Abstract
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.
Highlights
Next-Generation Sequencing (NGS) technologies allow the generation of vast amounts of genomic data, facilitating a variety of DNA sequencing approaches that range from single genome sequencing to large-scale metagenomic studies [1]
whole metagenome shotgun (WMGS) sequencing of animal stool samples produced approximately 79 million of paired-end reads with an average length of ~ 150 bp, which were analyzed through the METAnnotatorX pipeline
To identify genomic contigs that putatively belong to unclassified bifidobacterial taxa, a custom script employing the results of the METAnnotatorX pipeline was implemented (Additional file 3: Figure S2)
Summary
Next-Generation Sequencing (NGS) technologies allow the generation of vast amounts of genomic data, facilitating a variety of DNA sequencing approaches that range from single genome sequencing to large-scale metagenomic studies [1]. The focus of the current study was to apply WMGS sequencing in order to investigate the presence of novel gut commensals species belonging to the genus Bifidobacterium among the gut microbiota of animals. We employed a custom-made METAnnotatorX pipeline [16] to screen the sequencing data of each sample in order to retrieve genomic dark matter that was predicted to belong to the genus Bifidobacterium.
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