The Ecology and Evolution of Pangenomes

Cited by (393)

Items 201–300 of 393

  1. Genomic Background Governs Opposing Responses to Nalidixic Acid upon Megaplasmid Acquisition in Pseudomonas
    David A. Baltrus, Caitlin Smith, MacKenzie Derrick, Courtney Leligdon, Zoe Rosenthal, Madison Mollico, Andrew Moore, Meara Clark · 2021 · mSphere
  2. Comparative Genomics and Pathogenicity Analysis of Two Bacterial Symbionts of Entomopathogenic Nematodes: The Role of the GroEL Protein in Virulence
    Abraham Rivera-Ramírez, Rosalba Salgado-Morales, Alfredo Jiménez‐Pérez, Rebeca Pérez-Martínez, Blanca I. García‐Gómez, Edgar Dantán‐González · 2022 · Microorganisms
  3. Comparison of Genomes, Resistomes, and Antimicrobial Properties of the Three Lactococcus lactis Strains from Fermented Milk and Cereal Products of South Africa and Russia
    Moiseenko, K. V., Glazunova, O. A., Savinova, O. S., Fedorova, T. V. · 2024 · Applied Biochemistry and Microbiology
  4. Exploring and utilizing soil Microbiota: From dark to light
    Caiyu Lu, Luotian Lu, Luyao Zhang, Huiyun Dong, Xingmei Liu, Bin Ma · 2025 · Earth Critical Zone
  5. Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes
    Francisnei Pedrosa‐Silva, Thiago M. Venâncio · 2023 · Genes
  6. The evolutionary replacement of restriction-modification by Ssp antiviral systems is associated with the distribution of prophages in the major clonal group of Acinetobacter baumannii
    Antonio Moreno-Rodríguez, Alejandro Rubio, Andrés Garzón, Younes Smani, Antonio J. Pérez‐Pulido · 2025 · mBio
  7. Population Genetic Structure: Where, What, and Why?
    Adomas Ragauskas, Evelina Maziliauskaitė, Petras Prakas, Dalius Butkauskas · 2025 · Diversity
  8. High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons
    Luzia Stalder, M. Maurhofer, Daniel Croll · 2025 · Microbiome
  9. Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum
    David Vereau Gorbitz, Chase Schwarz, John George McMullen, Mario A. Cerón-Romero, Rebecca T. Doyle, Jennifer A. Lau, Rachel J. Whitaker, Carin K. Vanderpool, Katy D. Heath · 2025 · mBio
  10. Genomic insights into the functional and metabolic versatility of gut microbiome Anaerostipes species
    Disha Bhattacharjee, Lindy Millman, Meagan L. Seesengood, Lindsey Martineau, Anna Maria Seekatz · 2026 · Microbial Genomics
  11. Regulatory features determine the evolutionary fate of laterally acquired genes in plants
    Catherine F Collins, Benjamin T Alston, Samuel G. S. Hibdige, Pauline Raimondeau, Emily R Baker, Graciela Sotelo, Alexander S. T. Papadopulos, Pascal-Antoine Christin, Lara Pereira, Luke T. Dunning · 2026 · Molecular Biology and Evolution
  12. Beyond Adaptive Gene Transfers: A Primer on Horizontal Gene Transfer Across Scales
    Julia Van Etten, Matthew D. Johnson · 2026 · Integrative and Comparative Biology
  13. Multiple relaxases contribute to the horizontal transfer of the virulence plasmids from the tumorigenic bacterium Pseudomonas syringae pv. savastanoi NCPPB 3335
    Maite Añorga, Miriam Urriza, Cayo Ramos, Jesús Murillo · 2022 · Frontiers in Microbiology
  14. Global dominance of Haloquadratum walsbyi by a single genomovar with distinct gene content and viral cohorts from close relatives
    Esteban Bustos-Caparros, Tomeu Viver, Juan F. Gago, Juanita R. Avontuur, Souad Amiour, Bonnie K. Baxter, María Eugenia Llames, Mehmet Burçin Mutlu, Aharon Oren, Ana S. Ramírez et al. · 2025 · The ISME Journal
  15. Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae
    Rachana Banerjee, Narendrakumar M. Chaudhari, Abhishake Lahiri, Anupam Gautam, Debaleena Bhowmik, Chitra Dutta, Sujay Chattopadhyay, Daniel H. Huson, Sandip Paul · 2021 · Frontiers in Microbiology
  16. Evolutionary Genomics of Marine Bacteria and Archaea
    Carolina A. Martínez-Gutiérrez, Frank O. Aylward · 2022 · The microbiomes of humans, animals, plants, and the environment
  17. Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming
    Mallory J. Choudoir, Achala Narayanan, Damayanti Rodriguez-Ramos, Rachel Simoes, Alon Efroni, Abigail Sondrini, Kristen M. DeAngelis · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  18. Kin Recognition Systems and Their Role in Multicellular Behaviors
    Karina Yaniv, Karine A. Gibbs · 2025 · Annual Review of Microbiology
  19. Pangenomes as a framework for adaptive radiation, speciation, and adaptation
    Nicolò Tellini, Ole K. Tørresen, David Edwards, Loren H. Rieseberg, Kjetill S. Jakobsen, José Cerca · 2025 · American Journal of Botany
  20. Genomic and Metabolomic Insights Into the Probiotic Potential of Weissella viridescens
    Shuwei Zhang, Ruiting Lan, Ruiqing Zhao, Ruoshi Wang, Liyun Liu, Jianguo Xu · 2025 · Biology
  21. Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics
    Scott V. Edwards, Heng Li · 2026 · Proceedings of the Royal Society B Biological Sciences
  22. A universal and constant rate of gene content change traces pangenome flux to LUCA
    Katharina Trost, Michael R. Knopp, Jessica L. E. Wimmer, Fernando D. K. Tria, William F. Martin · 2024 · FEMS Microbiology Letters
  23. Navigating Host Immunity and Concurrent Ozone Stress: Strain‐Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation in Xanthomonas on Pepper
    Amanpreet Kaur, Ivory Russell, Ranlin Liu, Auston Holland, Rishi Bhandari, Neha Potnis · 2025 · Evolutionary Applications
  24. Fitness costs of plasmids carrying antibiotic resistance genes
    Yi Xu, Hao Cheng, Xiaojie Hu, Chao QIN, Yanzheng Gao · 2025 · Scientia Sinica Technologica
  25. Comparative Genomics Reveals Intra and Inter Species Variation in the Pathogenic Fungus Batrachochytrium dendrobatidis
    Mark N. Yacoub, Jason Stajich · 2025 · Genome Biology and Evolution
  26. A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes
    Jindan Guo, Erli Pang, Hongtao Song, Kui Lin · 2021 · BMC Bioinformatics
  27. Plasmid evolution in the clinic
    Rosanna C. T. Wright, Michael A. Brockhurst · 2022 · Nature Ecology & Evolution
  28. The contours of evolution: In defence of Darwin's tree of life paradigm
    Peter T. S. van der Gulik, Wouter D. Hoff, Dave Speijer · 2024 · BioEssays
  29. Integration of diverse DNA substrates by a casposase can be targeted to R-loops in vitro by its fusion to Cas9
    Chun Hang Lau, Edward L. Bolt · 2020 · Bioscience Reports
  30. Epistasis decreases with increasing antibiotic pressure but not temperature
    Ana‐Hermina Ghenu, André Amado, Isabel Gordo, Claudia Bank · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  31. Redefining paradigms in the archaeal virus-host arms race
    Laura Martínez-Álvarez, Xu Peng · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome
    Pan Zhang, Biliang Zhang, Yuanyuan Ji, Jian Jiao, Ziding Zhang, Chang Fu Tian · 2024 · mLife
  33. A genome-wide investigation of Mycoplasma hominis genes associated with gynecological infections or infertility
    Salim Chibani, Elhem Yacoub, Safa Boujemaa, Helmi Mardassi, Julien Guglielmini, Amaury Vaysse, Nadine Khadraoui, Béhija Mlik, Boutheina Ben Abdelmoumen Mardassi · 2025 · Frontiers in Microbiology
  34. Harnessing genomic insights to identify antimicrobial traits in Bacillus velezensis MJ06 from Korean soybean-fermented Meju
    Yeajin Song, Eunhye Jo, Min-Jeong Kim, Hyeyoung Lee, Jaeho Cha · 2025 · Food Science and Biotechnology
  35. Advances of Chinese herbal medicine and its active ingredients in the treatment of antibiotic-resistant Klebsiella pneumoniae infections: Therapeutic efficacy, mechanisms, and combination strategies
    Shuo Yang, Ping Su, Shuang Liu, Yi Wang · 2025 · Science of Traditional Chinese Medicine
  36. Multi-omics analysis reveals important role for microbial-derived metabolites from Botryllus schlosseri in metal interactions
    Dulce G. Guillén Matus, Caroline M. Donaghy, Nidhi Vijayan, Zachary T. Lane, Matthew Howell, George G. Glavin, Alfredo Milton Angeles-Boza, Spencer V. Nyholm, Marcy J. Balunas · 2025 · mSystems
  37. Bacterial immune systems as causes and consequences of microbiome structure
    Rafael Custódio, Ellinor Alseth, Michael A. Brockhurst, Sam P. Brown, Edze Rients Westra · 2025 · PLoS Biology
  38. Diversity and evolution of archaeal immune strategies
    Laura Martínez-Álvarez, Xu Peng · 2026 · Nucleic Acids Research
  39. Multi-scale ecological drivers shape the genome flexibility of soil-dwelling Listeria monocytogenes
    Ying‐Xian Goh, FNU Hardeep, Hailong Zhang, Jingqiu Liao · 2026 · ISME Communications
  40. Antimicrobial resistance and the human gut microbiome—a food safety perspective
    Carmen Diaz‐Amigo, Leticia Elisa Bartolomé Del Pino, Jeffrey Lejeune, Jorge Pinto Ferreira, Catherine Bessy · 2026 · Critical Reviews in Food Science and Nutrition
  41. Plant pan-transcriptomics: Integrating structural genomics, isoform diversity, and systems genetics for next-generation breeding
    Bahman Panahi, Rasmieh Hamid, Zahra Ghorbanzadeh · 2026 · Current Plant Biology
  42. Empirical evidence for metabolic drift in plant and algal lipid biosynthesis pathways
    Maëlle Zonnequin, Arnaud Belcour, Ludovic Delage, Anne Siegel, Samuel Blanquart, Catherine Leblanc, Gabriel V. Markov · 2024 · Frontiers in Plant Science
  43. Screening Marine Microbial Metabolites as Promising Inhibitors of Borrelia garinii: A Structural Docking Approach towards Developing Novel Lyme Disease Treatment
    Zarrin Basharat, Sadia Sattar, Ammar Abdulraheem Bahauddin, Abdulaziz K. Al Mouslem, Ghallab Alotaibi · 2024 · BioMed Research International
  44. Multivariate Divergence in Wild Microbes: No Evidence for Evolution along a Genetic Line of Least Resistance
    Emile Gluck‐Thaler, Muhammad Shaikh, Corlett W. Wood · 2024 · The American Naturalist
  45. Copper homeostasis in Streptococcus and Neisseria: Known knowns and unknown knowns
    Archie Howell, Safa Chogule, Karrera Y. Djoko · 2025 · Advances in microbial physiology/Advances in Microbial Physiology
  46. A Small RNA Derived From the 5′ End of the IS 200 tnpA Transcript Regulates Multiple Virulence Regulons in Salmonella typhimurium
    Ryan S. Trussler, Naomi‐Jean Q. Scherba, Hoda Kooshapour, Michael J. Ellis, Konrad U. Förstner, Matthew Albert, Alexander J. Westermann, David B. Haniford · 2025 · Molecular Microbiology
  47. Gene co-occurrence and its association with phage infectivity in bacterial pangenomes
    Anne Kupczok, Athina Gavriilidou, Emilian Paulitz, Lucía Guerrero-García, Franz Baumdicker · 2025 · Philosophical Transactions of the Royal Society B Biological Sciences
  48. Origins and evolution of biological novelty
    Kelly A. Carscadden, Rebecca T. Batstone, Frances E. Hauser · 2022
  49. Pangenome evolution in Escherichia coli is sequence type, not phylogroup, specific
    Elizabeth Cummins, Rebecca J Hall, Christopher H. Connor, James O. McInerney, Alan McNally · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  50. Genomic Distance-based Rapid Uncovering of Microbial Population Structures (GRUMPS): a reference free genomic data cleaning methodology
    Kaleb Z. Abram, Zulema Udaondo, Michael Scott Robeson, Se‐Ran Jun · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Origins and Evolution of Novel Bacteroides in Captive Apes
    Alex H. Nishida, Howard Ochman · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  52. Defense systems and horizontal gene transfer in bacteria
    Roman Kogay, Yuri I. Wolf, Eugene V. Koonin · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Evolutionary dynamics of genome structure and content among closely related bacteria
    Marco Molari, Liam P. Shaw, Richard A. Neher · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  54. Negative frequency-dependent selection contributes to modular structure of effector repertoires in Pseudomonas syringae
    Shuanger Li, Eric Laderman, Hanna Märkle, Yunze Yang, Joy M. Bergelson, Mercedes Pascual · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  55. The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
    Mahboobeh Behruznia, Maximillian G. Marin, Daniel James Whiley, Maha Reda Farhat, Jonathan C. Thomas, Maria Rosa Domingo-Sananes, Conor Joseph Meehan · 2025 · eLife
  56. Novel genes arise from genomic deletions across the bacterial tree of life
    Arya Kaul, Fernando W. Rossine, Karel Břinda, Michael Baym · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Women's health is a team effort: probiogenomics supports the development of a multi-species vaginal probiotic
    Calvanese, Chiara Maria, Valentino, Vincenzo, De Prisco, Annachiara, Allesina, Serena, Amoruso, Angela, Deidda, Francesca, Visciglia, Annalisa, Ercolini, Danilo, Pane, Marco, De Filippis, Francesca · 2026 · Cellular and Molecular Life Sciences
  58. Influence of genomic variations on glanders serodiagnostic antigens using integrative genomic and transcriptomic approaches
    Philippe Charron, Ruimin Gao, John Chmara, Emily Hoover, Susan A. Nadin‐Davis, Danielle Chauvin, Jennifer Hazelwood, Kennedy J Makondo, Marc‐Olivier Duceppe, Mingsong Kang · 2023 · Frontiers in Veterinary Science
  59. Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples
    Zhe Zhao, Federico Marotta, Min Wu · 2024 · Microorganisms
  60. Comparative Pan- and Phylo-Genomic Analysis of Ideonella and Thermobifida Strains: Dissemination of Biodegradation Potential and Genomic Divergence
    Arockiyajainmary Michealsamy, Saranya Jayapalan · 2025 · Biochemical Genetics
  61. Genomic Markers Distinguishing Shiga Toxin-Producing Escherichia coli: Insights from Pangenome and Phylogenomic Analyses
    Asmaa Elrefaey, Kingsley E. Bentum, Emmanuel Kuufire, Tyric James, Rejoice Nyarku, Viona Osei, Yilkal Asfaw Woube, Temesgen Samuel, Woubit Abebe · 2025 · Pathogens
  62. A comprehensive pangenome approach to exploring the probiotic potential of Weissella confusa
    Md. Saddam Hossain, Shanjana Rahman Tuli, Nigar Fatima, Sobur Ali, Shovan Basak Moon, Abu Hashem · 2025 · The Microbe
  63. Comprehensive Phylogenomic Analyses Support the Reclassification of Multiple Bacteroides Species
    Nawel Zaatout, Taha Menasria, Mabrouka Benhadj · 2025 · Current Microbiology
  64. Genomic comparative analysis of Bradyrhizobium elkanii strains: Exploring the diversity of nod factors
    Igor Daniel Alves Ribeiro, Anderson José Scherer, Manuel Megı́as, Francisco Javier Ollero, Luciane Maria Pereira Passaglia · 2026 · Rhizosphere
  65. The evolutionary genomics of novel endosymbiosis in wild rhizobia bacteria
    Angeliqua P. Montoya, Kyson T. Jensen, Joel S. Griffitts, Stephanie S. Porter · 2026 · Current Biology
  66. Metabolic diversity of Paenibacillus: Pan-genome insights on carbohydrate-active enzymes and biosynthetic gene clusters
    Muhammad Irfanul Islam, Md. Samrat Mohay Menul Islam, Hajara Akhter, Sumaiya Islam Chowdhury, Mohammed Ayaz, Md Murshed Hasan Sarkar, Saiful Islam · 2026 · The Microbe
  67. Comparative genomic analysis of Bacteroides fragilis from intestinal and extra-intestinal sites
    Renee E. Oles, Marvic Carrillo Terrazas, Luke R. Loomis, Simone Zuffa, Maxwell Neal, Chia-Yun Hsu, Adriana Vasquez Ayala, Caitlin Tribelhorn, Pedro Belda‐Ferre, Jianshu Zhao et al. · 2026 · Microbiology Spectrum
  68. How the social lives of bacteria affect their pangenome
    Fiona Whelan · 2026 · Essays in Biochemistry
  69. Genomics and Molecular Phylogenetics Tree Analysis of Actinopolyspora Iraqiensis
    Talal S. Salih, Raghad Riyadh Shafeek · 2021 · Ibn AL- Haitham Journal For Pure and Applied Science
  70. First Record of the Rare Species Aeromonas lusitana from Rainbow Trout (Oncorhynchus mykiss, Walbaum): Comparative Analysis with the Existing Strains
    Ana Fernández-Bravo, Vicente Vega-Sánchez, Alba Pérez‐Cataluña, Fadua Latif-Eugenín, Roxana Beaz‐Hidalgo, Antonio Martı́nez-Murcia, Edgardo Soriano‐Vargas, Omar Alejandro Cabrero-Martínez, Graciela Castro‐Escarpulli, María José Figueras · 2022 · Pathogens
  71. Decoding Ecuadorian Mycobacterium tuberculosis Isolates: Unveiling Lineage-Associated Signatures in Beta-Lactamase Resistance via Pangenome Analysis
    Gabriel Morey-León G, Juan Carlos Fernández‐Cadena, Derly Andrade-Molina, Luisa Berná · 2025 · Biomedicines
  72. Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris
    Hugh Gifford, Duncan Wilson, Johanna L. Rhodes, Rhys A. Farrer · 2025 · Methods in molecular biology
  73. Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA
    Lucy A. Weinert · 2021 · Apollo (University of Cambridge)
  74. A non-adaptive demographic mechanism for genome expansion in Streptomyces
    Mallory J. Choudoir, Marko J Järvenpää, Pekka Marttinen, Daniel H. Buckley · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  75. A systematic investigation of lactic acid bacteria-derived biosynthetic gene clusters reveals diverse antagonistic bacteriocins in the human microbiome
    Dengwei Zhang, Jian Zhang, Shanthini Kalimuthu, Jing Liu, Zhiman Song, Beibei He, Peiyan Cai, Zheng Zhong, Chenchen Feng, Prasanna Neelakantan et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  76. Repeat sequences limit the effectiveness of LGT and favoured the evolution of meiotic sex in early eukaryotes
    Marco Colnaghi, Nick J. Lane, Andrew Pomiankowski · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  77. Variation in the rate lateral gene transfers accumulate in a grass lineage
    Pauline Raimondeau, Matheus E. Bianconi, Lara Pereira, Christian Parisod, Pascal‐Antoine Christin, Luke T. Dunning · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  78. High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons
    Luzia Stalder, M. Maurhofer, Daniel Croll · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  79. Genomic sequencing should extend to diverse priority pathogens for effective study and surveillance of antimicrobial resistance: a systematic review of whole-genome sequencing studies from India
    Nazneen Gheewalla, Jaisri Jagannadham, Rintu Kutum, Shraddha Madhav Karve · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  80. How to measure bacterial genome plasticity? A novel time-integrated index helps gather insights on pathogens
    Greta Bellinzona, Gherard Batisti Biffignandi, Fausto Baldanti, Matteo Brilli, Davide Sassera, Stefano Gaiarsa · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  81. Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer
    Juken Hong, Wenzhi Xue, Teng Wang · 2025 · eLife
  82. 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)
  83. The information content of species: formal definitions of pangenome complexity track with bacterial lifestyle
    Apurva Narechania, Dean Bobo, Marcus Thomas P. Gilbert, Shyam Gopalakrishnan · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  84. Redefining paradigms in the archaeal virus-host arms race
    Laura Martínez-Álvarez, Xu Peng · 2025 · Research Square
  85. Corn rust population genomics reveals a cryptic virulent group and adaptive effectorome
    Yuanjie Li, Peng Zhao, Xiufeng Liu, Clement K. M. Tsui, Daniel Croll, Junmin Liang, Lei Cai · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  86. Endemic dark ocean microbiomes drive carbon cycling in the Southern Ocean
    Thulani Peter Makhalanyane, Oliver K. I. Bezuidt, Diego Castillo, Tiffany du Plessis, Marike Palmer, Philip Hugenholtz · 2025 · Research Square
  87. Mobile genetic elements shape the evolution of wild bacterial pangenomes in the face of biotic and abiotic selective pressures in the soil
    Angeliqua P. Montoya, Hanna Kehlet-Delgado, Kyson T. Jensen, Joel S. Griffitts, Stephanie S. Porter · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  88. The pangenome of Aspergillus fumigatus highlights the dynamics of gene gain-loss over evolutionary timescales in a human fungal pathogen
    Harry Chown, Johanna L. Rhodes, Matthew C Fisher (17773886), Michael Bromley · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  89. Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks
    Samuel Horsfield, Maciej Wiatrak, James O. McInerney, Stephen D. Bentley, Caroline Colijn, John A. Lees · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  90. Comparative Genomic Insights into Pangenome Diversity and Functional Adaptation of Akkermansia and Faecalibacterium as Gut-Associated Next-Generation Probiotics: A Systematic Review
    Arlan, La, Lestari, Rani Dwi, Israyusnita, Fami, Kotala, Sarmawaty, Adi, Noval Wahyu, Sari, Dewi Firda, Hanifah, Zuraidah, Rudiansyah, Rudiansyah, Khasanah, Fazrina, Tukan, Fenty Florentina D. L. et al. · 2026 · F1000Research
  91. Self-organisation and persistence of antibiotic resistance in evolving plasmid communities
    Martin Zwanzig, Uta Berger · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  92. Limited and strain-specific transcriptional and growth responses to acquisition of a multidrug resistance plasmid in genetically diverse Escherichia coli lineages
    Steven J. Dunn, Laura Carrilero, Michael A. Brockhurst, Alan McNally · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  93. Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA
    Marta Matuszewska, Gemma G. R. Murray, Xiaoliang Ba, Rhiannon Wood, Mark A. Holmes, Lucy A. Weinert · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  94. Comparative genomics of Xylella fastidiosa suggests determinants of host-specificity and expands its mobile genetic elements repertoire
    Guillermo Uceda-Campos, Oseias Rodrigues Feitosa-Junior, Caio R. N. Santiago, Paulo Marques Pierry, Paulo A. Zaini, Wesley Oliveira de Santana, Joaquim Martins, Deibs Barbosa, Luciano Antônio Digiampietri, João Carlos Setúbal et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  95. Faculty Opinions recommendation of Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events.
    David S. Stephens, Yih‐Ling Tzeng · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  96. Comparative genomics support reduced-genome Paraburkholderia symbionts of Dictyostelium discoideum amoebas are ancestrally adapted professional symbionts
    Suegene Noh, Benjamin J. Capodanno, Songtao Xu, Marisa C. Hamilton, Joan E. Strassmann, David C. Queller · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  97. Soil microbial dark matter explored from genome-resolved metagenomics
    Bin Ma, Caiyu Lu, Yiling Wang, Jingwen Yu, Kankan Zhao, Ran Xue, Xiaofei Lv, Ronghui Pan, Jiabao Zhang, Yong‐Guan Zhu et al. · 2023 · Research Square
  98. Co-fitness network connectivity determines a fuzzy essential zone in Sinorhizobium of canonical open pangenome
    Pan Zhang, Biliang Zhang, Yuanyuan Ji, Jian Jiao, Ziding Zhang, Chang Fu Tian · 2023 · Research Square
  99. Additional file 1 of A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome
    Dengwei Zhang, Jian Zhang, Shanthini Kalimuthu, Liu, Jing, Zhi‐Man Song, He, Bei-bei, Peiyan Cai, Zheng Zhong, Chenchen Feng, Prasanna Neelakantan et al. · 2023 · Figshare
  100. Additional file 1 of Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China
    Hongbin Chen, Yuyao Yin, Lucy van Dorp, Liam P. Shaw, Gao, Hua, Mislav Acman, Jizhen Yuan, Fengning Chen, Shijun Sun, Xiaojuan Wang et al. · 2021 · Figshare