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Culturomics has allowed the isolation of a significant number of new bacterial species from the human gut microbiota and proved to be a valuable complement to culture-independent techniques. Using this culture-based approach, a new bacterial species has been isolated from a stool sample of a 39-year-old healthy Pygmy male and described using the taxonogenomic strategy. Cells of strain Marseille-P4356 T are Gram-stain negative cocci. The strain grows optimally at 37 °C and is catalase positive but oxidase negative. Its 16S rRNA gene sequence exhibited 92.96% sequence similarity with Dysgonomonas gadei strain JCM 16698T (NR_113134.1), currently its phylogenetically closest species that has been validly named. The genome of strain Marseille-P4356 T is 3,472,011 bp long with 37.3 mol% G+C content. Phenotypic, biochemical, proteomic, genomic and phylogenetic analyses, clearly demonstrate that strain Marseille-P4356 T (= CCUG 71356 T  = CSUR P4356 T ) represents a new species within the genus Dysgonomonas, for which we propose the name Dysgonomonas massiliensis sp. nov.

With the aim of describing the human microbiota by the means of culture methods, culturomics was developed in order to target previously un-isolated bacterial species and describe it via the taxono-genomics approach. While performing a descriptive study of the human gut microbiota of the pygmy people, strain Marseille-P4678 T has been isolated from a stool sample of a healthy 39-year-old pygmy male. Cells of this strain were Gram-positive cocci, spore-forming, non-motile, catalase-positive and oxidase-negative, and grow optimally at 37°C under anaerobic conditions. Its 16S rRNA gene sequence exhibited 89.69% of sequence similarity with Parvimonas micra strain 3119B T (NR 036934.1), its phylogenetically closest species with standing in nomenclature. The genome of strain Marseille-P4678 T is 2,083,161 long with 28.26 mol% of G+C content. Based on its phenotypic, biochemical, genotypic and proteomic profile, this bacterium was classified as a new bacterial genus and species Miniphocibacter massiliensis gen. nov., sp. nov. with the type strain Marseille-P4678 T ., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Intensive efforts have been made to describe the human microbiome and its involvement in health and disease. Culturomics has been recently adapted to target formerly uncultured bacteria and other unclassified bacterial species. This approach enabled us to isolate in the current study a new bacterial species, Parabacteroides timonensis strain Marseille-P3236 T , from a stool sample of a healthy 39-year-old pygmy male. This strain, is an anaerobic, gram-negative, nonspore-forming motile rod. Its genome is made up of 6,483,434 bp with 43.41% G+C content, 5046 protein-encoding genes, and 84 RNA genes. We herein provide the full description of Parabacteroides timonensis strain Marseille-P3236 T through the taxonogenomic approach., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Eggerthella timonensis strain Marseille-P3135 is a new bacterial species, isolated from the stool sample of a healthy 8-year-old pygmy female. This strain (LT598568) showed a 16S rRNA sequence similarity of 96.95% with its phylogenetically closest species with standing in nomenclature Eggerthella lenta strain DSM 2243 (AF292375). This bacterium is a nonspore forming, Gram-positive, nonmotile rod with catalase but no oxidase activity. Its genome is 3,916,897 bp long with 65.17 mol% of G + C content. Of the 3,371 predicted genes, 57 were RNAs and 3,314 were protein-coding genes. Here, we report the main phenotypic, biochemical, and genotypic characteristics of E. timonensis strain Marseille-P3135 (=CSUR P3135, =CCUG 70327); ti.mo.nen'sis, N.L. masc. adj., with timonensis referring to La Timone, which is the name of the hospital in Marseille (France) where this work was performed). Strain is a nonmotile Gram-positive rod, unable to sporulate, oxidase negative, and catalase positive. It grows under anaerobic conditions between 25°C and 42°C but optimally at 37°C., (© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Using culturomics, a recently developed strategy based on diversified culture conditions for the isolation of previously uncultured bacteria, we isolated strain Marseille-P3296 T from a fecal sample of a healthy pygmy female. A multiphasic approach, taxono-genomics, was used to describe the major characteristics of this anaerobic and gram-positive bacillus that is unable to sporulate and is not motile. The genome of this bacterium is 1,878,572 bp-long with a 57.94 mol% G + C content. On the basis of these characteristics and after comparison with its closest phylogenetic neighbors, we are confident that strain Marseille-P3296 T (=CCUG 70328 =  CSUR P3296) is the type strain of a novel species for which we propose the name Collinsella bouchesdurhonensis sp. nov., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Strain Marseille-P3237 was isolated from a stool sample of a healthy 35-year-old Congolese pygmy female. This anaerobic, Gram-negative, non-spore-forming and non-motile coccus-shaped bacterium is a member of the order Coriobacteriales . It exhibits a 2 009 306-bp genome with a 65.46 mol% G+C content and is closely related to, but distinct from, members of the Olsenella genus. We propose the creation of the new genus Libanicoccus gen. nov. and of the new species Libanicoccus massiliensis sp. nov. [ABSTRACT FROM AUTHOR]

This study presents the main characteristics of ‘ Mobilibacterium massiliense ’ strain P2510 (CSUR P2510) and ‘ Mobilibacterium timonense ’ strain P3194 (CSUR P3194), isolated from a stool sample of a patient at the Timone hospital and from a stool sample of a healthy 50-year-old pygmy (Baka) woman, respectively. [ABSTRACT FROM AUTHOR]