M. Mailhe

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.

Treatment and Prophylactic Strategy for Coxiella burnetii Infection of Aneurysms and Vascular Grafts: A Retrospective Cohort Study

AbstractCoxiella burnetii vascular infections continue to be very severe diseases and no guidelines exist about their prevention. In terms of treatment, the benefit of the surgical removal of infected tissues has been suggested by 1 retrospective study.We present a case of a C burnetii abdominal aortic graft infection for which we observed a dramatic clinical and biological recovery after surgery. We thus performed a retrospective cohort study to evaluate the impact of surgery on survival and serological outcome for patients with Q fever vascular infections diagnosed in our center.Between 1986 and February 2015, 100 patients were diagnosed with Q fever vascular infections. The incidence of these infections has significantly increased over the past 5 years, in comparison with the mean annual incidence over the preceding 22 years (8.83 cases per year versus 3.14 cases per year, P = 0.001). A two-and-a-half-year follow-up was available for 66 patients, of whom 18.2% died. We observed 6.5% of deaths in the group of patients who were operated upon at 2 and a half years, in comparison with 28.6% in the group which were not operated upon (P = 0.02). Surgery was the only factor that had a positive impact on survival at 2 and a half years using univariate analysis [hazard ratio: 0.17 [95% CI]: [0.039–0.79]; P = 0.024]. Surgery was also associated with a good serological outcome (74.1% vs 57.1% of patients, P = 0.03). In the group of patients with vascular graft infections (n = 47), surgery had a positive impact on serological outcome at 2 and a half years (85.7% vs 42.9%, P < 0.001) [hazard ratio: 0.40 [95% CI]: [0.17–098]; P = 0.046] and tended to be associated with lower although not statistically significant mortality (11.1% vs 27.6% of deaths, P = 0.19).Surgical treatment confers a benefit in terms of survival following C burnetii vascular infections. However, given the high mortality of these infections and their rising incidence, we propose a strategy that consists of screening for vascular graft and aneurysms in the context of primary Q fever, to decide when to start prophylactic treatment, similar to the strategy recommended for the prophylaxis of Q fever endocarditis.

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.