Rumen Virus Populations: Technological Advances Enhancing Current Understanding
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Rumen Virus Populations: Technological Advances Enhancing Current Understanding
Authors
Keywords
-
Journal
Frontiers in Microbiology
Volume 11, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2020-03-26
DOI
10.3389/fmicb.2020.00450
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Targeting of temperate phages drives loss of type I CRISPR–Cas systems
- (2020) Clare Rollie et al. NATURE
- Recombination between phages and CRISPR−cas loci facilitates horizontal gene transfer in staphylococci
- (2019) Andrew Varble et al. Nature Microbiology
- (Ph)ighting Phages: How Bacteria Resist Their Parasites
- (2019) Jakob T. Rostøl et al. Cell Host & Microbe
- Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus
- (2019) Rebekah M. Dedrick et al. NATURE MEDICINE
- Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
- (2019) Jakub Barylski et al. SYSTEMATIC BIOLOGY
- Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA)
- (2019) Vsevolod L. Popov et al. Viruses-Basel
- Mining, analyzing, and integrating viral signals from metagenomic data
- (2019) Tingting Zheng et al. Microbiome
- Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants
- (2019) R. Heyer et al. Microbiome
- Defining the human gut host–phage network through single-cell viral tagging
- (2019) Mária Džunková et al. Nature Microbiology
- Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions
- (2019) Mohammad Mazharul Islam et al. Frontiers in Microbiology
- Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity
- (2018) Mariann Landsberger et al. CELL
- Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
- (2018) Rekha Seshadri et al. NATURE BIOTECHNOLOGY
- Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales
- (2018) Mikayla A. Borton et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Viruses of archaea: Structural, functional, environmental and evolutionary genomics
- (2018) Mart Krupovic et al. VIRUS RESEARCH
- Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations
- (2018) Emily McGovern et al. Frontiers in Microbiology
- Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation
- (2018) Thomas Hartinger et al. Journal of Animal Science and Biotechnology
- “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system
- (2018) A. E. Naas et al. Microbiome
- Host-linked soil viral ecology along a permafrost thaw gradient
- (2018) Joanne B. Emerson et al. Nature Microbiology
- Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities
- (2018) Prem Krishnan Raghupathi et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- A Linear Plasmid-Like Prophage of Actinomyces odontolyticus Promotes Biofilm Assembly
- (2018) Mengyu Shen et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- A metagenomic study of the rumen virome in domestic caprids
- (2018) Samuel Namonyo et al. ARCHIVES OF VIROLOGY
- Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria
- (2018) E. H. Hart et al. Scientific Reports
- Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future
- (2018) Sharon A. Huws et al. Frontiers in Microbiology
- Phage Therapy: Going Temperate?
- (2018) Rodrigo Monteiro et al. TRENDS IN MICROBIOLOGY
- New approaches to characterizing bacteria-phage interactions in microbial communities and microbiomes
- (2018) Britt Koskella Environmental Microbiology Reports
- ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis
- (2018) Andrey N. Shkoporov et al. Nature Communications
- Inhibition of Rumen Methanogens by a Novel Archaeal Lytic Enzyme Displayed on Tailored Bionanoparticles
- (2018) Eric Altermann et al. Frontiers in Microbiology
- Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
- (2018) Lindsey M. Solden et al. Nature Microbiology
- Taxonomic variability and functional stability in microbial communities infected by phages
- (2017) Stilianos Louca et al. ENVIRONMENTAL MICROBIOLOGY
- Lysogeny in nature: mechanisms, impact and ecology of temperate phages
- (2017) Cristina Howard-Varona et al. ISME Journal
- Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)
- (2017) Elliot J Lefkowitz et al. NUCLEIC ACIDS RESEARCH
- Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasiteLeishmania
- (2017) Danyil Grybchuk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- VirusSeeker, a computational pipeline for virus discovery and virome composition analysis
- (2017) Guoyan Zhao et al. VIROLOGY
- The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes
- (2017) Sergey A. Shmakov et al. mBio
- Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers
- (2017) Sophie Nguyen et al. mBio
- Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation
- (2017) Eric C. Keen et al. mBio
- Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria
- (2017) Rosalind A. Gilbert et al. Frontiers in Microbiology
- A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments
- (2017) Simon Deusch et al. Frontiers in Microbiology
- Electron Cryomicroscopy of Viruses at Near-Atomic Resolutions
- (2017) Jason T. Kaelber et al. Annual Review of Virology
- Dietary energy drives the dynamic response of bovine rumen viral communities
- (2017) Christopher L. Anderson et al. Microbiome
- VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
- (2017) Jie Ren et al. Microbiome
- Prophage-mediated defence against viral attack and viral counter-defence
- (2017) Rebekah M. Dedrick et al. Nature Microbiology
- Dynamic biofilm architecture confers individual and collective mechanisms of viral protection
- (2017) Lucia Vidakovic et al. Nature Microbiology
- Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay
- (2017) Martial Marbouty et al. Science Advances
- Heterogeneity in Induction Level, Infection Ability, and Morphology of Shiga Toxin-Encoding Phages (Stx Phages) from Dairy and Human Shiga Toxin-Producing Escherichia coli O26:H11 Isolates
- (2016) Ludivine Bonanno et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester
- (2016) Live H. Hagen et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers
- (2016) Karen Smith et al. BMC MICROBIOLOGY
- Rumen Virome:An Assessment of Viral Communities and their Functions in the Rumen of an Indian Buffalo
- (2016) Nidhi R. Parmar et al. CURRENT SCIENCE
- The sequence of sequencers: The history of sequencing DNA
- (2016) James M. Heather et al. GENOMICS
- Challenges in microbial ecology: building predictive understanding of community function and dynamics
- (2016) Stefanie Widder et al. ISME Journal
- Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
- (2016) François Enault et al. ISME Journal
- PHASTER: a better, faster version of the PHAST phage search tool
- (2016) David Arndt et al. NUCLEIC ACIDS RESEARCH
- Illuminating structural proteins in viral “dark matter” with metaproteomics
- (2016) Jennifer R. Brum et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Temperate phages both mediate and drive adaptive evolution in pathogen biofilms
- (2016) Emily V. Davies et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Bacterial Microbiome and Virome Milestones of Infant Development
- (2016) Efrem S. Lim et al. TRENDS IN MICROBIOLOGY
- Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131
- (2016) Nouri L. Ben Zakour et al. mBio
- The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing
- (2016) Jaime Iranzo et al. mBio
- Antimicrobial usage and resistance in beef production
- (2016) Andrew Cameron et al. Journal of Animal Science and Biotechnology
- Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh
- (2016) Shafiqul Alam Sarker et al. EBioMedicine
- Piggyback-the-Winner in host-associated microbial communities
- (2016) Cynthia B Silveira et al. npj Biofilms and Microbiomes
- Removal of Listeria monocytogenes Biofilms with Bacteriophage P100
- (2016) KAMLESH A. SONI et al. JOURNAL OF FOOD PROTECTION
- Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes
- (2015) Analice C. Azevedo et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- A new family of hybrid virophages from an animal gut metagenome
- (2015) Natalya Yutin et al. Biology Direct
- Development of an improved representation of rumen digesta outflow in a mechanistic and dynamic model of a dairy cow, Molly
- (2015) Pablo Gregorini et al. ECOLOGICAL MODELLING
- Enhanced virome sequencing using targeted sequence capture
- (2015) Todd N. Wylie et al. GENOME RESEARCH
- The Hitchhiker’s guide to Hi-C analysis: Practical guidelines
- (2015) Bryan R. Lajoie et al. METHODS
- A century of the phage: past, present and future
- (2015) George P. C. Salmond et al. NATURE REVIEWS MICROBIOLOGY
- Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters
- (2015) Jeremy J. Barr et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Bacteriophage lambda: Early pioneer and still relevant
- (2015) Sherwood R. Casjens et al. VIROLOGY
- Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells
- (2015) Inés Romero-Brey et al. Viruses-Basel
- Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
- (2015) Gemma Henderson et al. Scientific Reports
- Biochemical Characterisation of Phage Pseudomurein Endoisopeptidases PeiW and PeiP Using Synthetic Peptides
- (2015) Linley R. Schofield et al. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL
- Analysis of Bottlenecks in Experimental Models of Infection
- (2015) Sören Abel et al. PLoS Pathogens
- Virulence reduction in bacteriophage resistant bacteria
- (2015) Marcela León et al. Frontiers in Microbiology
- The human gut virome: a multifaceted majority
- (2015) Lesley A. Ogilvie et al. Frontiers in Microbiology
- Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations
- (2015) Paul J. Weimer Frontiers in Microbiology
- VirSorter: mining viral signal from microbial genomic data
- (2015) Simon Roux et al. PeerJ
- The vocabulary of microbiome research: a proposal
- (2015) Julian R. Marchesi et al. Microbiome
- The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
- (2015) Alejandra Escobar-Zepeda et al. Frontiers in Genetics
- Agriculture and food animals as a source of antimicrobial-resistant bacteria
- (2015) Vangelis Economou et al. Infection and Drug Resistance
- The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9
- (2015) William J Kelly et al. Standards in Genomic Sciences
- Differing Populations of Endemic Bacteriophages in Cattle Shedding High and Low Numbers of Escherichia coli O157:H7 Bacteria in Feces
- (2014) J. Hallewell et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Safely Coupling Livestock and Crop Production Systems: How Rapidly Do Antibiotic Resistance Genes Dissipate in Soil following a Commercial Application of Swine or Dairy Manure?
- (2014) Romain Marti et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut
- (2014) Patrick H. Degnan et al. Cell Host & Microbe
- Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities
- (2014) Jason M. Norman et al. GASTROENTEROLOGY
- A dynamic mechanistic model of lactic acid metabolism in the rumen
- (2014) J.A.N. Mills et al. JOURNAL OF DAIRY SCIENCE
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Environment
- (2014) Jose Luis Balcazar PLoS Pathogens
- The factors affecting effectiveness of treatment in phages therapy
- (2014) Mai Huong Ly-Chatain Frontiers in Microbiology
- Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies
- (2013) S. C. Leahy et al. Animal
- Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Human Fecal Samples
- (2013) Pablo Quirós et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- From deep sequencing to viral tagging: Recent advances in viral metagenomics
- (2013) Dana Willner et al. BIOESSAYS
- Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle
- (2013) Elizabeth M Ross et al. BMC MICROBIOLOGY
- Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron
- (2013) Elisa Deriu et al. Cell Host & Microbe
- Highlights of the DNA cutters: a short history of the restriction enzymes
- (2013) Wil A. M. Loenen et al. NUCLEIC ACIDS RESEARCH
- Presence of a Polymicrobial Endometrial Biofilm in Patients with Bacterial Vaginosis
- (2013) Alexander Swidsinski et al. PLoS One
- Bacteriophage adhering to mucus provide a non-host-derived immunity
- (2013) J. J. Barr et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Phage C2 Mediates Transduction of Tn6215, Encoding Erythromycin Resistance, between Clostridium difficile Strains
- (2013) S. Goh et al. mBio
- Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences
- (2013) Lesley A. Ogilvie et al. Nature Communications
- Diversity of gut methanogens in herbivorous animals
- (2012) B. St-Pierre et al. Animal
- A suggested new bacteriophage genus: “Viunalikevirus”
- (2012) Evelien M. Adriaenssens et al. ARCHIVES OF VIROLOGY
- Prokaryote viruses studied by electron microscopy
- (2012) H.-W. Ackermann et al. ARCHIVES OF VIROLOGY
- Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes
- (2012) D. M. Kristensen et al. JOURNAL OF BACTERIOLOGY
- Novel Biopolymer Matrices for Microencapsulation of Phages: Enhanced Protection Against Acidity and Protease Activity
- (2012) Cecilia Dini et al. MACROMOLECULAR BIOSCIENCE
- Tail morphology controls DNA release in two Salmonella phages with one lipopolysaccharide receptor recognition system
- (2012) Dorothee Andres et al. MOLECULAR MICROBIOLOGY
- Diversity, stability and resilience of the human gut microbiota
- (2012) Catherine A. Lozupone et al. NATURE
- Transforming clinical microbiology with bacterial genome sequencing
- (2012) Xavier Didelot et al. NATURE REVIEWS GENETICS
- Hypervariable loci in the human gut virome
- (2012) S. Minot et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Recent trends in counter-current chromatography
- (2012) Ruilin Hu et al. TRAC-TRENDS IN ANALYTICAL CHEMISTRY
- Purification of phage display-modified bacteriophage T4 by affinity chromatography
- (2011) Anna Oślizło et al. BMC BIOTECHNOLOGY
- Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
- (2011) Margret E. Berg Miller et al. ENVIRONMENTAL MICROBIOLOGY
- The human gut virome: Inter-individual variation and dynamic response to diet
- (2011) S. Minot et al. GENOME RESEARCH
- The diversity of cyanomyovirus populations along a North–South Atlantic Ocean transect
- (2011) Eleanor Jameson et al. ISME Journal
- Bacteriophage-mediated transduction of antibiotic resistance in enterococci
- (2011) R. Mazaheri Nezhad Fard et al. LETTERS IN APPLIED MICROBIOLOGY
- Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere
- (2011) M. Krupovic et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures
- (2011) Kurt E. Williamson et al. MICROSCOPY RESEARCH AND TECHNIQUE
- PHAST: A Fast Phage Search Tool
- (2011) Y. Zhou et al. NUCLEIC ACIDS RESEARCH
- Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Environmental Samples
- (2011) Marta Colomer-Lluch et al. PLoS One
- Identification of Diverse Antimicrobial Resistance Determinants Carried on Bacterial, Plasmid, or Viral Metagenomes from an Activated Sludge Microbial Assemblage
- (2010) L. C. Parsley et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Bacteriophage applications: where are we now?
- (2010) A.B. Monk et al. LETTERS IN APPLIED MICROBIOLOGY
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions
- (2010) Sinead C. Leahy et al. PLoS One
- Prophage Spontaneous Activation Promotes DNA Release Enhancing Biofilm Formation in Streptococcus pneumoniae
- (2010) Margarida Carrolo et al. PLoS One
- Cryptic prophages help bacteria cope with adverse environments
- (2010) Xiaoxue Wang et al. Nature Communications
- Metagenomic signatures of 86 microbial and viral metagenomes
- (2009) Dana Willner et al. ENVIRONMENTAL MICROBIOLOGY
- Viral control of bacterial biodiversity - evidence from a nutrient-enriched marine mesocosm experiment
- (2009) Ruth-Anne Sandaa et al. ENVIRONMENTAL MICROBIOLOGY
- The bacteriophages in human- and animal body-associated microbial communities
- (2009) A. Letarov et al. JOURNAL OF APPLIED MICROBIOLOGY
- The Secret Life of the Anthrax Agent Bacillus anthracis: Bacteriophage-Mediated Ecological Adaptations
- (2009) Raymond Schuch et al. PLoS One
- Preventing biofilms of clinically relevant organisms using bacteriophage
- (2009) Rodney M. Donlan TRENDS IN MICROBIOLOGY
- Amoxicillin and specific bacteriophage can be used together for eradication of biofilm of Klebsiella pneumoniae B5055
- (2009) Manmeet Sakshi Bedi et al. WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
- Analysis of the Methanobrevibacter ruminantium draft genome: understanding methanogen biology to inhibit their action in the rumen
- (2008) G. T. Attwood et al. Australian journal of experimental agriculture
- Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria
- (2008) P M Bennett BRITISH JOURNAL OF PHARMACOLOGY
- Portal protein diversity and phage ecology
- (2008) Matthew B. Sullivan et al. ENVIRONMENTAL MICROBIOLOGY
- Partial characterization of Enterococcus faecalis bacteriophage F4
- (2008) K. Nigutová et al. FOLIA MICROBIOLOGICA
- The biofilm life cycle and virulence of Pseudomonas aeruginosa are dependent on a filamentous prophage
- (2008) Scott A Rice et al. ISME Journal
- Modeling methane production from beef cattle using linear and nonlinear approaches1
- (2008) J. L. Ellis et al. JOURNAL OF ANIMAL SCIENCE
- Functional metagenomic profiling of nine biomes
- (2008) Elizabeth A. Dinsdale et al. NATURE
- Bacteriophages for prophylaxis and therapy in cattle, poultry and pigs
- (2008) R. P. Johnson et al. ANIMAL HEALTH RESEARCH REVIEWS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation