Polyphasic approach to detect, isolate and characterise Candidate Phyla Radiation in human saliva

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Benseddik, Fatma | Bedotto, Marielle | Caputo, Aurélia | Alou, Maryam, Tidjani | Baudoin, Jean- Pierre | Beye, Mamadou | Andrieu, Claudia | Raoult, Didier | Dubourg, Grégory

Edité par CCSD -

The vast majority of bacteria on earth have not yet been cultured, including most members of the Candidate Phyla Radiation. This emerging division of the bacterial domain accounts for 26% of the diversity of the human microbiota and consists of 73 phyla including Candidatus Saccharibacteria, formerly known as TM7. They are characterised by their small cell (100 to 400 nm) and size of their genome (1 Mb). These mini-microbes present obligatory symbiotic or parasitic activities with their bacterial hosts and are often associated with inflammatory mucosal pathologies such as gingivitis and periodontitis. Although ubiquitous in the human oral microbiome and widespread in the environment, TM7 cannot be cultured in axenic conditions and are only co-cultured with their bacterial host. In this study, we aimed to isolate new TM7 strains, maintain their viability, and characterise them using molecular and microscopic approaches. To this effect, we developed a new co-culture protocol to grow them with their host bacterium, Schaalia odontolytica, and designed a real-time quantitative PCR system targeting the 23S rRNA gene of TM7. We also conducted analyses using scanning and transmission electron microscopy, fluorescence in situ hybridisation, MALDI-TOF mass spectrometry, and next-generation sequencing. From one salivary sample, we identified potential bacterial hosts for TM7 and successfully isolated a new species of TM7 by co-culture with Schaalia odontolytica, maintaining viability after several passages. Analysis of the genomic sequences will improve the database and help us better understand their metabolisms and their currently poorly understood roles in both human physiology and pathology.

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