Genomic description and prevalence of two new Candidatus Saccharibacteria species from the human gut in different samples and countries

Abstract

Abstract 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.