The candidate phyla radiation (CPR) has been described as an obligatory group of ultrasmall bacteria associated with host bacteria. They phylogenetically represent a subdivision of bacteria distinct from other living organisms. Using polyphasic approaches, we screened human faecal samples for the detection of Saccharibacteria. The new sequences obtained by sequencing were compared to the complete CPR genomes available to date. Then, we attempted a co-culture of CPR-bacteria and non-CPR bacteria from human faecal samples. We finally aimed to evaluate the prevalence and distribution of these Saccharibacteria sequences in human sources in 16S amplicon datasets. We were able to reconstitute two high-quality Saccharibacteria genomes named Minimicrobia massiliensis and Minimicrobia timonensis. We have established, for the first time in human digestive samples, the coculture of Candidatus Saccharibacteria with two different bacterial hosts. Finally, we showed that 12.8% (610/4,756) of samples sequenced in our laboratory were positive for operational taxonomic units (OTUs) assigned to M.massiliensis. and significantly enriched in human respiratory and oral microbiota. Here, we reported the first genomes and coculture of Saccharibacteria from human gut specimens. This study opens a new field, particularly in the study of the involvement of CPR in the human intestinal microbiota.
AbstractWe used phenotypic, genomic and phylogenetic information following the taxono-genomics approach to demonstrate that strain Marseille–P3254, isolated from an ileal sample of a 76-year old woman who underwent upper and lower digestive tract endoscopy for esophagitis and colonic polyp, is representative of a novel bacterial genus within the family Erysipelotrichaceae in the phylum Firmicutes. It is an anaerobic Gram-negative bacterium without catalase and oxidase activities. The genome of strain Marseille–P3254 is 2,468,496-bp long with a 40.1% G + C content. This new bacterium is most closely related to Eubacterium dolichum, with which it shares 90.7% 16S rRNA sequence similarity. In addition, genomic comparison using the digital DNA–DNA hybridization and OrthoANI analyses between the novel organism and the E. dolichum type strain revealed identities of 25.2 and 68.91%, respectively. The major fatty acids were C16: 0, C18: 1n9 and C18: 0. Based on these data, we propose the creation of the new genus Merdibacter gen. nov., with strain Marseille-P3254T (=CSUR P3254 = DSM 103534) being the type strain of the new species Merdibacter massiliensis gen. nov., sp. nov.