Microbial Culturomics: Paradigm shift in the human gut microbiome study

We studied two lean African and one obese European stools using 212 different culture techniques (microbial culturomics). The 32,500 colonies obtained by culturomics were analyzed using mass-spectrometry and 16S rRNA amplification and sequencing, yielding 341 species of bacteria from 7 phyla and 117 genera, 5 fungi and a giant virus (Senegalvirus). The microbiome identified by culturomics included 175 species never described previously in the human gut including 32 new species and genera for which the genomes were sequenced. Among these, the new species Microvirga massiliensis have the largest bacterial genome so far obtained from a human, and Senegalvirus is the first giant virus detected in human gut. Concurent metagenomic analysis of the same samples produced 698 phylotypes including 282 known species of which 51 overlapped with the microbiome identified by culturomics.