The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses

Abstract

Graphical abstract

Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity

“…Almost all of our viral genomes represented tailed dsDNA phages from the order Caudovirales ( Babenko et al, 2020 ) and could be sub-classified into the families Siphoviridae (73%), Podoviridae or the newly delineated Schitoviridae ( Wittmann et al, 2020 ) (21%) and Myoviridae (6%). Seven genomes were assigned to ssDNA viruses from the family Microviridae , four of which cluster as part of the subfamily Gokushovirinae .…”

“…Thus, despite previous efforts—and drawing on comparisons with the human microbiome, where new species are still being discovered ( Almeida et al, 2019 ; Forster et al, 2019 )—the horse hindgut microbiome presents us with a vast, only superficially explored ( Di Pietro et al, 2021 ) landscape of taxonomic, ecological and functional diversity, certain to encompass important, yet undiscovered roles. Babenko et al (2020) emphasize this with their preliminary exploration of the equine faecal virome, presenting a rich taxonomically diverse viral community which is thought to be essential in shaping microbial ecology. As in studies of the human gut microbiome, faeces provides ready non-invasive access to the gut contents.…”

Equine intestinal O-seroconverting temperate coliphage Hf4s: genomic and biological characterization

“…The available data on the abundance of the virulent and temperate phages in the feces of other mammal species is scarce. However, in the metagenomes of the horse feces the fraction of the contigs attributed to temperate phages was moderate (6). The coliphages isolated from the pool of the free phage particles of horse feces were almost entirely represented by the virulent phages ( (11,(24)(25)(26)(27)(28) and our unpublished observations).…”

“…However, the data generated by the -omics approaches are currently hard to interpretation even in humans for which the diversity of intestinal bacteriophages has been extensively investigated over the last two decades (4,5). In other mammal species, the vast majority of the viral genomic sequences represent socalled "genomic dark matter" matching no close relatives in databases of sequenced bacteriophage genomes (6). Therefore, the culture-based research is still relevant for better understanding of the bacteriophage ecology in the gut (1,5).…”

From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs

“…The PhageClouds' graph database was built using phage genomic sequences obtained from the following sources: NCBI's GenBank database, the Gut Phage Database (GPD), 10 phages from the Global Ocean Viromes (GOV) reported by the TARA Oceans consortium, 9 phages in the Integrated Microbial Genome/Virus (IMG/VR) database 7 from samples categorized as terrestrial, prophages from bacterial genomes in the Genome Taxonomy Database (GTDB), 26 non-GOV entries in the Phages and Integrated Genomes Encapsidated Or Not (PIGEON) database, 27 the Cenote Human Virome Database (CHVD), 28 The Gut Virome Database (GVD), 29 phages from the cattle slurry virome, 30 phages from horse feces viromes, 31 and phages from marine samples taken at the U.K.'s south coast (MarineUKSouth) 32 ( Table 1 ).…”