Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes

(2022) Xiaoxuan Zheng et al.   ISME Journal

Life and death in the soil microbiome: how ecological processes influence biogeochemistry

(2022) Noah W. Sokol et al.   NATURE REVIEWS MICROBIOLOGY

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

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Diversity and ecological footprint of Global Ocean RNA viruses

(2022) Guillermo Dominguez-Huerta et al.   SCIENCE

RNA viromes from terrestrial sites across China expand environmental viral diversity

(2022) Yan-Mei Chen et al.   Nature Microbiology

Expansion of the global RNA virome reveals diverse clades of bacteriophages

(2022) Uri Neri et al.   CELL

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

(2022) George Muscatt et al.   Microbiome

Virus classification for viral genomic fragments using PhaGCN2

(2022) Jing-Zhe Jiang et al.   BRIEFINGS IN BIOINFORMATICS

PhaTYP: predicting the lifestyle for bacteriophages using BERT

(2022) Jiayu Shang et al.   BRIEFINGS IN BIOINFORMATICS

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

(2022) Xiao-Qing Luo et al.   Microbiome

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

(2021) Zexin Li et al.   ISME Journal

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

(2021) Christian Santos-Medellin et al.   ISME Journal

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

(2021) Jiarong Guo et al.   Microbiome

T4-like Phages Reveal the Potential Role of Viruses in Soil Organic Matter Mineralization

(2021) Xiaomeng Wei et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Diversity and distribution of viruses inhabiting the deepest ocean on Earth

(2021) Huahua Jian et al.   ISME Journal

Interactions between bacterial and phage communities in natural environments

(2021) Anne Chevallereau et al.   NATURE REVIEWS MICROBIOLOGY

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

(2021) Sungeun Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants

(2021) Yiqiang Chen et al.   Nature Communications

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

(2021) Kristopher Kieft et al.   Nature Communications

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

(2021) Akbar Adjie Pratama et al.   PeerJ

Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress

(2021) Dan Huang et al.   Microbiome

High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System

(2021) Anh D. Ha et al.   mSystems

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(2020) Basem Al-Shayeb et al.   NATURE

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

(2020) Lucas P. P. Braga et al.   Microbiome

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

Succession of the bacterial community structure and functional prediction in two composting systems viewed through metatranscriptomics

(2020) Jianli Ding et al.   BIORESOURCE TECHNOLOGY

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

(2020) Paraskevi Mara et al.   ISME Journal

Large freshwater phages with the potential to augment aerobic methane oxidation

(2020) Lin-Xing Chen et al.   Nature Microbiology

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

(2020) M. Consuelo Gazitúa et al.   ISME Journal

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

The degradation of organic matter coupled with the functional characteristics of microbial community during composting with different surfactants

(2020) Gen Li et al.   BIORESOURCE TECHNOLOGY

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

(2019) Gang Li et al.   ACS Synthetic Biology

Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity

(2019) Zhao Zhao et al.   ISME Journal

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen 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

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

(2019) Shuo Jiao et al.   ISME Journal

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

(2019) Amy E. Zimmerman et al.   NATURE REVIEWS MICROBIOLOGY

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

(2019) Evan P. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient reduction of antibiotic residues and associated resistance genes in tylosin antibiotic fermentation waste using hyperthermophilic composting

(2019) Hanpeng Liao et al.   ENVIRONMENT INTERNATIONAL

Phage combination therapies for bacterial wilt disease in tomato

(2019) Xiaofang Wang et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant

(2018) Zhen Yu et al.   BIORESOURCE TECHNOLOGY

Succession of bacterial community function in cow manure composing

(2018) Ke Wang et al.   BIORESOURCE TECHNOLOGY

A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments

(2018) Jacob H. Munson-McGee et al.   ISME Journal

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

(2018) Paula Dalcin Martins et al.   Microbiome

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The structure and function of the global citrus rhizosphere microbiome

(2018) Jin Xu et al.   Nature Communications

Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing

(2018) Rebecca A. Daly et al.   Nature Microbiology

Hyperthermophilic Composting Accelerates the Removal of Antibiotic Resistance Genes and Mobile Genetic Elements in Sewage Sludge

(2017) Hanpeng Liao et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing

(2017) Polina Galitskaya et al.   PLoS One

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(2016) B. Knowles et al.   NATURE

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

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DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8

(2016) Yuko Nagayoshi 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

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

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

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Viral activities and life cycles in deep subseafloor sediments

(2015) Tim Engelhardt et al.   Environmental Microbiology Reports

Deep sequencing of the viralphoHgene reveals temporal variation, depth-specific composition, and persistent dominance of the same viralphoHgenes in the Sargasso Sea

(2015) Dawn B. Goldsmith et al.   PeerJ

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Metagenomic analysis of double-stranded DNA viruses in healthy adults

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Consequences of biodiversity loss for litter decomposition across biomes

(2014) I. Tanya Handa et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

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Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

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

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SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

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Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION