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. 2019 Jun;8(6):e00758.
doi: 10.1002/mbo3.758. Epub 2019 Jan 30.

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

Sory Ibrahima Traore  1 , Melhem Bilen  1   2 , Mamadou Beye  3 , Awa Diop  3 , Maxime Descartes Mbogning Fonkou  1 , Mamadou Lamine Tall  1 , Caroline Michelle  1 , Muhammad Yasir  4 , Esam Ibraheem Azhar  4   5 , Fehmida Bibi  4 , Fadi Bittar  1 , Asif Ahmad Jiman-Fatani  6 , Ziad Daoud  6 , Fréderic Cadoret  1 , Pierre-Edouard Fournier  3 , Sophie Edouard  1
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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

Sory Ibrahima Traore et al. Microbiologyopen. 2019 Jun.

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.

Keywords: Raoultibacter massiliensis; Raoultibacter timonensis; culturomics; human gut microbiota; new bacterial species; taxonogenomics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Gel view comparing Raoultibacter massiliensis gen. nov., sp. nov. strain Marseille‐P2849T and strain Raoultibacter timonensis gen. nov., sp. nov. strain Marseille‐P3277T with other closely related species present in our matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry spectrum database. The gel view displays the raw spectra of loaded spectrum files arranged in a pseudo‐gel like look. The x‐axis records the m/z value. The left y‐axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a gray scale scheme code. The color bar and the right y‐axis indicate the relation between the color of the peak and its intensity, in arbitrary units. Displayed species are indicated on the left
Figure 2
Figure 2
Phylogenetic tree highlighting the position of Raoultibacter massiliensis strain gen. nov., sp. nov. strain Marseille‐P2849T and Raoultibacter timonensis gen. nov., sp. nov. strain Marseille‐P3277T relative to other closely related species. Strains and their GenBank accession numbers of 16S rRNA gene are indicated in brackets. Sequences were aligned using ClustalW, with default parameters and phylogenetic inferences obtained using the neighbor‐joining method with 500 bootstrap replicates, within MEGA7 software. The scale bar represents a 2% nucleotide sequence divergence
Figure 3
Figure 3
Gram staining of (a) Raoultibacter massiliensis gen. nov., sp. nov. strain Marseille‐P2849T and (b) Raoultibacter timonensis gen. nov., sp. nov strain Marseille‐P3277T. Transmission electron microscopy images of R. massiliensis gen. nov., sp. nov. strain Marseille‐P2849T (c) and R. timonensis gen. nov., sp. nov strain Marseille‐P3277T (d) using a Tecnai G20 transmission electron microscope (FEI Company). The scale bar represents 200 nm
Figure 4
Figure 4
Graphical circular map of the genome of (a) Raoultibacter massiliensis gen. nov., sp. nov. strain Marseille‐P2849T and (b) strain Raoultibacter timonensis gen. nov., sp. nov. strain Marseille‐P3277T. From the outside to the center, contigs (red/gray), clusters of orthologous groups (COGs) category of genes on the forward strand (three circles), genes on the forward strand (blue circle), genes on the reverse strand (red circle), COG category of genes on the reverse strand (three circles), G+C skew (purple indicates positive values and olive negative values)
Figure 5
Figure 5
Distribution of functional classes of predicted genes according to the clusters of orthologous groups of proteins of Raoultibacter massiliensis gen. nov., sp. nov. strain Marseille‐P2849T and strain Raoultibacter timonensis gen. nov., sp. nov. strain Marseille‐P3277T among other closely related species
See this image and copyright information in PMC

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