Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description ofBeduini massiliensisgen. nov., sp. nov.

Abstract

Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase-and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.

Discovery of a new species within Bacillus genus in a stool sample from Gabon: “Bacillus massiliogabonensis” sp. nov.

“…Succinctly, strain Marseille P2639 was isolated using a Marine medium culture bottle (bioMérieux, Marcy l'Etoile, France) followed by subculture in 5% sheep’s blood–enriched Columbia agar (bioMérieux) in an aerobic atmosphere at 37°C [3], [4], [5]. The Gram-negative bacillus, strain Marseille P2639, is motile and catalase positive.…”

“…The set of primers used included fD1-rP2 [3], [4], [5]. Correction and assembly of the 16S rRNA sequences were done using CodonCode Aligner.…”

“Intestinimonas gabonensis” sp. nov., a new bacterium detected from a Gabonese stool specimen

“…Strain GM5 was isolated after the stools were cultured in a blood culture bottle (bioMérieux, Marcy l’Etoile, France), followed by a subculture in 5% sheep’s blood–enriched Columbia agar (bioMérieux) under anaerobic conditions at 37°C [3], [4], [5]. A fusiform Gram-negative bacterium, strain GM5 is nonmotile without oxidase and catalase activities.…”

Description of Clostridium phoceensis sp. nov., a new species within the genus Clostridium

“…A Color Gram 2 Kit (bioMérieux) was used to perform the Gram coloration observed with a 100× oil-immersion objective lens using the DM1000 photonic microscope (Leica, Wetzlar, Germany) [12], [13].…”