Microbial culturomics: paradigm shift in the human gut microbiome study

摘要: Comprehensive determination of the microbial composition gut microbiota and relationships with health disease are major challenges in 21st century. Metagenomic analysis human detects mostly uncultured bacteria. We studied stools from two lean Africans one obese European, using 212 different culture conditions (microbial culturomics), tested colonies by mass spectrometry 16S rRNA amplification sequencing. In parallel, we analysed same three samples pyrosequencing amplicons targeting V6 region. The 32 500 obtained culturomics have yielded 340 species bacteria seven phyla 117 genera, including rare (Deinococcus-Thermus Synergistetes, five fungi, a giant virus (Senegalvirus). microbiome identified included 174 never described previously gut, 31 new genera for which genomes were sequenced, generating c. 10 000 unknown genes (ORFans), will help future molecular studies. Among these, Microvirga massiliensis has largest bacterial genome so far human, Senegalvirus is reported gut. Concurrent metagenomic produced 698 phylotypes, 282 known species, 51 overlapped culturomics. Thus, complements metagenomics overcoming depth bias inherent approaches.