Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction

(2022) Alessandro Rossi et al.   Microbiome

Phage-host interactions: The neglected part of biological wastewater treatment

(2022) Xiang Tang et al.   WATER RESEARCH

Soil viral diversity, ecology and climate change

(2022) Janet K. Jansson et al.   NATURE REVIEWS MICROBIOLOGY

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

(2021) Jiarong Guo et al.   Microbiome

Bacteriophage ecology in biological wastewater treatment systems

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

Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems

(2021) Bingbing Du et al.   JOURNAL OF HAZARDOUS MATERIALS

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

(2021) Yiqiang Chen et al.   Nature Communications

Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers

(2021) Mo-Lian Chen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity

(2020) Xiaolong Liang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes

(2020) Lin Ye et al.   Microbiome

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils

(2020) Li Bi et al.   ENVIRONMENTAL MICROBIOLOGY

Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

(2020) Matthew J. Tuttle et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Evolution of microbial community and drug resistance during enrichment of tetracycline-degrading bacteria

(2019) Qiang Wang et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Coupled virus - bacteria interactions and ecosystem function in an engineered microbial system

(2019) M.R. Brown et al.   WATER RESEARCH

Lysogeny is prevalent and widely distributed in the murine gut microbiota

(2018) Min-Soo Kim et al.   ISME Journal

High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems

(2018) Yulin Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

Impact of food-to-microorganisms ratio on the stability of aerobic granular sludge treating high-strength organic wastewater

(2018) Rania Ahmed Hamza et al.   WATER RESEARCH

Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses

(2017) Amir Mohaghegh Motlagh et al.   Frontiers in Microbiology

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

(2016) Nathan A. Ahlgren et al.   NUCLEIC ACIDS RESEARCH

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics

(2015) Jennifer R Brum et al.   ISME Journal

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils

(2014) Olivier Zablocki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Sludge bulking impact on relevant bacterial populations in a full-scale municipal wastewater treatment plant

(2014) Juan Wang et al.   PROCESS BIOCHEMISTRY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Intermittent filtration and gas bubbling for fouling reduction in anaerobic membrane bioreactors

(2012) A. Cerón-Vivas et al.   JOURNAL OF MEMBRANE SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Bacteriophage ecology in environmental biotechnology processes

(2011) Orr H Shapiro et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Genome Sequence and Characterization of theTsukamurellaBacteriophage TPA2

(2010) Steve Petrovski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evidence for bacteriophage activity causing community and performance changes in a phosphorus-removal activated sludge

(2010) Jeremy J. Barr et al.   FEMS MICROBIOLOGY ECOLOGY

Viral and microbial community dynamics in four aquatic environments

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

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Various physico-chemical stress factors cause prophage induction in Nitrosospira multiformis 25196- an ammonia oxidizing bacteria

(2010) Jeongdong Choi et al.   WATER RESEARCH

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater

(2009) Orr H Shapiro et al.   ISME Journal

Determination of virus abundance, diversity and distribution in a municipal wastewater treatment plant

(2008) Qinglong Wu et al.   WATER RESEARCH