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

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Lugli, Gabriele Andrea
Milani, Christian
Duranti, Sabrina
Alessandri, Giulia
Turroni, Francesca
Mancabelli, Leonardo
Tatoni, Danilo
Ossiprandi, Maria Cristina
van Sinderen, Douwe
Ventura, Marco
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BioMed Central Ltd.
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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.
Genomics , Metagenomics , Microbiota , Human gut commensals
Lugli, G.A., Milani, C., Duranti, S., Alessandri, G., Turroni, F., Mancabelli, L., Tatoni, D., Ossiprandi, M.C., van Sinderen, D. and Ventura, M. (2019). 'Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches'. Genome biology, 20(1), 96. (6pp.) DOI:10.1186/s13059-019-1711-6