Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

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Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

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Degradation of host translational machinery drives tRNA acquisition in viruses

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Closely related Lak megaphages replicate in the microbiomes of diverse animals

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Clades of huge phages from across Earth’s ecosystems

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Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

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VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

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Seeker: alignment-free identification of bacteriophage genomes by deep learning

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CheckV assesses the quality and completeness of metagenome-assembled viral genomes

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Megaphages infect Prevotella and variants are widespread in gut microbiomes

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Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

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A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

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Predicting effects of changed antimicrobial usage on the abundance of antimicrobial resistance genes in finisher’ gut microbiomes

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A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

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Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

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A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision

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Minimum Information about an Uncultivated Virus Genome (MIUViG)

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dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

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Communication between viruses guides lysis–lysogeny decisions

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MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

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A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

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Measurement of bacterial replication rates in microbial communities

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Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

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The Phyre2 web portal for protein modeling, prediction and analysis

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Subsistence strategies in traditional societies distinguish gut microbiomes

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Social networks predict gut microbiome composition in wild baboons

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Phage lysis: Three steps, three choices, one outcome

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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Stop codon reassignments in the wild

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Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat

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UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

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The Spanin Complex Is Essential for Lambda Lysis

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(2012) Ben Langmead et al.   NATURE METHODS

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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