The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens

Abstract

Although the prokaryotic communities of the rumen microbiome are being uncovered through genome sequencing, little is known about the resident viral populations. Whilst temperate phages can be predicted as integrated prophages when analyzing bacterial and archaeal genomes, the genetics underpinning lytic phages remain poorly characterized. To the five genomes of bacteriophages isolated from rumen-associated samples sequenced and analyzed previously, this study adds a further five novel genomes and predictions gleaned from them to further the understanding of the rumen phage population. Lytic bacteriophages isolated from fresh ovine and bovine fecal and rumen fluid samples were active against the predominant fibrolytic ruminal bacterium Butyrivibrio fibrisolvens. The double stranded DNA genomes were sequenced and reconstructed into single circular complete contigs. Based on sequence similarity and genome distances, the five phages represent four species from three separate genera, consisting of: (1) Butyrivibrio phages Arian and Bo-Finn; (2) Butyrivibrio phages Idris and Arawn; and (3) Butyrivibrio phage Ceridwen. They were predicted to all belong to the Siphoviridae family, based on evidence in the genomes such as size, the presence of the tail morphogenesis module, genes that share similarity to those in other siphovirus isolates and phylogenetic analysis using phage proteomes. Yet, phylogenomic analysis and sequence similarity of the entire phage genomes revealed that these five phages are unique and novel. These phages have only been observed undergoing the lytic lifecycle, but there is evidence in the genomes of phages Arawn and Idris for the potential to be temperate. However, there is no evidence in the genome of the bacterial host Butyrivibrio fibrisolvens of prophage genes or genes that share similarity with the phage genomes.

Ruminal Phages – A Review

“…Also, sequencing of DNA from isolated viruses is a powerful strategy to obtain the genomic information, functional prediction, and a better understanding of phages and its interaction with bacteria. Together, Gilbert et al (2017) and Friedersdorff et al (2020) , reported the entire genome of 10 ruminal phages. According to Friedersdorff et al (2020) , sequenced phages were in a lytic life cycle; however, the functional genomic analysis enabled to infer that some of the phages had lysogeny-associated genes, which suggest that some of these phages could have a temperate life cycle as well.…”

“…Together, Gilbert et al (2017) and Friedersdorff et al (2020) , reported the entire genome of 10 ruminal phages. According to Friedersdorff et al (2020) , sequenced phages were in a lytic life cycle; however, the functional genomic analysis enabled to infer that some of the phages had lysogeny-associated genes, which suggest that some of these phages could have a temperate life cycle as well. Gilbert et al (2017) , provided insights on how lytic phages interact with the host bacteria in the rumen environment.…”

“…Another recent study reported five more phage genomes isolated from the ruminal environment, which double the currently available phage genomes ( Friedersdorff et al, 2020 ). These phages have been observed in a lytic lifestyle, as a free phage; however, genomic analysis indicates that some have a potential to undergo temperate lifecycle.…”

“…The CRISPR/Cas process occurs in a large number of species of archaea and almost all species of bacteria in the rumen and horizontal gene transfer is a common and important evolutionary practice of the living organisms in the ruminal environment ( Berg Miller et al, 2012 ). The presence of CRISPR/Cas genes can provide historic information of phage-bacteria interaction and metagenomic analysis of the rumen microbiome ( Berg Miller et al, 2012 ) and genomic analysis of bacterial host have detected CRISPR/Cas genes ( Gilbert et al, 2017 ; Friedersdorff et al, 2020 ) suggesting previous interactions between phages and bacterial host.…”

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

“…For example, phages have been used to control bacterial infections in dairy cattle with mastitis, which is a common and costly disease in the dairy industry [24]. Despite tremendous success in identifying viruses from various environmental sources such as the ruminants rumen [25][26][27][28][29][30][31],…”