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

Genome Biology

Giulia Alessandri¹  Maria Cristina Ossiprandi²  Christian Milani³  Gabriele Andrea Lugli³  Danilo Tatoni³  Leonardo Mancabelli³  Sabrina Duranti³  Marco Ventura⁴  Francesca Turroni⁴  Douwe van Sinderen⁵ 

[1] 0000 0004 1758 0937, grid.10383.39, Department of Veterinary Medical Science, University of Parma, Parma, Italy;0000 0004 1758 0937, grid.10383.39, Department of Veterinary Medical Science, University of Parma, Parma, Italy;0000 0004 1758 0937, grid.10383.39, Microbiome Research Hub, University of Parma, Parma, Italy;0000 0004 1758 0937, grid.10383.39, Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy;0000 0004 1758 0937, grid.10383.39, Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy;0000 0004 1758 0937, grid.10383.39, Microbiome Research Hub, University of Parma, Parma, Italy;0000000123318773, grid.7872.a, APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland;

关键词: Genomics;    Metagenomics;    Microbiota;    Human gut commensals;   

DOI  :  10.1186/s13059-019-1711-6

来源: publisher

【 摘 要 】

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.

【 授权许可】

CC BY