D. Ricaboni

Romboutsia timonensis, a new species isolated from human gut

The exploration of the human microbiome was recently revolutionized by microbial culturomics and taxonogenomics. Thanks to this approach, we report here the main characteristics of Romboutsia timonensis strain Marseille-P326, a new bacterium isolated from the right human colon by colonoscopy in a 63-year-old French man with severe anaemia with melaena.

Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach

Strain Marseille-P2915T, a Gram-positive, facultative anaerobic and nonmotile coccus, was isolated from the gastric lavage of a patient with severe anaemia. The 16S rRNA and rpoB gene comparison exhibited a sequence identity of 98.7 and 92.6% with Streptococcus infantis strain JCM 10157T, respectively, collocating it within the ‘Streptococcus mitis’ group. On the basis of phenotypic and genomic analysis, we propose the validation of the type strain Streptococcus timonensis sp. nov. Marseille-P2915T (= DSM 103349 = CSUR P2915).

‘Merdibacter massiliensis’ gen. nov., sp. nov., isolated from human ileum

We report here the main characteristics of ‘Merdibacter massiliensis’ strain Marseille-P3254T (= CSUR P3254 = DSM 103475), which was isolated from human ileum.

Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum

The strain Marseille-P2749T (= CSUR P2749 = DSM 103085) was isolated as part of culturomics study from a liquid duodenum sample from a French man. Bacterial cells were Gram-negative bacilli, fusiform shaped and non–spore forming, and they grew in microaerophilic and anaerobic atmosphere. Its genome is 1 809 169 bp long and contains 1646 protein-coding genes. The DNA G+C content was 27.33 mol%. This strain exhibited a 95.9% sequence similarity with Fusobacterium periodonticum, the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2749T is suggested to be a novel species belonging to the genus Fusobacterium, for which the name Fusobacterium massiliense sp. nov. is proposed.

‘Mediterranea massiliensis’ gen. nov., sp. nov., a new human-associated bacterium isolated from the right and left colon lavage of a 58-year-old patient

We report here the main characteristics of ‘Mediterranea massiliensis’ strain Marseille-P2645T (CSURP2645) that was isolated from stored samples of gut.

Draft Genome Sequence of Blautia faecis Strain Marseille-P328, Isolated from the Human Ascending Colon

ABSTRACT Blautia faecis strain Marseille P328 was isolated from the ascending colon of a French patient. We sequenced the 4.45-Mb genome of the strain and compared it with that of other species of the Blautia genus.

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.

Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon

Strain Marseille-P2645T was isolated in a colon sample from a Frenchwoman who underwent a colonoscopy. Bacterial cells were Gram negative, non–spore forming, mobile and strictly anaerobic. The genome of strain Marseille-P2645T is 3 950 441 bp long and contains 3374 protein-coding genes. The DNA G+C content is of 51.66 mol%. Strain Marseille-P2645T exhibited a 92.9% sequence similarity with Bacteroides helcogenes strain P36-108T (GenBank accession no. CP002352), the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2645T (= CSUR P2645 = DSM 103034) is therefore a candidate as a type species of a new genus belonging to the Bacteroidaceae family, for which the name of Mediterranea massiliensis gen. nov., sp. nov., is proposed.

Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics

Culturomics is a concept developing different culture conditions in order to enlarge our knowledge of the human microbiota through the discovery of previously uncultured bacteria. This enabled us to isolate six new species of the Bacteroides genus: Bacteroides mediterraneensis strain Marseille-P2644, Bacteroides ihuae strain Marseille-P2824, Bacteroides togonis strain Marseille-P3166, Bacteroides ndongoniae strain Marseille-P3108, Bacteroides ilei strain Marseille-P3208 and Bacteroides congonensis strain Marseille-P3132. Those bacteria are Gram-negative anaerobic bacilli. We describe here their phenotypic features, together with phylogenetic analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum, fatty acid composition, and genome sequencing and annotation.

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing

BackgroundMost studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.ResultsUsing culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02).Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).ConclusionSignificant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.