S. Ndongo

Culture of previously uncultured members of the human gut microbiota by culturomics

Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism1. The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms2. We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization–time of flight and 16S rRNA for identification2. Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies3–5. We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut.

Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia

The strain GD9T is the type strain of the newly proposed species Blautia massiliensis sp. nov., belonging to the family Lachnospiraceae. It was isolated from a fresh stool sample collected from a healthy human using the culturomics strategy. Cells are Gram-negative rods, oxygen intolerant, non-motile and non-spore forming. The 16S rRNA gene sequencing showed that strain GD9T was closely related to Blautia luti, with a 97.8% sequence similarity. Major fatty acids were C14:0 (19.8%) and C16:0 (53.2%). Strain GD9T exhibits a genome of 3,717,339 bp that contains 3,346 protein-coding genes and 81 RNAs genes including 63 tRNAs. The features of this organism are described here, with its complete genome sequence and annotation. Compared with other Blautia species which are Gram positive, the strain was Gram negative justifying an emended description of the genus Blautia.

Christensenella timonensis, a new bacterial species isolated from the human gut.

We propose a new species, Christensenella timonensis, strain Marseille-P2437T (CSUR P2437T), which was isolated from gut microbiota of a 66-year-old patient as a part of culturomics study. C. timonensis represents the second species isolated within the Christensenella genus.

‘Collinsella phocaeensis’ sp. nov., ‘Clostridium merdae’ sp. nov., ‘Sutterella massiliensis’ sp. nov., ‘Sutturella timonensis’ sp. nov., ‘Enorma phocaeensis’ sp. nov., ‘Mailhella massiliensis’ gen. nov., sp. nov., ‘Mordavella massiliensis’ gen. nov., sp. nov. and ‘Massiliprevotella massiliensis’ gen. nov., sp. nov., 9 new species isolated from fresh stool samples of healthy French patients

Here we report of summary of the characteristics of ‘Collinsella phocaeensis’ strain Marseille-P3245T sp. nov., ‘Clostridium merdae’ strain Marseille-P2953T, ‘Sutterella massiliensis’ strain Marseille-P2435T sp. nov., ‘Sutturella timonensis’ strain Marseille-P3282T sp. nov., ‘Enorma phocaeensis’ Marseille-P3242T sp. nov., ‘Mailhella massiliensis’ strain Marseille-P3199T gen. nov., sp. nov., ‘Mordavella massiliensis’ strain Marseille-P3246T sp. nov. and ‘Massiliprevotella massiliensis’ strain Marseille-P2439T sp. nov. isolated from fresh stool samples of healthy French patients.

‘Actinomyces provencensis’ sp. nov., ‘Corynebacterium bouchesdurhonense’ sp. nov., ‘Corynebacterium provencense’ sp. nov. and ‘Xanthomonas massiliensis’ sp. nov., 4 new species isolated from fresh stools of obese French patients

We report the main characteristics of ‘Actinomyces provencensis’ strain SN12T sp. nov., ‘Corynebacterium bouchesdurhonense’ strain SN14T sp. nov., ‘Corynebacterium provencense’ strain SN15T sp. nov. and ‘Xanthomonas massiliensis’ strain SN8T sp. nov., which were all isolated from stool samples from obese French patients.

Emergencia timonensis, a new bacterium isolated from the stool of a healthy patient.

We present the essential characteristics of “Emergencia timonensis” strain SN18 (= CSUR P2260), a new member of the order Clostridiales that was isolated from the stool of healthy patient.

‘Cellulomonas timonensis’ sp. nov., taxonogenomics description of a new bacterial species isolated from human gut

‘Cellulomonas timonensis’ sp. nov. strain sn7T is a new species within the Cellulomonas genus. We present the main phenotypic characteristics and provide a complete annotation of its genome sequence. This facultative anaerobic bacterium, isolated from the stool of 38-year-old obese Frenchman, is Gram-positive, has motile rods and is sporulating. The genome is 4 057 828 bp long with 72.42% G + C content. Of the 3732 predicted genes, 3667 were protein-coding genes and 65 were RNAs.

Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces

Xanthomonas massiliensis strain SN6T is a Gram-negative bacterium which is aerobic, motile and nonsporulating. This new species isolated from human faeces exhibited the characteristic traits of members of this genus, such as yellow pigmentation and viscosity. Here we present the main phenotypic characteristics and the taxonogenomics description of this strain. The genome is 3 690 720 bp long with DNA G + C content of about 70.52%.

Gorillibacterium timonense sp. nov. and Vitreoscilla massiliensis sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients

We report the main characteristics of Gorillibacterium timonense strain SN4T sp. nov. and Vitreoscilla massiliensis strain SN6T sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients.

Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics

The taxonogenomic approach, including the culturomics techniques, is now currently used to isolate and characterize new bacteria. These approaches notably allowed us to discover six new species of the Actinomyces genus: Actinomyces ihuae strain SD1, Actinomyces bouchesdurhonensis strain Marseille-P2825, Actinomyces urinae strain Marseille-P2225, Actinomyces marseillensis strain Marseille-P2818, Actinomyces mediterranea strain Marseille-P3257 and Actinomyces oralis strain Marseille-P3109. Each is the type strain of the corresponding bacterial species. 16S ribosomal RNA gene sequence comparison was used to classify these strains among the Actinomyces genus. These strains are all Gram positive, rod shaped and facultative aerobic. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.