TAXONOGENOMICS: GENOME OF A NEW ORGANISM Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut M. Tidjani Alou 1 , T.-T. Nguyen 1 , N. Armstrong 1 , J. Rathored 1 , S. Khelaifia 1 , D. Raoult 1,2 , P.-E. Fournier 1 and J.-C. Lagier 1 1) Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France and 2) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Numidum massiliense gen. nov., sp. nov., strain mt3 T is the type strain of Numidum gen. nov., a new genus within the family Bacillaceae. This strain was isolated from the faecal flora of a Tuareg boy from Algeria. We describe this Gram-positive facultative anaerobic rod and provide its complete annotated genome sequence according to the taxonogenomics concept. Its genome is 3 755 739 bp long and contains 3453 protein-coding genes and 64 RNA genes, including eight rRNA genes. © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. Keywords: Bacillaceae, Culturomics, gut microbiota, Numidum massiliense genome, taxonogenomics Original Submission: 15 April 2016; Revised Submission: 10 May 2016; Accepted: 12 May 2016 Article published online: 17 May 2016 Corresponding author: J.-C. Lagier, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France E-mail: jclagier@yahoo.fr Introduction Several microbial ecosystems are harboured by the human body, among which is the human gut microbiota. This particular ecosystem is so vast that its cell count (10 14 cells) is evaluated at ten times the number of human cells in the human body, and its collective bacterial genome size is 150 times larger than the human genome [1 – 4]. Over the years, with the evolution of exploratory techniques of microbial ecosystems from culture to metagenomics, the gut microbiota has been shown to be involved in many conditions such as obesity, inflammatory bowel disease and irritable bowel disease [1]. It has also been shown to play key roles in digestion as well as metabolic and immunologic functions [1 – 3]. A better knowledge of the gut microbiota’s composition is thus required for an improved understanding of its functions. In order to extend the gut microbiota repertoire and bypass the noncultivable bacteria issue, the culturomics concept was developed in order to cultivate as exhaustively as possible the viable population of a bacterial ecosystem; it consists in the multiplication of culture conditions, as well as varying of media, temperature and atmosphere [5]. Using this technique, strain mt3 T was isolated and identified as a previously unknown member of the Bacillaceae family. Currently there are 53 vali- dated genera in the Bacillaceae family. This family was created by Fisher in 1895 (http://www.bacterio.net/Bacillaceae.html). The genus Bacillus was described as its type genus. The genera that belong to this family are rod shaped, mostly aerobic and facultative anaerobic bacteria. They are found in various eco- systems like the human body, soil, water, air and other envi- ronmental ecosystems [6]. Bacterial classification is currently based on a polyphasic approach with phenotypic and genotypic characteristics such as DNA-DNA hybridization, G+C content and 16S rRNA sequence similarity [7 – 9]. Nevertheless, this classification sys- tem has its limits, among which is the high cost of the DNA- DNA hybridization technique and its low reproducibility [7,10]. With the recent development of genome sequencing technology [11], a new concept of bacterial description was developed in our laboratory [12 – 16]. This taxonogenomics New Microbe and New Infect 2016; 12: 76– 85 © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) http://dx.doi.org/10.1016/j.nmni.2016.05.009