Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches

Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.