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Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome

https://doi.org/10.1101/144642
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Fast gapped-read alignment with Bowtie 2
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Fast and sensitive protein alignment using DIAMOND
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The gut microbiota shapes intestinal immune responses during health and disease
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The skin microbiome
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Phage-mediated horizontal transfer of a Staphylococcus aureus virulence-associated genomic island
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Statistical structure of host–phage interactions
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Rapid evolution of the human gut virome
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WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
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Computational approaches to predict bacteriophage–host relationships
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The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases
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Resource availability affects the structure of a natural bacteria–bacteriophage community
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Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes
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Microbial Ecology of the Skin in the Era of Metagenomics and Molecular Microbiology
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The human gut virome: Inter-individual variation and dynamic response to diet
inferredcites →https://doi.org/10.1111/1574-6976.12072openalex-snapshot
Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities
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The dissimilarity of species interaction networks
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A Broad‐Host‐Range Vibriophage, KVP40, Isolated from Sea Water
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Topographical and Temporal Diversity of the Human Skin Microbiome
inferredcites →https://doi.org/10.1126/science.1177486openalex-snapshot
Bacterial Community Variation in Human Body Habitats Across Space and Time
inferredcites →https://doi.org/10.1126/science.1261498openalex-snapshot
Patterns and ecological drivers of ocean viral communities
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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
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Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses
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Pseudomonas aeruginosa Bacteriophage PA1Ø Requires Type IV Pili for Infection and Shows Broad Bactericidal and Biofilm Removal Activities
inferredcites →https://doi.org/10.1128/aem.01275-08openalex-snapshot
Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil
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Prevalence of Broad-Host-Range Lytic Bacteriophages of Sphaerotilus natans , Escherichia coli , and Pseudomonas aeruginosa
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Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
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Impact of Phages on Two-Species Bacterial Communities
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General Transduction in Vibrio cholerae
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Altered Oral Viral Ecology in Association with Periodontal Disease
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The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
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The Human Gut Microbiome as a Screening Tool for Colorectal Cancer
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Regularized gene selection in cancer microarray meta-analysis
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PILER-CR: Fast and accurate identification of CRISPR repeats
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Structure of the gut microbiome following colonization with human feces determines colonic tumor burden
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Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes
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Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
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Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla
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Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection
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Conservation of Gene Cassettes among Diverse Viruses of the Human Gut
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Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes
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Prophage Induction Is Enhanced and Required for Renal Disease and Lethality in an EHEC Mouse Model
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The human urine virome in association with urinary tract infections
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HostPhinder: A Phage Host Prediction Tool
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Bacteriophage behavioral ecology
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VirSorter: mining viral signal from microbial genomic data
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