Enhanced Bacterium–Phage Symbiosis in Attached Microbial Aggregates on a Membrane Surface Facing Elevated Hydraulic Stress

RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Moddels Alongside the PDB Structures Enabled by Architectural Advances

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

(2023) Ruyin Liu et al.   WATER RESEARCH

Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants

(2023) Ling Yuan et al.   Environmental Science & Technology

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

(2023) Hanpeng Liao et al.   ISME Journal

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

(2023) Rong Xia et al.   ISME Journal

Prokaryotic community interchange between distinct microhabitats causes community pressure on anammox biofilm development

(2023) Weiwei Cai et al.   WATER RESEARCH

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

(2023) Yunha Hwang et al.   Nature Microbiology

A social niche breadth score reveals niche range strategies of generalists and specialists

(2023) F. A. Bastiaan von Meijenfeldt et al.   Nature Ecology & Evolution

Disentangling direct from indirect relationships in association networks

(2022) Naijia Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiome differential abundance methods produce different results across 38 datasets

(2022) Jacob T. Nearing et al.   Nature Communications

CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model

(2022) Jiayu Shang et al.   BRIEFINGS IN BIOINFORMATICS

Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature

(2022) Faizan Ahmed Sadiq et al.   FEMS MICROBIOLOGY REVIEWS

Pseudomonas aeruginosa polysaccharide Psl supports airway microbial community development

(2022) Sara N. Stoner et al.   ISME Journal

A mixed blessing of viruses in wastewater treatment plants

(2022) Ling-Dong Shi et al.   WATER RESEARCH

Community assembly of microbial habitat generalists and specialists in urban aquatic ecosystems explained more by habitat type than pollution gradient

(2022) Mamun Abdullah Al et al.   WATER RESEARCH

Flocculation with heterogeneous composition in water environments: A review

(2022) Que Nguyen Ho et al.   WATER RESEARCH

GTDB-Tk v2: memory friendly classification with the genome taxonomy database

(2022) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

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

(2022) Xiang Tang et al.   WATER RESEARCH

PhaTYP: predicting the lifestyle for bacteriophages using BERT

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IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

(2022) Antonio Pedro Camargo et al.   NUCLEIC ACIDS RESEARCH

UniProt: the Universal Protein Knowledgebase in 2023

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

(2022) Xiao-Qing Luo et al.   Microbiome

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

(2021) Jiarong Guo et al.   Microbiome

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

(2021) Ya-Jou Chen et al.   ISME Journal

Diversity and distribution of viruses inhabiting the deepest ocean on Earth

(2021) Huahua Jian et al.   ISME Journal

Bacillus subtilis biofilm formation and social interactions

(2021) Sofia Arnaouteli et al.   NATURE REVIEWS MICROBIOLOGY

Interactions between bacterial and phage communities in natural environments

(2021) Anne Chevallereau et al.   NATURE REVIEWS MICROBIOLOGY

Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern

(2021) Chenxiang Sun et al.   WATER RESEARCH

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

(2021) Yiqiang Chen 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

Understanding the Complex Phage-Host Interactions in Biofilm Communities

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

DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach

(2021) Shufang Wu et al.   GigaScience

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

(2021) Dan Huang et al.   Microbiome

Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function

(2021) Viviane Runa et al.   Frontiers in Microbiology

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

(2021) Oliver Schwengers et al.   Microbial Genomics

Molecular Insights into Extracellular Polymeric Substances in Activated Sludge

(2020) Han-Qing Yu   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Biofilm Matrixome: Extracellular Components in Structured Microbial Communities

(2020) L. Karygianni et al.   TRENDS IN MICROBIOLOGY

Biofouling and me: My Stockholm syndrome with biofilms

(2020) Hans-Curt Flemming   WATER RESEARCH

Water Treatment: Are Membranes the Panacea?

(2020) Matthew R. Landsman et al.   Annual Review of Chemical and Biomolecular Engineering

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

Hormetic Promotion of Biofilm Growth by Polyvalent Bacteriophages at Low Concentrations

(2020) Bo Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The environment drives microbial trait variability in aquatic habitats

(2020) Sara Beier et al.   MOLECULAR ECOLOGY

Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization

(2020) Zhuodong Yu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review

(2020) Monika Sharma et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Host-hijacking and planktonic piracy: how phages command the microbial high seas

(2019) Joanna Warwick-Dugdale et al.   Virology Journal

Bacteria and archaea on Earth and their abundance in biofilms

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

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

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

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

Global diversity and biogeography of bacterial communities in wastewater treatment plants

(2019) Linwei Wu et al.   Nature Microbiology

Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant

(2019) Muhammad Ali et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A novel mode of air recycling favored stable operation of the aerobic granular sludge process via calcium accumulation

(2019) Zhiming Zhang et al.   CHEMICAL ENGINEERING JOURNAL

Deciphering links between bacterial interactions and spatial organization in multispecies biofilms

(2019) Wenzheng Liu et al.   ISME Journal

Temperature-dependent changes to host–parasite interactions alter the thermal performance of a bacterial host

(2019) Daniel Padfield et al.   ISME Journal

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

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

Characterization of stratified EPS and their role in the initial adhesion of anammox consortia

(2019) Weigang Wang et al.   WATER RESEARCH

Phage or foe: an insight into the impact of viral predation on microbial communities

(2018) Lucía Fernández et al.   ISME Journal

A strong link between marine microbial community composition and function challenges the idea of functional redundancy

(2018) Pierre E. Galand et al.   ISME Journal

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee 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

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization

(2018) Yongxin Lin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2018) Gherman V. Uritskiy et al.   Microbiome

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Aquatic organic matter: Classification and interaction with organic microcontaminants

(2018) Vanda Artifon et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome

(2017) Gerald K. Matar et al.   WATER RESEARCH

Dominance of Sulfuritalea species in nitrate-depleted water of a stratified freshwater lake and arsenate respiration ability within the genus

(2017) Tomohiro Watanabe et al.   Environmental Microbiology Reports

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors

(2016) Sung Jun Jo et al.   WATER RESEARCH

Attached biofilms and suspended aggregates are distinct microbial lifestyles emanating from differing hydraulics

(2016) Robert Niederdorfer et al.   Nature Microbiology

Microbial dynamics and properties of aerobic granules developed in a laboratory-scale sequencing batch reactor with an intermediate filamentous bulking stage

(2015) H. Aqeel et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing

(2015) Qiao Ma et al.   BIORESOURCE TECHNOLOGY

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Microbial degradation of 2,4-dichlorophenoxyacetic acid: Insight into the enzymes and catabolic genes involved, their regulation and biotechnological implications

(2014) Ajit Kumar et al.   CRITICAL REVIEWS IN MICROBIOLOGY

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Bacterial biofilm development as a multicellular adaptation: antibiotic resistance and new therapeutic strategies

(2013) César de la Fuente-Núñez et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2012) Limin Fu et al.   BIOINFORMATICS

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Vibrio biofilms: so much the same yet so different

(2009) Fitnat H. Yildiz et al.   TRENDS IN MICROBIOLOGY