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In recent years, metagenomics and then culturomics, which consists of the multiplication of media and culture conditions and the rapid identification of all bacterial colonies, have generated renewed interest in the human microbiota, and diseases associated with modifications in its composition in particular. The sample transport media included in diverse swab transport systems and the storage conditions are among the factors that influence the results of the culturomics. In this study, we compared the results of culturomics from paired skin, oral and rectal swabs from intensive care unit (ICU) patients using Culture Top sample transport medium as compared to our routine one. From 152 clinical samples, we were able to isolate and identify 45 600 colonies, belonging to 338 different bacterial species. The transport system Culture Top identified 282 different bacterial species, while 244 were identified by our routine system. Of these, 188 different bacterial species were commonly identified using both transport systems, while 94 (27.8 %) and 56 (16.5 %) were only identified using Culture Top and our routine system, respectively (P

To date, the axenic culture of

BackgroundTreponema species as commensals of the human microbiome have a prevalence and function depending on the studied niche. In the oral cavity, treponemes are ubiquitous while they have been strictly linked to rural and ancestral populations in the gastro-intestinal tract and are undetected in urban populations. In this study, an in silico analysis of 1481 metagenomes, selected based on the previous detection of treponemes in such sample types, was conducted to predict putative bacterial antagonists of treponemes, i.e. bacteria present when treponemes are lacking and vice versa. Predicted antagonists were subsequently tested in-vitro against Treponema denticola CSUR P7640.ResultsMost frequent predicted antagonists included members of the Bifidobacteriaceae family (23.3%) among which Bifidobacterium longum was the most significant (63.3% in T- group, p Bacteroides (6.7%) and Streptococcus (13.3%) genera. The relative abundance of the aforementioned taxa was also anticorrelated with that of the Treponema genus in the metagenomes analyzed in this study. B. longum CSUR P7400, Bifidobacterium bifidum CSUR P1194, Bifidobacterium breve CSUR P7882, Bacteroides ovatus CSUR P4577, Bacteroides uniformis CSUR P2248 and Bacteroides thetaiotaomicron CSUR P7324 were able to inhibit the growth of T. denticola with B. longum being the most efficient.ConclusionsThese results highlight an antagonism between Bifidobacterium species, known probiotics and bio-preservatives, and Treponema spp. This may help to explain the variation of Treponema prevalence in high-income countries and middle- and low-income countries which might linked to the differential consumption of fermented dairy foodstuff and processed food and therefore to the phenomenon of nutrition transition.

International audience; Using a taxonogenomics method, we describe here a Gram-negative bacterium named Prevotella rectalis sp. nov., strain Marseille-P4334 T (= CSUR P4334) isolated from the rectum. Strain Marseille-P4334 T has a genome that measure 3.03 Mbp with 43.3 mol% G + C content.

We report the main characteristics of ‘Selenomonas massiliensis’ sp. nov., strain Marseille-P4036T (= CSUR P4036). The culturomic combined with taxonogenomic methods were used to identify and characterize this new anaerobic bacterial species, which was isolated from an oral sample of a 25-year-old healthy woman. Keywords: Culturomics, oral microbiota, ‘Selenomonas massiliensis’, taxonogenomics

We present here a new passive-filtration-based culture device combined with rapid identification with a new electron microscope (Hitachi TM4000) for the detection and culture of Treponema species from the human oral cavity. Of the 44 oral samples cultivated, 15 (34%) were found to be positive for Treponema using electron microscopy and were also culture positive. All were subcultured on agar plates; based on genome sequencing and analyses, 10 were strains of Treponema pectinovorum and 5 were strains of Treponema denticola. The 29 samples that were negative for Treponema remained culture negative. In addition, 14 Treponema species ordered from the DSMZ collection were cultured in the T-Raoult culture medium optimized here. Finally, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) was used and 30 novel spectra were added to the MALDI-TOF MS database. We have successfully developed a new and effective method for treponemal detection, culture, and identification.

We report the main characteristics of ‘Bacteroides cutis’ sp. nov., strain Marseille-P4118T (= CSUR P4118), a new species within the genus Bacteroides. This strain was isolated from a skin sample of a 75-year-old man from Marseille. Keywords: Bacteroides cutis, culturomics, intensive care unit patient, skin microbiota, taxonogenomics

Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28 consenting peri-implantitis patients. PCR-sequencing of the 16S rRNA gene was used as a broad-spectrum screening method and results were further confirmed by real-time quantitative PCR targeting the mcrA genes. Results showed a methanogen community dominated by Methanobrevibacter oralis in 31/58 (51%) samples including 16/28 (57%) control samples and 15/30 (50%) peri-implantitis samples. Methanobrevibacter massiliense was detected in 5/58 (8.6%) samples including 3/28 (1%) control samples and 2/30 (6.7%) peri-implantitis samples. The prevalence of M. oralis or M. massiliense did not significantly differ in peri-implantitis and control samples (exact Fisher test, P = 0.61 and P = 0.67, respectively). Further ponderation of the methanogen load by the real-time quantitative PCR for actin human gene again indicated non-significant difference (Wilcoxon-Mann-Whitney test, P = 0.48 and P = 0.40, respectively). These data show that the prevalence of methanogens does not differ in peri-implantitis lesions and healthy sites, when individuals are their own control. These data do not allow assigning a specific pathogenic role to methanogens in peri-implantitis; methanogens rather are part of the commensal and normal flora of the oral cavity.