Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut.

Abstract

Metagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains uncharacterized. In this study, we mined a collection of 1090 metagenome assembled "high quality" viral genomes (> 90% completeness, as determined by CheckV) derived from human fecal samples. Sequence analysis revealed eight new species spanning seven genera within the class, Caudoviricetes and nineteen new species from fourteen genera within the ssDNA virus family, Microviridae. Additionally, four "high quality" genomes were not found in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation and KEGG pathway analysis of the "high-quality" genomes identified seven core genes (antB, dnaB, DNMT1, DUT, xlyAB, xtmB and xtmA) associated with metabolism and fundamental viral processes. Moreover, genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also detected. Host prediction analysis suggest bacterial hosts for approximately 40% of the genomes. Overall, this study reports the discovery of novel viral genomes and provides a comprehensive genome profiling of human gut viruses in a subpopulation from India. These findings serve as a foundation for future biological investigations to elucidate the role of these viruses in host physiology.