Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

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Snakemake—a scalable bioinformatics workflow engine

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ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages

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A comprehensive and quantitative exploration of thousands of viral genomes

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A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

(2018) Kathryn M. Kauffman et al.   NATURE

A common trick for transferring bacterial DNA

(2018) Alan R. Davidson   SCIENCE

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

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The enigmatic archaeal virosphere

(2017) David Prangishvili et al.   NATURE REVIEWS MICROBIOLOGY

MVP: a microbe–phage interaction database

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The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

Outer Membrane Proteome of Veillonella parvula: A Diderm Firmicute of the Human Microbiome

(2017) Daniel I. Poppleton et al.   Frontiers in Microbiology

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice

(2016) Min-Soo Kim et al.   ENVIRONMENTAL MICROBIOLOGY

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Sporulation, bacterial cell envelopes and the origin of life

(2016) Elitza I. Tocheva et al.   NATURE REVIEWS MICROBIOLOGY

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes

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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

TagDust2: a generic method to extract reads from sequencing data

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Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

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Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

(2015) Chantal Campbell et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Bacteriophage lambda: Early pioneer and still relevant

(2015) Sherwood R. Casjens et al.   VIROLOGY

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

Trimmomatic: a flexible trimmer for Illumina sequence data

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Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

(2014) K. G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Transposable Mu-like phages in Firmicutes: new instances of divergence generating retroelements

(2013) Ariane Toussaint   RESEARCH IN MICROBIOLOGY

Veillonella, Firmicutes: Microbes disguised as Gram negatives

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CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Adaptation of Temperate Bacteriophages to Their Host Genomes

(2012) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Peptidoglycan Remodeling and Conversion of an Inner Membrane into an Outer Membrane during Sporulation

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Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

BEDTools: a flexible suite of utilities for comparing genomic features

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

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Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

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Characterization of tet(32) Genes from the Oral Metagenome

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Bacteriophage genomics

(2008) Graham F Hatfull   CURRENT OPINION IN MICROBIOLOGY