Explaining Microbial Population Genomics through Phage Predation

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2. Species-Specific Viromes in the Ancestral Holobiont Hydra
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3. Phage-host interactions: The neglected part of biological wastewater treatment
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4. Genomes of the “ Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria
   Mario López‐Pérez, Jose Manuel Haro-Moreno, Jaime Iranzo, Francisco Rodríguez‐Valera · 2020 · mSystems
5. Bacteriophages of the lower urinary tract
   Andrea Garretto, Taylor Miller-Ensminger, Alan J. Wolfe, Catherine Putonti · 2019 · Nature Reviews Urology
6. Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool
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7. A case for the protection of saline and hypersaline environments: a microbiological perspective
   Varun G. Paul, Melanie R. Mormile · 2017 · FEMS Microbiology Ecology
8. Bacteriophage ecology in environmental biotechnology processes
   Orr H. Shapiro, Ariel Kushmaro · 2011 · Current Opinion in Biotechnology
9. Systems biology of lactic acid bacteria: a critical review
   Bas Teusink, Herwig Bachmann, Douwe Molenaar B · 2011 · Microbial Cell Factories
10. T4-like Phages Reveal the Potential Role of Viruses in Soil Organic Matter Mineralization
    Xiaomeng Wei, Tida Ge, Chuanfa Wu, Shuang Wang, Kyle Mason‐Jones, Yong Li, Zhenke Zhu, Yajun Hu, Chao Chu Liang, Jianlin Shen et al. · 2021 · Environmental Science & Technology
11. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions
    Christopher P Belnap, Chongle Pan, Vincent J. Denef, Nagiza F. Samatova, Robert L. Hettich, Jillian F. Banfield · 2011 · The ISME Journal
12. Genomic Diversity of “Deep Ecotype” Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames
    Mario López‐Pérez, Aitor Gonzaga, Francisco Rodríguez‐Valera · 2013 · Genome Biology and Evolution
13. Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber
    Lejla Pašić, Beltran Rodriguez-Mueller, Ana-Belén Martín-Cuadrado, Álex Mira, Forest L. Rohwer, Francisco Rodríguez‐Valera · 2009 · BMC Genomics
14. Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion
    Jordan Vacheron, Clara Margot Heiman, Christoph Keel · 2021 · Communications Biology
15. Individual bacteria in structured environments rely on phenotypic resistance to phage
    Erin L. Attrill, Rory Claydon, Urszula Łapińska, Mario Recker, Sean Meaden, Aidan T. Brown, Edze Rients Westra, Sarah V. Harding, Stefano Pagliara · 2021 · PLoS Biology
16. Convergent evolution toward an improved growth rate and a reduced resistance range in Prochlorococcus strains resistant to phage
    Sarit Avrani, Debbie Lindell · 2015 · Proceedings of the National Academy of Sciences
17. Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System
    Connor T. Skennerton, Florent E. Angly, Mya Breitbart, Lauren M. Bragg, Shaomei He, Katherine D. McMahon, Philip Hugenholtz, Gene W. Tyson · 2011 · PLoS ONE
18. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake
    Alberto López-Bueno, Alberto Rastrojo, Ramón Peiró‐Pastor, Miguel Arenas, Antonio Alcamı́ · 2015 · Molecular Ecology
19. Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health
    Yuan Huang, Wenlong Lu, Min Zeng, Xiaoyue Hu, Zhanhao Su, Yiwei Liu, Zeye Liu, Jianhui Yuan, Li Li, Xiaoling Zhang et al. · 2022 · Microbiome
20. Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean
    Hagay Enav, Shay Kirzner, Debbie Lindell, Yael Mandel‐Gutfreund, Oded Béjà · 2018 · Nature Communications
21. Towards an Evolutionary Model of Animal-Associated Microbiomes
    Carl J. Yeoman, Nicholas Chia, Süleyman Yıldırım, Margret E. Berg Miller, Angela D. Kent, Rebecca M. Stumpf, Steven R. Leigh, Karen E. Nelson, Bryan A. White, Brenda Anne Wilson · 2011 · Entropy
22. Microbial Arsenal of Antiviral Defenses – Part I
    Artem B. Isaev, Olga S. Musharova, Konstantin Severinov · 2021 · Biochemistry (Moscow)
23. Functional Strain Redundancy and Persistent Phage Infection in Swiss Hard Cheese Starter Cultures
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24. Comparative genomics of Lactobacillus sakei with emphasis on strains from meat
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25. Prokaryote Genome Fluidity: Toward a System Approach of the Mobilome
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26. Adding a cost of resistance description extends the ability of virus–host model to explain observed patterns in structure and function of pelagic microbial communities
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27. Evolutionary Genomics of a Temperate Bacteriophage in an Obligate Intracellular Bacteria (Wolbachia)
    Bethany N. Kent, Lisa J. Funkhouser-Jones, Shefali Setia, Seth R. Bordenstein · 2011 · PLoS ONE
28. The virus’s tooth: cyanophages affect an African flamingo population in a bottom-up cascade
    Peter Peduzzi, Martin Gruber, Michael Gruber, Michael Schagerl · 2014 · The ISME Journal
29. Ongoing Phenotypic and Genomic Changes in Experimental Coevolution of RNA Bacteriophage Qβ and Escherichia coli
    Akiko Kashiwagi, Tetsuya Yomo · 2011 · PLoS Genetics
30. Evidence of bacterioplankton community adaptation in response to long-term mariculture disturbance
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31. “Candidatus Nitrosotenuis aquarius,” an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter
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32. The dynamic interplay of bacteriophage, bacteria and the mammalian host during phage therapy
    Jacopo Marchi, Sophia Zborowsky, Laurent Debarbieux, Joshua S. Weitz · 2023 · iScience
33. Polyclonality of Concurrent Natural Populations of Alteromonas macleodii
    Aitor Gonzaga, Ana-Belén Martín-Cuadrado, Mario López‐Pérez, Carolina Megumi Mizuno, Inmaculada García-Heredia, Nikole E. Kimes, Purificación López‐García, David Moreira, David Wayne Ussery, Mila Zaballos et al. · 2012 · Genome Biology and Evolution
34. Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus : From Genotype to Ecotype
    Mario López‐Pérez, Jane M. Jayakumar, Jose Manuel Haro-Moreno, Asier Zaragoza-Solas, Geethika Reddi, Francisco Rodríguez‐Valera, Orr H. Shapiro, Munirul Alam, Salvador Almagro‐Moreno · 2019 · mBio
35. CRISPR-Cas Systems
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36. Effects of bacteriophages on gut microbiome functionality
    Kurilovich, Elena, Geva-Zatorsky, Naama · 2025 · Gut Microbes
37. Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation
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38. The Deep Viriosphere: Assessing the Viral Impact on Microbial Community Dynamics in the Deep Subsurface
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39. Deciphering the Symbiotic Plant Microbiome: Translating the Most Recent Discoveries on Rhizobia for the Improvement of Agricultural Practices in Metal-Contaminated and High Saline Lands
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40. How can microbial population genomics inform community ecology?
    David VanInsberghe, Philip Arevalo, Diana M. Chien, Martin F. Polz · 2020 · Philosophical Transactions of the Royal Society B Biological Sciences
41. Microbial Arsenal of Antiviral Defenses. Part II
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42. Deep sequencing of the viralphoHgene reveals temporal variation, depth-specific composition, and persistent dominance of the same viralphoHgenes in the Sargasso Sea
    Dawn B. Goldsmith, Rachel J. Parsons, Damitu Beyene, Peter Salamon, Mya Breitbart · 2015 · PeerJ
43. Genomes of “Spiribacter”, a streamlined, successful halophilic bacterium
    Mario López‐Pérez, Rohit Ghai, María José León, Ángel Rodríguez-Olmos, José Luis Copa-Patiño, Juán Soliveri, Cristina Sánchez‐Porro, António Ventosa, Francisco Rodríguez‐Valera · 2013 · BMC Genomics
44. Host‐dependent differences in abundance, composition and host range of cyanophages from the R ed S ea
    Naama P. Dekel‐Bird, Gazalah Sabehi, Bar Mosevitzky Lis, Debbie Lindell · 2014 · Environmental Microbiology
45. Ancestral gene acquisition as the key to virulence potential in environmental Vibrio populations
    Maxime Bruto, Yannick Labreuche, Adèle James, Damien Piel, Sabine Chenivesse, Bruno Petton, Martin F. Polz, Frédérique Le Roux · 2018 · The ISME Journal
46. Review article: bacteriophages in gastroenterology—from biology to clinical applications
    João Sabino, Robert P. Hirten, Jean‐Frédéric Colombel · 2019 · Alimentary Pharmacology & Therapeutics
47. Intestinal virome in patients with alcohol use disorder and after abstinence
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48. Phables: from fragmented assemblies to high-quality bacteriophage genomes
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49. Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation
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50. Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil
    Yunha Hwang, Janina Rahlff, Dirk Schulze‐Makuch, Michael Schloter, Alexander J. Probst · 2021 · mSystems
51. Ecological and genetic interactions between cyanobacteria and viruses in a low‐oxygen mat community inferred through metagenomics and metatranscriptomics
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52. Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection
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53. Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns
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54. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples
    Jakob Thannesberger, Hans-Jörg Hellinger, Ingeborg Klymiuk, Marie-Theres Kastner, Franz J. J. Rieder, Martina Schneider, Susanne Fister, Thomas Lion, Karin Kosulin, Johannes Laengle et al. · 2017 · The FASEB Journal
55. Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community
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56. Ecological and genomic features of two widespread freshwater picocyanobacteria
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57. Viruses in colorectal cancer
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58. Archaeal Viruses Multiply: Temporal Screening in a Solar Saltern
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59. Analysis of metagenomic data reveals common features of halophilic viral communities across continents
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60. New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake
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61. Simple models combining competition, defence and resource availability have broad implications in pelagic microbial food webs.
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62. Coupled virus - bacteria interactions and ecosystem function in an engineered microbial system
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63. Isolation, engineering and ecology of temperate phages from the human gut
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64. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano
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65. From deep sequencing to viral tagging: Recent advances in viral metagenomics
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66. The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria
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67. Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov
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68. Evidence for metaviromic islands in marine phages
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69. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis
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70. Metatranscriptomic analysis of extremely halophilic viral communities
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71. The impact of bacteriophages on probiotic bacteria and gut microbiota diversity
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72. Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea
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73. Taxonomic variability and functional stability in microbial communities infected by phages
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74. Genetic hurdles limit the arms race betweenProchlorococcusand the T7-like podoviruses infecting them
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75. The Prokaryotic Species Concept and Challenges
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76. The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective
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77. Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents
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78. Systems Biology for Ecology
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79. Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea
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80. Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics
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81. Scratching the Surface of Biology’s Dark Matter
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82. A phage parasite deploys a nicking nuclease effector to inhibit viral host replication
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83. Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking
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84. The history and market impact of CRISPR RNA-guided nucleases
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85. Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration
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86. Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples
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87. Optimal Defense Strategies in an Idealized Microbial Food Web under Trade-Off between Competition and Defense
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88. Complementary and Alternative Medicine Strategies for Therapeutic Gut Microbiota Modulation in Inflammatory Bowel Disease and their Next-Generation Approaches
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89. Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory
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90. Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean
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91. Haloviruses of archaea, bacteria, and eukaryotes
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92. Conservation of Gene Cassettes among Diverse Viruses of the Human Gut
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93. Is the pan-genome also a pan-selectome?
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94. Bacteriophage ecology in biological wastewater treatment systems
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95. Genomic variation and biogeography of Antarctic haloarchaea
    Bernhard Tschitschko, Susanne Erdmann, Matthew Z. DeMaere, Simon Roux, Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Sarah Brazendale, Alyce M. Hancock, Emiley A. Eloe‐Fadrosh et al. · 2018 · Microbiome
96. Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs
    Sergio Guajardo‐Leiva, Carlos Pedrós‐Alió, Oscar Salgado, Fabián Pinto, Beatriz Dı́ez · 2018 · Frontiers in Microbiology
97. Genomes of Alteromonas australica,a world apart
    Mario López‐Pérez, Aitor Gonzaga, Elena Pavlovna Ivanova, Francisco Rodríguez‐Valera · 2014 · BMC Genomics
98. Homologous recombination is involved in the diversity of replacement flexible genomic islands in aquatic prokaryotes
    Mario López‐Pérez, Ana-Belén Martín-Cuadrado, Francisco Rodríguez‐Valera · 2014 · Frontiers in Genetics
99. Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth
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100. Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages
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