Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Abstract

Background Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut. Results A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, “Flandersviridae” and “Quimbyviridae”, include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides, and Prevotella. The third proposed family, “Gratiaviridae,” consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae, and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some “Quimbyviridae” phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several “Flandersviridae” phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The “Gratiaviridae” phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. Conclusions Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse, and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes.

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

“…4 A). The terL gene is a single-copy viral marker gene [ 12 ] that is commonly used for phylogenetic tree construction of Caudovirales phages [ 83 , 84 ], due to its ubiquity and relatively high sequence conservation across diverse phages [ 84 ]. Overall, the tree revealed two large superclades, one with predominantly RefSeq viral sequences and one with predominantly soil viral sequences (phylogenetic dispersion, D = − 0.25), with D < 0 indicating significant phylogenetic separation of RefSeq and soil sequences [ 85 , 86 ].…”

Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

“…Although the contribution of each route to the total number of horizontally transferred genes in a given genome is an outstanding question ( 7 – 9 ), examining the genes mobilized via each pathway offers the opportunity to identify trends universal to all routes. Recent large-scale analyses of horizontally transferred genes have either not considered the molecular pathway of transfer ( 10 – 12 ) or focused on a particular class of mobile genetic elements (MGEs), such as plasmids ( 13 , 14 ), integrative and conjugative elements ( 15 ), or viruses ( 16 – 18 ). However, to the best of our knowledge, the diversity of genes mobilized via transposition has not been comprehensively characterized.…”

Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing

“…The automated vMAG extraction and host attribution features of ProxiPhage make it the first software capable of such analysis, and its accuracy and high throughput have the potential to aid the study of viruses and their cellular hosts. In both environmental and host-associated metagenomic studies, this platform can accelerate the discovery of novel viral clades and improve our understanding of the role of phages in the composition dynamics and nutrient cycling of their respective communities (50). Finally, our platform could be applied in clinical settings for efficacy and safety screenings of fecal microbiota transplantations (FMT) and phage therapies, and for predicting the effects of such treatments on specific patients (51,52).…”