J. Rathored

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov.

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.

Identification of virulence factors and antibiotic resistance markers using bacterial genomics

In recent years, the number of multidrug-resistant bacteria has increased rapidly and several epidemics were signaled in different regions of the world. Faced with this situation that presents a major global public health concern, the development and the use of new and rapid technologies is more than urgent. The use of the next-generation sequencing platforms by microbiologists and infectious disease specialists has allowed great progress in the medical field. Here, we review the usefulness of whole-genome sequencing for the detection of virulence and antibiotic resistance associated genes.

Noncontiguous finished genome sequence and description of Kallipyga gabonensis sp. nov.

Taxonogenomics coupled with culturomics promotes the isolation and characterization of bacteria. Kallipyga gabonensis sp. nov. strain GM4 is a strictly anaerobic, Gram-positive, and non motile coccus isolated from the stool of a Gabonese male teenager. The genome is 1,621,211 bp long with 50.01% G+C content and two scaffolds. Of the 1,536 predicted genes, 1,475 were protein-coding genes and 61 were RNA genes. A total of 931 genes were assigned a putative function, and 79 genes were identified as ORFans.

Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut

Virgibacillus senegalensis SK-1T (= CSUR P1101 = DSM 28585) is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man. Here we describe the genomic and phenotypic characteristics of this isolate. The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes.

Noncontiguous finished genome sequence and description of Gabonia massiliensis gen. nov., sp. nov.

Culturomics coupled with taxonogenomics is currently used to isolate and characterize new bacteria. Here we describe the features and complete genome sequence of Gabonia massiliensis strain GM3, an anaerobic Gram negative, non-spore-forming and catalase-positive bacillus isolated from a stool specimen of a healthy Gabonese male youth. Belonging to a new genus called Gabonia, it exhibits a genome of 4 261 752 bp including 37.9% GC content and 3,288 predicted genes.

Bacillus rubiinfantis sp. nov. strain mt2T, a new bacterial species isolated from human gut

Bacillus rubiinfantis sp. nov. strain mt2T is the type strain of B. rubiinfantis sp. nov., isolated from the fecal flora of a child with kwashiorkor in Niger. It is Gram-positive facultative anaerobic rod belonging to the Bacillaceae family. We describe the features of this organism alongside the complete genome sequence and annotation. The 4 311 083 bp long genome (one chromosome but no plasmid) contains 4028 protein-coding gene and 121 RNA genes including nine rRNA genes.

Paenibacillus phocaensis sp. nov., isolated from the gut microbiota of a healthy infant

Paenibacillus phocaensis sp. nov. strain mt24T (= CSUR P2238 = DSM 101777) is a Gram-negative, facultative anaerobic, spore-forming and motile bacilli. This strain was isolated from the stool sample of a healthy infant from Niger. Its genome was estimated to a size of 5 521 415 bp with a 53.54% GC content. It contains 4835 protein-coding genes and 89 RNAs, among which two were 16S rRNA genes. There were also 101 genes (2.09%) identified as ORFans.

Drancourtella massiliensis gen. nov., sp. nov. isolated from fresh healthy human faecal sample from South France

Strain GD1T gen. nov., sp. nov., is the type strain of the newly proposed genus and species Drancourtella massiliensis, belonging to the Clostridiales order. This strain, isolated from the stool of a healthy person, is a Gram-positive rod, oxygen intolerant and nonmotile, with spore-forming activity. The features of this organism and its genome sequence are described. The draft genome is 3 057 334 bp long with 45.24% G + C content; it contains 2861 protein-coding genes and 64 RNA genes.

Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut.

Numidum massiliense gen. nov., sp. nov., strain mt3T 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.

Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut

Massilibacterium senegalense gen. nov., sp. nov., strain mt8T, is the type strain of Massilibacterium gen. nov., a new genus within the Bacillaceae family. This Gram-negative facultative anaerobic rod was isolated from the gut microbiota of a severely malnourished boy. Its phenotypic description is hereby presented with a complete annotation of its genome sequence. This genome is 5 697 950 bp long and contains 5615 protein-coding genes and 178 RNA genes, among which are 40 rRNA genes.