Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

  title={Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens},
  author={Ryan Cook and Steven P T Hooton and Urmi H. Trivedi and Liz King and Christine E R Dodd and Jon L. Hobman and Dov J. Stekel and Michael A. Jones and Andrew D. Millard},
Background Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as… 
Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere
Background The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their
Global composition of the bacteriophage community in honeybees
The study along with the two previous bee virome studies shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriaphages that primarily infect four of the dominant bacterial phylotypes in the bee Gut.
Global Composition of the Bacteriophage Community in Honey Bees
This study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacter iophages that primarily infect four of the dominant bacterial phylotypes in the bee Gut.
Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts
Prophages in the infant gut are largely unique to the individual and not shared, and most of them appear to be induced and so may be key drivers in shaping the bacterial microbiome.
Antimicrobial resistance in dairy slurry tanks: a critical point for measurement and control
Waste from dairy production is one of the world’s largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs). However, studies to date do not provide necessary
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
The Virion2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples, and the VirION2 assemblies combined with short-read based data provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes.
INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of phage genomes
An automated retrieval and analysis system for bacteriophage genomes, INPHARED, is developed that provides data in a consistent format and provides a mechanism to reproducibly extract complete phage genomes and highlights some of the biases within this data, that underpins the current understanding of phages.
hafeZ: Active prophage identification through read mapping
HafeZ is presented, a tool able to identify ‘active’ prophages within bacterial genomes through genomic read mapping and it is shown that hafeZ can accurately identify their presence and location in the host chromosomes.
Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate
Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas, gut microbiome maturation during the first three years of life was characterized and the role of maternal effects in shaping offspring microbiome assembly was assessed.


Phage-specific metabolic reprogramming of virocells
It is suggested that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently, and related phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models are related.
Uncovering Earth’s virome
Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups, and detailed insight into viral habitat distribution and host–virus interactions is provided.
Comparative metagenomics of microbial traits within oceanic viral communities
Previously undetected microbial metabolic capabilities concealed within the genomes of uncultured marine viral communities are characterized using a unique search strategy on the GOS metagenomes in combination with marine virome and microbiome pyrosequencing-based datasets.
Riding the wave of genomics to investigate aquatic coliphage diversity and activity
Genomics and proteomic analysis combined with host range analysis allowed the identification of a putative tail fibre that is likely responsible for the observed differences in host range of phages vB_Eco_mar003J3 and vB-Eco-mar004NP2.
Diversities and potential biogeochemical impacts of mangrove soil viruses
Viral metagenomics sequencing and virome-specific bioinformatics tools showed that mangrove viruses are diverse and probably directly manipulate carbon cycling by participating in biomass recycling of complex polysaccharides, providing the knowledge essential in revealing the ecological roles of viruses in mangroves ecosystems.
Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.
Abundant SAR11 viruses in the ocean
The isolation of diverse SAR11 viruses belonging to two virus families in culture disproves the theory that SAR11 cells are immune to viral predation and is consistent with the interpretation that the success of this highly abundant microbial clade is the result of successfully evolved adaptation to resource competition.
Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes
It is suggested that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions and showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities.
Phage puppet masters of the marine microbial realm
The ‘royal family model’ is proposed as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem.
Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean
Data showed that the uncultured vSAG 37-F6 population represents the Pelagibacter phages that inhabit the sunlit ocean better, and contains a vast unrecognized microdiversity.