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

• Published in: Genome Biology Vol. 20; no. 1; p. 96
• Main Authors: Lugli, Gabriele Andrea, Milani, Christian, Duranti, Sabrina, Alessandri, Giulia, Turroni, Francesca, Mancabelli, Leonardo, Tatoni, Danilo, Ossiprandi, Maria Cristina, van Sinderen, Douwe, Ventura, Marco
• Format: Journal Article
• Language: English
• Published: London BioMed Central 16.05.2019; BMC
• Subjects: Animal Genetics and Genomics; Animals; Bifidobacterium; Bifidobacterium - genetics; Bifidobacterium - isolation & purification; Bioinformatics; Biomedical and Life Sciences; Callimico; Callithrix; Cattle; computer simulation; Dark matter; Deoxyribonucleic acid; digestive system; DNA; Evolutionary Biology; Gastrointestinal Microbiome; Genetic engineering; genome; Genomes; Genomics; Human Genetics; Human gut commensals; Life Sciences; Metagenomics; Microbial Genetics and Genomics; Microbiome Biology; Microbiota; Microorganisms; Phylogenetics; Pipelines; Plant Genetics and Genomics; prediction; Short Report; species; Metagenomics; Microbiota; Human gut commensals; Genomics
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-019-1711-6

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.