Taxonogenomics description of Parabacteroides timonensis sp. nov. isolated from a human stool sample
Authors: Enora Tomei
Fr√©d√©ric Cadoret
Maxime Descartes Mbogning Fonkou
Pierre-Edouard Fournier
Gregory Dubourg
Nicholas Armstrong
Fadi Bittar
Melhem Bilen
Didier Raoult
Ziad Daoud
Saber Khelaifia
Journal: MicrobiologyOpen (2019)
Discipline: MICROBIOLOGY
Keywords: Parabacteroides timonensis; culturomics; human; microbiome; new species.
Affiliations: Aix Marseille University, IRD, AP-HM, MEPHI, IHU M√©diterran√©e-Infection, Marseille, France., Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon., Aix Marseille University, IRD, AP-HM, SSA, VITROME, IHU M√©diterran√©e-Infection, Marseille, France., Assistance Publique H√¥pitaux de Marseille (AP-HM), IHU M√©diterran√©e-Infection, Marseille, France., Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.

Abstract:  Intensive efforts have been made to describe the human microbiome and its involvement in health and disease. Culturomics has been recently adapted to target formerly uncultured bacteria and other unclassified bacterial species. This approach enabled us to isolate in the current study a new bacterial species, Parabacteroides timonensis strain Marseille-P3236T , from a stool sample of a healthy 39-year-old pygmy male. This strain, is an anaerobic, gram-negative, nonspore-forming motile rod. Its genome is made up of 6,483,434 bp with 43.41% G+C content, 5046 protein-encoding genes, and 84 RNA genes. We herein provide the full description of Parabacteroides timonensis strain Marseille-P3236T through the taxonogenomic approach. 

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 from subjects 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 39y old Pygmy man 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 sample was collected in Congo, the strain was named after Marseille, where the strain was discovered. 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 Genbank Entry LT598573 does not mention that the isolate came from a man in Congo either. Rather it says that it was isolated in the hospital of Timone (Marseille). * How did the authors manage to transport this stool sample from Congo to the laboratory in France? Some details appear to be missing. Was the stool 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 *an approval from the ethic commit- tee of the Institut Fu00e9du00e9ratif de Recherche IFR48 (Marseille, France) carrying the number 09-022 was obtained before launching the study.* 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? ,