Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
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Title
Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
Authors
Keywords
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Journal
Viruses-Basel
Volume 9, Issue 6, Pages 127
Publisher
MDPI AG
Online
2017-05-25
DOI
10.3390/v9060127
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Note: Only part of the references are listed.- Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations
- (2017) Leonardo Mancabelli et al. ENVIRONMENTAL MICROBIOLOGY
- Virus taxonomy in the age of metagenomics
- (2017) Peter Simmonds et al. NATURE REVIEWS MICROBIOLOGY
- VirusSeeker, a computational pipeline for virus discovery and virome composition analysis
- (2017) Guoyan Zhao et al. VIROLOGY
- Translational Aspects of the Human Respiratory Virome
- (2016) Alicia B. Mitchell et al. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
- Prophages of the genusBifidobacteriumas modulating agents of the infant gut microbiota
- (2016) Gabriele Andrea Lugli et al. ENVIRONMENTAL MICROBIOLOGY
- iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure
- (2016) Benjamin Bolduc et al. ISME Journal
- The human gut microbiota and its interactive connections to diet
- (2016) C. Milani et al. JOURNAL OF HUMAN NUTRITION AND DIETETICS
- Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
- (2016) Simon Roux et al. NATURE
- Uncovering Earth’s virome
- (2016) David Paez-Espino et al. NATURE
- Healthy human gut phageome
- (2016) Pilar Manrique et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing
- (2016) Yu-Chih Tsai et al. mBio
- Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
- (2016) Juan Jovel et al. Frontiers in Microbiology
- Bacteriophage T4 Infection of Stationary Phase E. coli: Life after Log from a Phage Perspective
- (2016) Daniel Bryan et al. Frontiers in Microbiology
- Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
- (2016) Simon Roux et al. PeerJ
- Metagenomics insights into food fermentations
- (2016) Francesca De Filippis et al. Microbial Biotechnology
- MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets
- (2016) Vanessa Isabell Jurtz et al. PLoS One
- Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses
- (2016) M. Tangherlini et al. Scientific Reports
- Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study
- (2016) Christian Milani et al. Scientific Reports
- Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community
- (2016) Stephan Thies et al. Scientific Reports
- Topographic Diversity of the Respiratory Tract Mycobiome and Alteration in HIV and Lung Disease
- (2015) Lijia Cui et al. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
- Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community
- (2015) Robert M. Bowers et al. BMC GENOMICS
- Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes
- (2015) Manuel Kleiner et al. BMC GENOMICS
- CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
- (2015) Rachid Ounit et al. BMC GENOMICS
- Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease
- (2015) Jason M. Norman et al. CELL
- Next-generation sequencing as an approach to dairy starter selection
- (2015) Philip Kelleher et al. Dairy Science & Technology
- The effects of variable sample biomass on comparative metagenomics
- (2015) Meghan Chafee et al. ENVIRONMENTAL MICROBIOLOGY
- Composition and temporal stability of the gut microbiota in older persons
- (2015) Ian B Jeffery et al. ISME Journal
- Counts and sequences, observations that continue to change our understanding of viruses in nature
- (2015) K. Eri Wommack et al. JOURNAL OF MICROBIOLOGY
- Rising to the challenge: accelerated pace of discovery transforms marine virology
- (2015) Jennifer R. Brum et al. NATURE REVIEWS MICROBIOLOGY
- Gut microbiota and aging
- (2015) P. W. OToole et al. SCIENCE
- Application of metagenomics in the human gut microbiome
- (2015) Wei-Lin Wang et al. WORLD JOURNAL OF GASTROENTEROLOGY
- The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
- (2015) Geoffrey D. Hannigan et al. mBio
- The role of the microbiota in ageing: current state and perspectives
- (2015) Denise B. Lynch et al. Wiley Interdisciplinary Reviews-Systems Biology and Medicine
- Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
- (2015) Simon Roux et al. eLife
- Biotechnological applications of functional metagenomics in the food and pharmaceutical industries
- (2015) Laura M. Coughlan et al. Frontiers in Microbiology
- VirSorter: mining viral signal from microbial genomic data
- (2015) Simon Roux et al. PeerJ
- Bacteriophage and their potential roles in the human oral cavity
- (2015) Anna Edlund et al. Journal of Oral Microbiology
- Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut
- (2015) Josué L. Castro-Mejía et al. Microbiome
- Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome
- (2015) Shirley Bikel et al. Computational and Structural Biotechnology Journal
- Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis
- (2015) Sébastien Boutin et al. PLoS One
- Viral Metagenomics Reveal Blooms of Anelloviruses in the Respiratory Tract of Lung Transplant Recipients
- (2014) J. C. Young et al. AMERICAN JOURNAL OF TRANSPLANTATION
- Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
- (2014) Simon Roux et al. BMC BIOINFORMATICS
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome
- (2014) Bonnie L Hurwitz et al. ISME Journal
- Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research
- (2014) Deepak Sharma et al. JOURNAL OF VIROLOGY
- Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities
- (2014) Matthew B. Sullivan JOURNAL OF VIROLOGY
- Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
- (2014) B. L. Hurwitz et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Characterization of virus-like particles associated with the human faecal and caecal microbiota
- (2014) Lesley Hoyles et al. RESEARCH IN MICROBIOLOGY
- A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
- (2014) Bas E. Dutilh et al. Nature Communications
- Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
- (2014) Agata Wesolowska-Andersen et al. Microbiome
- From deep sequencing to viral tagging: Recent advances in viral metagenomics
- (2013) Dana Willner et al. BIOESSAYS
- Previously unknown and highly divergent ssDNA viruses populate the oceans
- (2013) Jessica M Labonté et al. ISME Journal
- Evaluation of commercial kits for the extraction and purification of viral nucleic acids from environmental and fecal samples
- (2013) Brandon C. Iker et al. JOURNAL OF VIROLOGICAL METHODS
- Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery
- (2013) Richard J. Hall et al. JOURNAL OF VIROLOGICAL METHODS
- Improved Bacteriophage Genome Data is Necessary for Integrating Viral and Bacterial Ecology
- (2013) Kyle Bibby MICROBIAL ECOLOGY
- Resident viruses and their interactions with the immune system
- (2013) Breck A Duerkop et al. NATURE IMMUNOLOGY
- The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology
- (2013) Bonnie L. Hurwitz et al. PLoS One
- Metagenomics and novel gene discovery
- (2013) Eamonn P Culligan et al. Virulence
- The global virome: not as big as we thought?
- (2013) J Cesar Ignacio-Espinoza et al. Current Opinion in Virology
- Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences
- (2013) S. Roux et al. Open Biology
- Expanding the Marine Virosphere Using Metagenomics
- (2013) Carolina Megumi Mizuno et al. PLoS Genetics
- Metabolic reprogramming by viruses in the sunlit and dark ocean
- (2013) Bonnie L Hurwitz et al. GENOME BIOLOGY
- A method for evaluating the host range of bacteriophages using phages fluorescently labeled with 5-ethynyl-2′-deoxyuridine (EdU)
- (2012) Sayaka Ohno et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Reference-independent comparative metagenomics using cross-assembly: crAss
- (2012) Bas E. Dutilh et al. BIOINFORMATICS
- Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
- (2012) Bonnie L. Hurwitz et al. ENVIRONMENTAL MICROBIOLOGY
- Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method
- (2012) Melissa B. Duhaime et al. ENVIRONMENTAL MICROBIOLOGY
- Bacteriophage endolysins as novel antimicrobials
- (2012) Mathias Schmelcher et al. Future Microbiology
- Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities
- (2012) Yan Wei Lim et al. Journal of Cystic Fibrosis
- Going viral: next-generation sequencing applied to phage populations in the human gut
- (2012) Alejandro Reyes et al. NATURE REVIEWS MICROBIOLOGY
- Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme
- (2012) Michael J. Moser et al. PLoS One
- Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing
- (2012) Jana Sachsenröder et al. PLoS One
- Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell
- (2012) C. Zong et al. SCIENCE
- Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline
- (2012) Melissa B. Duhaime et al. VIROLOGY
- Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging
- (2012) L. Deng et al. mBio
- VIROME: a standard operating procedure for analysis of viral metagenome sequences
- (2012) K. Eric Wommack et al. Standards in Genomic Sciences
- Metagenomics and future perspectives in virus discovery
- (2012) John L Mokili et al. Current Opinion in Virology
- Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA
- (2011) Rachel Marine et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces
- (2011) Min-Soo Kim et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses
- (2011) Kyoung-Ho Kim et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
- (2011) Bo Liu et al. BMC GENOMICS
- The human gut virome: Inter-individual variation and dynamic response to diet
- (2011) S. Minot et al. GENOME RESEARCH
- Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome
- (2011) David T Pride et al. ISME Journal
- Linear amplification for deep sequencing
- (2011) Wieteke A M Hoeijmakers et al. Nature Protocols
- Consider something viral in your research
- (2011) Forest Rohwer et al. NATURE REVIEWS MICROBIOLOGY
- IMG: the integrated microbial genomes database and comparative analysis system
- (2011) V. M. Markowitz et al. NUCLEIC ACIDS RESEARCH
- Single Virus Genomics: A New Tool for Virus Discovery
- (2011) Lisa Zeigler Allen et al. PLoS One
- Bacteria-Phage Antagonistic Coevolution in Soil
- (2011) P. Gomez et al. SCIENCE
- TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
- (2011) Hernan A. Lorenzi et al. Standards in Genomic Sciences
- A Holistic Approach to Marine Eco-Systems Biology
- (2011) Eric Karsenti et al. PLOS BIOLOGY
- Identifying Active Phage Lysins through Functional Viral Metagenomics
- (2010) J. E. Schmitz et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- Viruses in the faecal microbiota of monozygotic twins and their mothers
- (2010) Alejandro Reyes et al. NATURE
- Multiple displacement amplification compromises quantitative analysis of metagenomes
- (2010) Suzan Yilmaz et al. NATURE METHODS
- Bacteriophage resistance mechanisms
- (2010) Simon J. Labrie et al. NATURE REVIEWS MICROBIOLOGY
- Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes
- (2010) Matthew R. Henn et al. PLoS One
- A simple and efficient method for concentration of ocean viruses by chemical flocculation
- (2010) Seth G. John et al. Environmental Microbiology Reports
- WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
- (2009) Wolfgang Gerlach et al. BMC BIOINFORMATICS
- Functional metagenomics for enzyme discovery: challenges to efficient screening
- (2009) Taku Uchiyama et al. CURRENT OPINION IN BIOTECHNOLOGY
- Laboratory procedures to generate viral metagenomes
- (2009) Rebecca V Thurber et al. Nature Protocols
- Explaining microbial population genomics through phage predation
- (2009) Francisco Rodriguez-Valera et al. NATURE REVIEWS MICROBIOLOGY
- Assembling the Marine Metagenome, One Cell at a Time
- (2009) Tanja Woyke et al. PLoS One
- Phage-Mediated Intergeneric Transfer of Toxin Genes
- (2009) J. Chen et al. SCIENCE
- Functional viral metagenomics and the next generation of molecular tools
- (2009) Thomas Schoenfeld et al. TRENDS IN MICROBIOLOGY
- Metagenetics: spending our inheritance on the future
- (2009) Jo Handelsman Microbial Biotechnology
- Randomly Amplified Polymorphic DNA PCR as a Tool for Assessment of Marine Viral Richness
- (2008) D. M. Winget et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Phylogenetic Diversity of Sequences of Cyanophage Photosynthetic Gene psbA in Marine and Freshwaters
- (2008) C. Chenard et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Bacteriophage lysins as effective antibacterials
- (2008) Vincent A Fischetti CURRENT OPINION IN MICROBIOLOGY
- The Capsid of the T4 Phage Superfamily: The Evolution, Diversity, and Structure of Some of the Most Prevalent Proteins in the Biosphere
- (2008) A. M. Comeau et al. MOLECULAR BIOLOGY AND EVOLUTION
- Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities
- (2008) A. F. Andersson et al. SCIENCE
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