Explaining microbial population genomics through phage predation

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Items 501–600 of 666

1. Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster
   Kaixin Diao, Guohui Li, Xueqin Sun, Hao Yi, Shiying Zhang, Wei Xiao · 2023 · Viruses
2. Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments
   Pranjal Bharali, Bhagyudoy Gogoi, Viphrezolie Sorhie, Shiva Aley Acharjee, Bendangtula Walling, Alemtoshi, Vinita Vishwakarma, Maulin Pramod Shah · 2023 · Biodegradation
3. Microdiversity in marine pelagic ammonia‐oxidizing archaeal populations in a Mediterranean long‐read metagenome
   Pablo Suárez‐Moo, Jose Manuel Haro-Moreno, Francisco Rodríguez‐Valera · 2024 · Environmental Microbiology
4. Bacterial Virus Ontology; Coordinating across Databases
   Chantal Hulo, Patrick Masson, Ariane Toussaint, David Osumi-Sutherland, Edouard de Castro, Andrea H Auchincloss, Sylvain Poux, Lydie Bougueleret, Ioannis Xénarios, Philippe Le Mercier · 2017 · Viruses
5. Mechanisms of multi-strain coexistence in host–phage systems with nested infection networks
   Luis F. Jover, Michael H. Cortez, Joshua S. Weitz · 2013 · Journal of Theoretical Biology
6. Helicobacter pylori and Related Virulence Factors for Gastrointestinal Diseases
   Evariste Tshibangu‐Kabamba, Yoshio Yamaoka · 2018 · Springer eBooks
7. From Genomics to Microevolution and Ecology: The Case of Salinibacter ruber
   Arantxa Peña, Hanno Teeling, Jaime Huerta‐Cepas, Fernando Santos, Inmaculada Meseguer, Marianna Lucio, Philippe Schmitt‐Kopplin, Joaquı́n Dopazo, Ramon A. Rossello-Mora, Margarete Schüler et al. · 2011 · Springer eBooks
8. DNA Reassociation Yields Broad‐Scale Information on Metagenome Complexity and Microbial Diversity
   Vigdis Lid Torsvik, Lise Øvreås · 2011
9. Systems Microbiology and Engineering of Aerobic-Anaerobic Ammonium Oxidation
   David Gregory Weissbrodt, George Wells, Michele Laureni, Shelesh Agrawal, Ramesh K. Goel, Giancarlo Russo, Yujie Men, David R. Johnson, Magnus Christensson, Susanne Lackner et al. · 2020 · ChemRxiv
10. Illuminating the Black Box: Trace Element Biogeochemistry from a Microbial Perspective
    Benjamin D. Peterson, Brett A. Poulin · 2025 · Environmental Science & Technology
11. Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters
    Bishav Bhattarai, Ananda Shankar Bhattacharjee, Felipe H. Coutinho, Ramesh K. Goel · 2023 · Chemosphere
12. Being Selective in the Prochlorococcus Collective
    Chris Bowler, David John Scanlan · 2014 · Science
13. Demographics of lytic viral infection of coastal ocean Vibrio
    Kathryn M. Kauffman · 2014
14. Enterobacter-infecting phages in nitrogen-deficient paddy soil impact nitrogen-fixation capacity and rice growth by shaping the soil microbiome
    Yu Liu, Yajiao Wang, Wenchong Shi, Nan Wu, Wénwén Liú, Frédéric Francis, Xifeng Wang · 2024 · The Science of The Total Environment
15. Two Tales of Prokaryotic Genomic Diversity: Escherichia coli and Halophiles
    Lejla Pašić, Jerneja Ambrožič Avguštin, Marjanca Starčič Erjavec, Blagajana Herzog‐Velikonja, Zdravko Podlesek, Darja Žgur‐Bertok · 2014 · DOAJ (DOAJ: Directory of Open Access Journals)
16. Metabolic and microbial perspectives on the “evolution of evolution”
    Russell Powell, Maureen A. O’Malley · 2019 · Journal of Experimental Zoology Part B Molecular and Developmental Evolution
17. Complete genome sequence of Neptunomonas concharum JCM17730T: An acetate assimilating bacterium isolated from a dead ark clam
    Nan Pu, Wei Li, Zhengjun Li · 2020 · Marine Genomics
18. Evolutionary Genomics of Marine Bacteria and Archaea
    Carolina A. Martínez-Gutiérrez, Frank O. Aylward · 2022 · The microbiomes of humans, animals, plants, and the environment
19. Deconstructing the association between abiotic factors and species assemblages in the global ocean microbiome
    Xiaoyu Shan, Otto X. Cordero · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
20. Phylogenomics of SAR116 clade reveals two subclades with different evolutionary trajectories and important role in the ocean sulfur cycle
    Juan J. Roda‐Garcia, Jose Manuel Haro-Moreno, Lukas A. Huschet, Francisco Rodríguez‐Valera, Mario López‐Pérez · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
21. Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments
    Judith Villamor, María Dolores Ramos‐Barbero, Mercedes Moreno‐Paz, Cristian Villena‐Alemany, Manuel Martínez‐García, Vı́ctor Parro, Josefa Antón, Fernando Santos · 2025 · The ISME Journal
22. The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity
    Jose Manuel Haro-Moreno, Juan J. Roda‐Garcia, Carmen Molina-Pardines, Mario López‐Pérez · 2025 · Environmental Microbiome
23. Intestinal dysbiosis associated with non-nutritive sweeteners intake: an effect without a cause?
    Luigi Marongiu, Ewa Brzozowska, Svetlana Hetjens, Ludwig Eduard Hoelzle, Sascha Venturelli · 2025 · Frontiers in Nutrition
24. RNA virus diversity highlights the potential biosecurity threat posed by Antarctic krill
    Tingting Xu, Xianyong Zhao, Thomas P. Loch, Jiancheng Zhu, Wei Wang, Xinliang Wang, Chong Wang, Gangzhou Fan, Bin Hao, Jichang Zhang et al. · 2025 · Marine Life Science & Technology
25. The Dynamic Genomes of Acidophiles
    Francisco J. López de Saro, Manuel J. Gómez, Enrique González-Tortuero, Vı́ctor Parro · 2013 · Cellular origin, life in extreme habitats and astrobiology
26. CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes
    Lei Sun, Jinbiao Wang, Yan Fu, Gongming Wang, Yun Li, Jinlin Huang · 2022 · BMC Bioinformatics
27. New tRNA-targeting transposons that hijack phage and vesicles
    Emily R. Dart, Nathan A. Ahlgren · 2023 · Trends in Genetics
28. How Big Is Big? The Effective Population Size of Marine Bacteria
    Haiwei Luo · 2024 · Annual Review of Marine Science
29. High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel
    L. F. M. Kop, Hanna Koch, Paula Dalcin Martins, C. Suarez, Sabina Karačić, F. Persson, B. Wilén, P. Hagelia, M. S. M. Jetten, S. Lücker · 2025 · FEMS Microbiology Ecology
30. Current understanding of the Streptococcus bovis/equinus complex and its bacteriophages in ruminants: a review
    Seon Young Park, Seongwon Seo, Ji Hyung Kim · 2025 · Frontiers in Veterinary Science
31. Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium
    Clafy Fernandes, Markus Haber, Paul Layoun, Maria‐Cecilia Chiriac, Paul‐Adrian Bulzu, Rohit Ghai, Vojtěch Kasalický, Tanja Shabarova, Hans‐Peter Grossart, Jason Nicholas Woodhouse et al. · 2025 · Nature Microbiology
32. Viral Nature of the Aquatic Ecosystems
    Daichi Morimoto, Kento Tominaga, Hiroaki Takebe, Sigitas Šulčius, Takashi Yoshida · 2022 · Advances in environmental microbiology
33. MAFLD under the lens: the role of gut microbiota
    Patrícia Sousa, Mariana Verdelho Machado · 2022 · Metabolism and Target Organ Damage
34. Ecological Aspects on Rumen Microbiome
    Emiliana Manesco Romagnoli, Maria Carolina Pezzo Kmit, Josiane Barros Chiaramonte, Maike Rossmann, Rodrigo Mendes · 2017 · Springer eBooks
35. Virus Interactions in the Aquatic World
    Stéphan Jacquet, Kevin Xu Zhong, Peter Peduzzi, Tron Frede Thingstad, Kaarle Joonas Parikka, Markus G. Weinbauer · 2018 · Caister Academic Press eBooks
36. Bacteria–Virus Interactions
    Takashi Yoshida, Daichi Morimoto, Shigeko Kimura · 2019 · Springer eBooks
37. Phages - bacteria interactions network of the healthy human gut
    Martial Marbouty, Agnès Thierry, Romain Koszul · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
38. Stable Isotope Probing and the Human Gut
    Koen Venema · 2014 · ASM Press eBooks
39. Effect of different HbA1c levels on the gut microbiota in patients with type 2 diabetes mellitus
    Yanxia Chen, Rongfei Mou, Mian Wang · 2021 · World Academy of Sciences Journal
40. Phage Probiotics
    Shirley Lau Wong · 2016 · SpringerBriefs in biochemistry and molecular biology
41. 682: INTESTINAL VIROME IN PATIENTS WITH ALCOHOL USE DISORDER AND AFTER ABSTINENCE
    Cynthia L. Hsu, Xinlian Zhang, Lu Jiang, Sonja Lang, Phillipp Hartmann, David T. Pride, Derrick E. Fouts, Peter Stärkel, Bernd Schnabl · 2022 · Gastroenterology
42. Exploring the Potential of Bacteriophages on Earth and Beyond
    Anurup Mohanty, Biswanath Shaw, Nikhil Pradeep, Nitin Kumar Singh, Kasthuri Venkateswaran · 2023 · Journal of the Indian Institute of Science
43. Novel adaptive immune systems in pristine Antarctic soils
    Marc W. Van Goethem, Oliver K. I. Bezuidt, Rian Pierneef, Surendra Vikram, DAVID W. HOPKINS, Thomas J. Aspray, Grant Hall, Stephan M Woodborne, Ian D. Hogg, Trent R. Northen et al. · 2025 · Scientific Reports
44. Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity
    Claudia Teso-Pérez, Areli López-Gazcón, Juan Manuel Peralta‐Sánchez, Manuel Martínez‐Bueno, Eva Valdivia, María Esther Fárez‐Vidal, Antonio Manuel Martín-Platero · 2024 · Microbial Ecology
45. Human Microbiome and Bacteriophages: Impacts on Health and Disease
    Muhammad Abdullah Sheraz, Hongyan Shi, Santasree Banerjee · 2025 · Current Clinical Microbiology Reports
46. Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus–host pairing of freshwater bacteria
    Yusuke Okazaki, Yohei Nishikawa, Ryota Wagatsuma, Haruko Takeyama, Shin‐ichi Nakano · 2025 · ISME Communications
47. Single cell genomics of deep ocean bacteria
    Weizhou Zhao, Siv G. E. Andersson · 2014 · Trends in Microbiology
48. Marine Microbial Diversity
    2016 · CRC Press eBooks
49. Frequency-Dependent Selection in Light of Phage Exposure
    Stephen Tobias Abedon · 2022 · Springer eBooks
50. Bacterial resistance response and resource availability mediate viral coexistence
    Lisa Butt, Justin R. Meyer, Richard J. Lindsay, Robert Beardmore, Ivana Gudelj · 2024 · Journal of Evolutionary Biology
51. Microbial subnetworks related to short-term diel O2 fluxes within geochemically distinct freshwater wetlands
    Dean J. Horton, Matthew J. Cooper, Anthony J. Wing, Peter Stefanov Kourtev, Donald G Uzarski, Deric R. Learman · 2018 · FEMS Microbiology Letters
52. Daily and Seasonal Rhythms of Marine Phages of Cyanobacteria
    Gur Hevroni, Alon Philosof · 2021 · Springer eBooks
53. Monitoring biodegradation capacity of organic pollutants in the environment
    Bas M. van der Zaan · 2010
54. The virome in adult monozygotic twins with concordant or discordant gut microbiomes
    J. Leonardo Moreno-Gallego, Shao‐Pei Chou, Sara C. Di Rienzi, Julia K. Goodrich, Tim D. Spector, Jordana T. Bell, Youngblut, Ian Hewson, Alejandro Reyes, Ruth E. Ley · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
55. Evolutionary ecology of natural comammox Nitrospira populations
    Alejandro Palomo, Arnaud Dechesne, Otto X. Cordero, Barth F. Smets · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
56. Genetics of Phage Lysis
    Madalena Pimentel · 2015 · ASM Press eBooks
57. Ecogenomics and limnological dynamics of a new Thiocapsa species blooming in the whole water column of a karstic lake
    Pedro J. Cabello‐Yeves, Antonio Picazo, Carlos Rochera, Daniel Morant, Eduardo Vicente, David John Scanlan, Richard John Puxty, Antonio Camacho · 2025 · Limnology and Oceanography
58. Cultivation, genomics, and giant viruses of a ubiquitous and heterotrophic freshwater cryptomonad
    Indranil Mukherjee, Paul‐Adrian Bulzu, Roudaina Boukheloua, Usman Asghar, Hongjae Park, Helena Henriques Vieira, Maria‐Cecilia Chiriac, Vojtěch Kasalický, Petr Znachor, Pavel Rychtecký et al. · 2025 · The ISME Journal
59. Dynamics and Eco‐Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness
    Sukki Sookyoung Kim, Elisa D'Agostino, David M. Needham · 2026 · Environmental Microbiology
60. Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease
    Deepika Dinesh, Xochitl C. Morgan, Jordan Jensen, Kjetil Bjørnevik, Michael A. Schwarzschild, Alberto Ascherio, Curtis Huttenhower, Natalia Palacios · 2026 · Annals of Neurology
61. Remodelling of the gut virome after long-term fasting
    Natalie Falshaw, Quinten R. Ducarmon, Alexandra King, Franziska Grundler, Robin Mesnage · 2026 · npj Biofilms and Microbiomes
62. In vitro lytic efficiency of Staphylococcus aureus bacteriophages in bacteria from bovine mastitis: a meta-analysis
    Bibiana Martins Barasuol, Valessa Lunkes Ely, Antônio Francisco Igor Magalhães de Matos, Luís Antônio Sangioni, Águeda Castagna de Vargas, Daniela Isabel Brayer Pereira, Amanda Carneiro Martini, Luciana Pötter, Sônia de Ávila Botton · 2021 · Ciência Rural
63. Viral Prevalence and Genomic Xenology in the Coevolution of HzNV-2 (Nudiviridae) with Host Helicoverpa zea (Lepidoptera: Noctuidae)
    Luke R. Tembrock, Frida A. Zink, Todd M. Gilligan · 2023 · Insects
64. 20. The Deep Viriosphere: Assessing the Viral Impact on Microbial Community Dynamics in the Deep Subsurface
    Rika E. Anderson, William J. Brazelton, John A. Baross · 2013 · De Gruyter eBooks
65. Bacteriophage and Viral Ecology as Seen Through the Lens of Nucleic Acid Sequence Data
    Eric G Sakowski, W. Kress, E. Wommack · 2011
66. Evolution of complex phenotypes through successions of adaptive steps
    Tin Yau Pang, Martin J. Lercher · 2015 · arXiv (Cornell University)
67. The evolution of bacterial cell differentiation and multicellular organization
    Jordi van Gestel · 2016 · University of Groningen research database (University of Groningen / Centre for Information Technology)
68. Prokaryotic Viruses: Intriguing Players in the Aquatic Realm
    Johannes Sergej Schweichhart · 2021 · Elsevier eBooks
69. Microdiversity in marine pelagic ammonia-oxidizing archaeal populations
    Pablo Suárez‐Moo, Jose Manuel Haro-Moreno, Francisco Rodríguez‐Valera · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
70. Disentangling the impacts of abiotic and biotic environmental factors and dispersal dynamics on the pangenome fluidity of bacterial pathogens
    Ying‐Xian Goh, FNU Hardeep, Hailong Zhang, Jingqiu Liao · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
71. Approches génomiques de l’interaction Ostreococcus tauri-Prasinovirus
    Julie Thomy · 2022 · theses.fr (ABES)
72. Evolution And Dynamics Of The H uman Gut Virome
    Samuel S. Minot · 2012 · ScholarlyCommons (University of Pennsylvania)
73. Variabilidad genómica del ecotipo profundo de la bacteria marina alteromonas macleodii
    Aitor Gonzaga · 2015
74. Microbial diversity beyond E. coli: new microbial worlds, new concepts in biology
    John A. Fuerst · 2011 · Microbiology Australia
75. DOCTEUR DE L'UNIVERSITÉ DE GRENOBLE
    Chimie Biologie, Yves Jouanneau · 2011
76. New approaches indicate constant viral diversity despite shifts in assemblage な
    Joanne Emerson, Brian C. Thomas, Karen Andrade, Karla B. Heidelberg, Jillian, Jillian F. Banfield · 2013
77. Persisting anti-phage CRISPR immunity in multiple human gut microbiomes
    Eran Mick, Adi Stern, Rotem Sorek · 2013
78. The evolutionary selective pressures exerted on A3 actinobacteriophages
    Cheyenne Weeks‐Galindo · 2015 · JMU Scholoraly Commons (James Madison University)
79. Mechanism and engineering of CRISPR-associated endonucleases
    Samuel H. Sternberg · 2014 · eScholarship (California Digital Library)
80. Molecular basis of cyanophage resistance in marine Synechococcus
    Blanca M. Perez-Sepulveda · 2026 · Warwick Research Archive Portal (University of Warwick)
81. Metagenomic characterisation of the gastrointestinal virome of neonatal pigs
    Oskar Karlsson Lindsjö · 2016 · Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences))
82. Haloarchaeal Species Genesis: Diversity, Recombination, and Evolution
    Nikhil Ram-Mohan · 2016
83. Molecular characterization of new archaeal viruses from high salinity environments
    Tatiana A. Demina · 2016 · Työväentutkimus Vuosikirja
84. Phage--Bacteria Infection networks: from nestedness to modularity and back again
    F. Morata Garcia, O César · 2014
85. Reconstrução e análise de genomas de bactérias de compostagem a partir de dados metagenômicos
    Leandro Nascimento Lemos · 2016
86. Composition and Diversity of Human Oral Microbiome
    Preethi Balan, Chaminda Jayampath Seneviratne · 2017 · CRC Press eBooks
87. Assembly of Deeply Sequenced Metagenomes Yields Insight into Viral and Microbial Ecology in Two Natural Systems
    Joanne Emerson · 2012 · eScholarship (California Digital Library)
88. Dynamics in coastal RNA viruses and bacteriophages are driven by shifts in the community phylogenetic structure
    Julia Gustavsen, Curtis A. Suttle · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
89. Associations between depth and micro-diversity within marine viral communities revealed through metagenomics
    Felipe H. Coutinho, Riccardo Rosselli, Francisco Rodríguez‐Valera · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
90. High-Throughput Cultivation of Bacterioplankton from the Gulf of Mexico and Genomics of the First Cultured LD12 Representative
    Michael W. Henson · 2019
91. Coevolving parasites improve host evolutionary search on structured fitness landscapes
    Hywel T. P. Williams · 2012 · Conference on Artificial Life (ALIFE)
92. The role of bacteriophages in mixed microbial communities and populations of Pseudomonas aeruginosa
    Hafiz Ismail Muhammad · 2019
93. The virus integrations in gut microbes associated with dysbiosis of microbial community in tumorigenesis of colorectal carcinoma
    Boyu Cui, Xiaodan Wang, Wenqiu Xu, Caihong Zheng, Jun Cai · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
94. Peer Review #2 of "Benchmarking protocols for the metagenomic analysis of stream biofilm viromes (v0.2)"
    2019 · PeerJ
95. Streamlined freshwater bacterioplankton Nanopelagicales (acI) and “ Ca . Fonsibacter” (LD12) thrive in functional cohorts
    Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
96. An insight into bacteriophages' response to various physical and chemical conditions: temperature, pH, salts
    Tabassum Tasnim Auroni, Md Deen Islam, Mst Salma Khatun, Md Shifat E Monjur, Mahmuda Yasmin, Chowdhury Rafiqul Ahsan, Jamalunnessa · 2016 · Dhaka University Journal of Biological Sciences
97. Peer Review #2 of "Mimicking prophage induction in the body: induction in the lab with pH gradients (v0.1)"
    2020 · PeerJ
98. The worm affair: Genetic diversity in two species of symbionts that co-occur in tubeworms from the Mediterranean Sea
    Tal Zvi‐Kedem, Eli Shemesh, Dan Tchernov, Maxim Rubin‐Blum · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
99. Микробный арсенал противовирусной защиты. Глава I
    Artem B. Isaev, Olga S. Musharova, Konstantin Severinov · 2021 · Biochemistry (Moscow)
100. Isolation and characterization of novel temperate virus Aeropyrum globular virus 1 infecting hyperthermophilic archaeon Aeropyrum
     Maho Yumiya, Yuto Fukuyama, Yoshihiko Sako, Takashi Yoshida · 2021 · bioRxiv (Cold Spring Harbor Laboratory)