approved by the Ethics Committee of Senegal which is a program of identification of emergent pathogens. The objective seems different from the exploration of the human gut microflora in 1 healthy child. We can note that this approval number (No. 00.87 MSP DS CNERS) is also used for several other papers with different types of objectives and different types of designs. For example, in this paper * [Common Epidemiology of Rickettsia felis Infection and Malaria, Africa]  *, the authors mention no stool sample in the study. Only blood samples have been taken. Furthermore, the same ethic approval number is used in the article * [The detection of vector-borne-disease-related DNA in human stool paves the way to large epidemiological studies]  *. In this article, the same author mention that the recruitment start in 2008, before to get the Senegalese approval in 2010. * feces were collected during a period from 2008 to 2010 * If the authors consider that the same protocol started in 2008, it means the approval number (No. 00.87 MSP DS CNERS) is a retrospective approval number and all papers with this number may be reviewed considering this fact. In accordance with Editors guidances and Helsinki Declaration, retrospective ethics approval cannot be obtained and it may not be possible to consider the manuscript for peer review. Can the authors provide more details about the scope of the protocol approved by Senegalese Ethics Committee with the No. 00.87 MSP DS CNERS: - Did the recruitment start in 2008 ? If not, why one of the study with a recruitment started in 2008 referred to this approval number? - Did the protocol include blood sample ? - Did the protocol include second reuse of the data ? - Have the patients been informed about the second reuse of their data ? - Did the CNERS approve the second reuse of the data ? ,