Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut
Authors: Asif Ahmad Jiman-Fatani
Sory Ibrahima Traore
Fehmida Bibi
Fadi Bittar
Melhem Bilen
Sophie Edouard
Esam Ibraheem Azhar
Mamadou Lamine Tall
Maxime Descartes Mbogning Fonkou
Pierre-Edouard Fournier
Mamadou Beye
Awa Diop
Caroline Michelle
Muhammad Yasir
Ziad Daoud
Fréderic Cadoret
Journal: MicrobiologyOpen (2019)
Discipline: MICROBIOLOGY
Keywords: Raoultibacter massiliensis; Raoultibacter timonensis; culturomics; human gut microbiota; new bacterial species
Affiliations: UMR MEPHI, IRD, APHM, IHU Méditerranée-Infection, Aix-Marseille Université, Marseille, France., Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon., UMR VITROME, IRD, AP-HM, SSA, IHU Méditerranée-Infection, Aix-Marseille Université, Marseille, France., Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia., Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia., Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.

Abstract:  As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively. 

Retracted: No

PubPeer comments:
 Unexpectedly, this paper does not mention that both strains had been described in two separate papers from some of the same authors. Both strains are described in this paper as novel, without citing the previous papers: * Raoultibacter massiliensis appears to have already been described in SI Traore et al., New Microbe and New Infect 2016; 14: 1u20133, DOI: 10.1016 j.nmni.2016.06.013 (same Genbank number, LT576395). * Raoultibacter timonensis appears to have already been described in M Bilen et al., New Microbe and New Infect 2017; 16: 45u201346, DOI: 10.1016 j.nmni.2016.12.016 (same Genbank number, LT623894). , 
 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. This paper describes the genome sequence of two Raoultibacter strains, one isolated from a healthy 19u2010yearu2010old Saudi Bedouin, and the other one from an 11u2010yearu2010old pygmy female living in Congo. The article offers few details, so I hope the authors could answer some questions here, in particular for the sample collected from a child in Congo. * What was the approximate place of residence of the subjects? The text says that the sample from the girl was 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 subjects? There is only limited value to describe a novel human-associated bacterial species if those details about the human host are not given. * How did the authors manage to incubate the specimen in a blood culture bottle under anaerobic conditions? Some details appear to be missing, in particular for the sample isolated in Congo. Was the sample transported from Congo back to France at some cold temperature, and then added to the blood culture bottle, or was the sample processed locally? Did local researchers or authorities participate? * The study mentions *the study was validated by the ethics committee of the Institut Federatif de Recherche 48 under number 09u2010022.* But that is a committee in France, not in one of the Congo republics or in Saudi Arabiaa. 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 from Congo to contribute. * Of particular concern, there is no statement about parents of the 11-year old girl giving consent. ,