Rumen Virome:An Assessment of Viral Communities and their Functions in the Rumen of an Indian Buffalo

Parmar, Nidhi; Jakhesara, Subhash J.; Mohapatra, Amitbikram; Joshi, Chaitanya G.

doi:10.18520/cs/v111/i5/919-925

Cited by 10 publications

(7 citation statements)

References 17 publications

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“…In comparison, the metagenomic approach used in the current study provides improved resolution into the response of viruses to dietary change. Others that have taken a metagenomic approach to study rumen viral communities have explored the variation between animals on the same diet [ 32 – 34 ]. Consequently, prior to the current study, the relative importance of dietary factors in structuring rumen viral communities had not been demonstrated.…”

Section: Resultsmentioning

confidence: 99%

“…However, metagenomics would provide a deeper understanding of the potential effect of diet on rumen viruses. Those that have utilized a metagenomic approach to study rumen viruses have focused on characterizing the composition and variation in the virome between animals fed the same diet and not identified ecological drivers of viral communities [ 32 – 34 ]. These previously published metagenomes indicate that rumen viruses potentially encode AMGs associated with a variety of pathways.…”

Section: Introductionmentioning

confidence: 99%

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Dietary energy drives the dynamic response of bovine rumen viral communities

2017

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BackgroundRumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen. To this end, we investigated how rumen bacterial and viral community structure and function responded in five steers fed four randomized dietary treatments in a crossover design.ResultsTotal digestible nutrients (TDN), a measure of dietary energy, best explained the variation in bacterial and viral communities. Additional ecological drivers of viral communities included dietary zinc content and microbial functional diversity. Using partial least squares regression, we demonstrate significant associations between the abundances of 267 viral populations and variables driving the variation in rumen viral communities. While rumen viruses were dynamic, 14 near ubiquitous viral populations were identified, suggesting the presence of a core rumen virome largely comprised of novel viruses. Moreover, analysis of virally encoded auxiliary metabolic genes (AMGs) indicates rumen viruses have glycosidic hydrolases to potentially augment the breakdown of complex carbohydrates to increase energy production. Other AMGs identified have a role in redirecting carbon to the pentose phosphate pathway and one carbon pools by folate to boost viral replication.ConclusionsWe demonstrate that rumen bacteria and viruses have differing responses and ecological drivers to dietary perturbation. Our results show that rumen viruses have implications for understanding the structuring of the previously identified core rumen microbiota and impacting microbial metabolism through a vast array of AMGs. AMGs in the rumen appear to have consequences for microbial metabolism that are largely in congruence with the current paradigm established in marine systems. This study provides a foundation for future hypotheses regarding the dynamics of viral-mediated processes in the rumen.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0374-3) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dietary energy drives the dynamic response of bovine rumen viral communities

2017

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“…Under these assumptions we may be missing vital functions and relationships. Lower abundance viral families have been identified in the rumen, which have been putatively assigned as large DNA viruses (Mimiviridae, Phycodnaviridae), filamentous lysogenic viruses of bacteria and archaea (Inoviridae), archaeal viruses (Bicaudaviridae) and animal viruses (including; Baculoviridae, and Adenoviridae) (Berg Miller et al, 2012;Parmar et al, 2016;Anderson et al, 2017). Although they have been detected in rumen virome datasets, the animal viruses identified often represent lineages which would not normally infect rumen microbes.…”

Section: Metagenomic Approaches For Studying Rumen Virusesmentioning

confidence: 99%

Rumen Virus Populations: Technological Advances Enhancing Current Understanding

et al. 2020

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The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often outnumbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.

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“…Another metagenomic study of the viral populations in the rumen of steers fed different diets revealed that although there are changes in viral communities with a change in diet, there were abundant populations of phages found across all samples, indicating a core virome (Anderson et al, 2017). An analysis of DNA viruses in buffalo revealed the order Caudovirales, the tailed bacteriophages, formed the largest community, and within this the Siphoviridae and Myoviridae families were predominant (Parmar et al, 2016). A similar study of rumen fluid from sheep and goats also revealed that of the reads that could be identified, the highest proportion shared similarity to the Siphoviridae family, yet the majority of the reads were unidentified (Namonyo et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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.

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Rumen Virome:An Assessment of Viral Communities and their Functions in the Rumen of an Indian Buffalo

Cited by 10 publications

References 17 publications

Dietary energy drives the dynamic response of bovine rumen viral communities

Dietary energy drives the dynamic response of bovine rumen viral communities

Rumen Virus Populations: Technological Advances Enhancing Current Understanding

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

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