Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition
Authors: Claudia Andrieu
Pierre-Edouard Fournier
Cheikh Sokhna
Matthieu Million
Aldiouma Diallo
Nicholas Armstrong
Maryam Tidjani Alou
Caroline Michelle
Fadi Bittar
Didier Raoult
Saber Khelaifia
Journal: Anaerobe (2016)
Discipline: MICROBIOLOGY
Keywords: Anaerococcus rubiinfantis; Culturomics; Gut microbiota; Malnutrition; Taxono-genomics.
Affiliations: Unit√© de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Universit√©, Marseille, France., Unit√© de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal., Unit√© de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Universit√©, Marseille, France; Unit√© de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia., Unit√© de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Universit√©, Marseille, France. Electronic address: .

Abstract:  Anaerococcus rubiinfantis sp. nov. strain mt16(T) is a new species within the genus Anaerococcus, which was isolated by the culturomics approach from the gut microbiota of an infant suffering from kwashiorkor. A phenotypic, biochemical and proteomic description of this strain is hereby presented alongside a complete annotation of its genome. This strictly anaerobic species forms Gram-positive non-sporeforming cocci. The major fatty acid was hexadecanoic acid. The phylogenetic analysis of strain mt16(T) showed a 97.9% similarity level with Anaerococcus vaginalis, the closest validly published species. Its genome is 1,929,161 bp long with 29.5% G + C content and contains 1808 protein-coding genes and 56 RNA genes, among which are six rRNA genes. Genomic analysis identified 41/1864 coding genes as ORFans (2.2%) and at least 620/1808 (34.9%) orthologous proteins which are not shared with the closest phylogenetic species. We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease. 

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. In this paper, a novel bacterial species is described, isolated from the stool of a malnourished 7-month-old child living in Senegal. The article offers few details about the subject, so I hope the authors could answer some questions here. * How did the authors manage to transport this stool sample from Senegal 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 paper only gives us  the sample was frozen at -80 C upon reception at the hospital La Timone in Marseille, France. * After obtaining the stool sample, was the malnourished child treated, and the family helped? * The study mentions *Approval for this study was given by the Institut Feu0019deu0019ratif de Recherche 48 (Faculty of Medicine, Marseille, France) under agreement number 09e022.* But that is a committee in France, not in Senegal. There is no word about obtaining IRB approval e.g. on consent wording with the local authorities. ,