Insights into the phage community structure and potential function in silage fermentation.

[1]  Shangang Jia,et al.  Characterization of phyllosphere endophytic lactic acid bacteria reveals a potential novel route to enhance silage fermentation quality , 2024, Communications biology.

[2]  F. Aylward,et al.  Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems , 2023, ISME communications.

[3]  K. Yu,et al.  Metagenomic analysis unveils the underexplored roles of prokaryotic viruses in a full-scale landfill leachate treatment plant. , 2023, Water research.

[4]  Min Zhao,et al.  Engineered phage with cell-penetrating peptides for intracellular bacterial infections , 2023, mSystems.

[5]  Ying Zhu,et al.  Viral community structure and functional potential vary with lifestyle and altitude in soils of Mt. Everest. , 2023, Environment international.

[6]  Vivek K. Mutalik,et al.  Geochemical constraints on bacteriophage infectivity in terrestrial environments , 2023, bioRxiv.

[7]  Zhen Yu,et al.  Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting , 2023, The ISME journal.

[8]  M. Walker.  Skeleton keys in the phage world , 2022, Communications Biology.

[9]  Wenjun Li,et al.  Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts , 2022, Microbiome.

[10]  Hong Zhou,et al.  Ensiling vine tea (Ampelopsis grossedentata) residue with Lactobacillus plantarum inoculant as an animal unconventional fodder , 2022, Journal of Integrative Agriculture.

[11]  Eoin L. Brodie,et al.  Life and death in the soil microbiome: how ecological processes influence biogeochemistry , 2022, Nature Reviews Microbiology.

[12]  Xusheng Guo,et al.  Microbial mechanisms of using feruloyl esterase-producing Lactobacillus plantarum A1 and grape pomace to improve fermentation quality and mitigate ruminal methane emission of ensiled alfalfa for cleaner animal production. , 2022, Journal of environmental management.

[13]  Hang Hu.  Faculty Opinions recommendation of Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. , 2022, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

[14]  Jinhe Kang,et al.  Alfalfa Silage Treated With Sucrose Has an Improved Feed Quality and More Beneficial Bacterial Communities , 2021, Frontiers in Microbiology.

[15]  Z. Dong,et al.  Recycling deteriorated silage to remove hazardous mycotoxins and produce a value-added product. , 2021, Journal of hazardous materials.

[16]  E. Westra,et al.  Interactions between bacterial and phage communities in natural environments , 2021, Nature Reviews Microbiology.

[17]  Tom O. Delmont,et al.  VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses , 2021, Microbiome.

[18]  Mercè Llabrés,et al.  VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families , 2021, Bioinform..

[19]  Alexander J. Probst,et al.  Virus-associated organosulfur metabolism in human and environmental systems , 2021, bioRxiv.

[20]  N. Kyrpides,et al.  CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.

[21]  S. Hallam,et al.  Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters , 2020, The ISME Journal.

[22]  S. Hallam,et al.  Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages , 2020, Nature Communications.

[23]  J. Emerson,et al.  Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities , 2020, The ISME Journal.

[24]  G. Cochrane,et al.  Tara Oceans: towards global ocean ecosystems biology , 2020, Nature Reviews Microbiology.

[25]  Lucas P. P. Braga,et al.  Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios , 2020, Microbiome.

[26]  S. Moineau,et al.  Phage diversity, genomics and phylogeny , 2020, Nature Reviews Microbiology.

[27]  Z. Dong,et al.  Dynamics of microbial community and fermentation quality during ensiling of sterile and nonsterile alfalfa with or without Lactobacillus plantarum inoculant. , 2019, Bioresource technology.

[28]  D. Hoyt,et al.  Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing , 2018, Nature Microbiology.

[29]  Y. Li,et al.  Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China. , 2018, Bioresource technology.

[30]  Changsheng Li,et al.  Host-linked soil viral ecology along a permafrost thaw gradient , 2018, Nature Microbiology.

[31]  R. Muck,et al.  Silage review: Recent advances and future uses of silage additives. , 2018, Journal of dairy science.

[32]  R. Grant,et al.  Silage review: Interpretation of chemical, microbial, and organoleptic components of silages. , 2018, Journal of dairy science.

[33]  C. Rensing,et al.  Hyperthermophilic Composting Accelerates the Removal of Antibiotic Resistance Genes and Mobile Genetic Elements in Sewage Sludge. , 2018, Environmental science & technology.

[34]  M. Sullivan,et al.  Dietary energy drives the dynamic response of bovine rumen viral communities , 2017, Microbiome.

[35]  Junxiang Yang,et al.  Effects of lactic acid bacteria and molasses additives on the microbial community and fermentation quality of soybean silage. , 2017, Bioresource technology.

[36]  A. Adesogan,et al.  Meta-analysis of effects of inoculation with homofermentative and facultative heterofermentative lactic acid bacteria on silage fermentation, aerobic stability, and the performance of dairy cows. , 2017, Journal of dairy science.

[37]  S. Abedon,et al.  Lysogeny in nature: mechanisms, impact and ecology of temperate phages , 2017, The ISME Journal.

[38]  Peer Bork,et al.  Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses , 2016, Nature.

[39]  Georgios A. Pavlopoulos,et al.  Uncovering Earth’s virome , 2016, Nature.

[40]  Hing-Fung Ting,et al.  MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. , 2016, Methods.

[41]  R. Feiner,et al.  A new perspective on lysogeny: prophages as active regulatory switches of bacteria , 2015, Nature Reviews Microbiology.

[42]  H. Ducklow,et al.  Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics , 2015, The ISME Journal.

[43]  Dong Li,et al.  Effect of microalgae supplementation on the silage quality and anaerobic digestion performance of Manyflower silvergrass. , 2015, Bioresource technology.

[44]  P. Bork,et al.  Patterns and ecological drivers of ocean viral communities , 2015, Science.

[45]  Maureen L. Coleman,et al.  A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes , 2015, The ISME Journal.

[46]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[47]  Alison Buchan,et al.  The elemental composition of virus particles: implications for marine biogeochemical cycles , 2014, Nature Reviews Microbiology.

[48]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[49]  J. Colprim,et al.  Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate. , 2013, Water research.

[50]  Frederic D Bushman,et al.  Rapid evolution of the human gut virome , 2013, Proceedings of the National Academy of Sciences.

[51]  S. Chisholm,et al.  Marine Viruses Exploit Their Host's Two-Component Regulatory System in Response to Resource Limitation , 2012, Current Biology.

[52]  Amos Bairoch,et al.  ViralZone: a knowledge resource to understand virus diversity , 2010, Nucleic Acids Res..

[53]  T. Nishino,et al.  Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of microbial community structure in landfill leachate. , 2009, Journal of hazardous materials.

[54]  C. Suttle.  Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.

[55]  S. Dowd,et al.  Natural mummification of the human gut preserves bacteriophage DNA. , 2016, FEMS microbiology letters.

[56]  I. Alli,et al.  Proteolysis Associated with the Ensiling of Chopped Alfalfa , 1988 .