Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

(2022) Zhichao Zhou et al.   Microbiome

Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes

(2022) Maria Cristina Gagliano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

vRhyme enables binning of viral genomes from metagenomes

(2022) Kristopher Kieft et al.   NUCLEIC ACIDS RESEARCH

Systematic and quantitative view of the antiviral arsenal of prokaryotes

(2022) Florian Tesson et al.   Nature Communications

Phage–host coevolution in natural populations

(2022) Damien Piel et al.   Nature Microbiology

Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations

(2022) Yunha Hwang et al.   mSystems

Defensive symbiosis against giant viruses in amoebae

(2022) Patrick Arthofer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

(2022) Vincent Somerville et al.   Microbiome

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

(2021) Martial Marbouty et al.   eLife

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

(2021) Jiarong Guo et al.   Microbiome

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil

(2021) Yunha Hwang et al.   mSystems

Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution

(2021) Bert Engelen et al.   Frontiers in Microbiology

Understanding the Complex Phage-Host Interactions in Biofilm Communities

(2021) Diana P. Pires et al.   Annual Review of Virology

Patterns of syntrophic interactions in methanogenic conversion of propionate

(2021) Liu Cao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Multi-species host range of staphylococcal phages isolated from wastewater

(2021) Pauline C. Göller et al.   Nature Communications

Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics

(2020) Liping Hao et al.   ISME Journal

Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes

(2020) Mon Oo Yee et al.   Scientific Reports

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

(2020) Alexander J. Probst et al.   ISME Journal

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Kristopher Kieft et al.   Microbiome

A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase

(2020) Alaina R. Weinheimer et al.   Nature Communications

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Bacteria and archaea on Earth and their abundance in biofilms

(2019) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

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

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Defining the human gut host–phage network through single-cell viral tagging

(2019) Mária Džunková et al.   Nature Microbiology

The pan-immune system of bacteria: antiviral defence as a community resource

(2019) Aude Bernheim et al.   NATURE REVIEWS MICROBIOLOGY

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

It Takes a Village: Microbial Communities Thrive through Interactions and Metabolic Handoffs

(2018) Laura A. Hug et al.   mSystems

Marine microbial metagenomes sampled across space and time

(2018) Steven J. Biller et al.   Scientific Data

High-quality genome sequences of uncultured microbes by assembly of read clouds

(2018) Alex Bishara et al.   NATURE BIOTECHNOLOGY

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

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

(2017) Matthew R Olm et al.   ISME Journal

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes

(2017) Abraham G. Moller et al.   PeerJ

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments

(2017) Nina Dombrowski et al.   Microbiome

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

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

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

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

(2016) Maggie C. Y. Lau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Communications

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

(2016) David Burstein et al.   Nature Communications

The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation

(2016) Andreas Teske et al.   Frontiers in Microbiology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity

(2015) Danielle L. Peters et al.   BMC GENOMICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

(2015) Kema Malki et al.   Virology Journal

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

(2014) Alejandro Caro-Quintero et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages

(2014) Alexander P. Hynes et al.   Nature Communications

Understanding Bacteriophage Specificity in Natural Microbial Communities

(2013) Britt Koskella et al.   Viruses-Basel

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

(2012) Limin Fu et al.   BIOINFORMATICS

Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond

(2011) Susanne Golby et al.   FEMS MICROBIOLOGY ECOLOGY

Sulfur Metabolisms in Epsilon- and Gamma-Proteobacteria in Deep-Sea Hydrothermal Fields

(2011) Masahiro Yamamoto et al.   Frontiers in Microbiology

Interdomain Conjugal Transfer of DNA from Bacteria to Archaea

(2010) J. A. Dodsworth et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS