Coevolution with Bacteriophages Drives Genome-Wide Host Evolution and Constrains the Acquisition of Abiotic-Beneficial Mutations

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,962 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992) · Genetics · doi:10.1093/genetics/131.2.479 · Cited by 13,929 · see citing works

A new method for non-parametric multivariate analysis of variance

Anderson, M. J. (2001) · Austral Ecology · doi:10.1111/j.1442-9993.2001.01070.pp.x · Cited by 13,828 · see citing works

Molecular Evolution and Phylogenetics

Nei, M., & Kumar, S. (2000) · doi:10.1093/oso/9780195135848.001.0001 · Cited by 8,012 · see citing works

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingPreprint

Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,822 · see citing works

A NEW EVOLUTIONARY LAW.

Valen, L. V. (1973) · Medical Entomology and Zoology · Cited by 2,468 · see citing works

THE EVOLUTIONARY ADVANTAGE OF RECOMBINATION

Felsenstein, J. (1974) · Genetics · doi:10.1093/genetics/78.2.737 · Cited by 1,711 · see citing works

Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins

Weinreich, D. M., Delaney, N. F., DePristo, M. A., & Hartl, D. L. (2006) · Science · doi:10.1126/science.1123539 · Cited by 1,418 · see citing works

Sexual reproduction as an adaptation to resist parasites (a review).

Hamilton, W. D. O., Axelrod, R., & Tanese, R. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.9.3566 · Cited by 1,277 · see citing works

Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities

Koskella, B. L., & Brockhurst, M. A. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12072 · Cited by 894 · see citing works

Biological and biomedical implications of the co-evolution of pathogens and their hosts

Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B., & Levin, B. R. (2002) · Nature Genetics · doi:10.1038/ng1202-569 · Cited by 869 · see citing works

The fate of competing beneficial mutations in an asexual population

Gerrish, P. J., & Lenski, R. E. (1998) · Genetica · doi:10.1023/a:1017067816551 · Cited by 783 · see citing works

The fate of competing beneficial mutations in an asexual population

Gerrish, P. J., & Lenski, R. E. (1998) · Contemporary issues in genetics and evolution · doi:10.1007/978-94-011-5210-5_12 · Cited by 721 · see citing works

PERSPECTIVE:SIGN EPISTASIS AND GENETIC CONSTRAINT ON EVOLUTIONARY TRAJECTORIES

Weinreich, D. M., Watson, R. A. R., & Chao, L. (2005) · Evolution · doi:10.1554/04-272 · Cited by 640 · see citing works

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

Khan, A., Dinh, D. M., Schneider, D., Lenski, R. E., & Cooper, T. F. (2011) · Science · doi:10.1126/science.1203801 · Cited by 581 · see citing works

Cyclic Diguanylate Is a Ubiquitous Signaling Molecule in Bacteria: Insights into Biochemistry of the GGDEF Protein Domain

Ryjenkov, D. A., Tarutina, M. G., Moskvin, O. V., & Gomelsky, M. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.5.1792-1798.2005 · Cited by 577 · see citing works

Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage

Bohannan, B. J. M., & Lenski, R. E. (2000) · Ecology Letters · doi:10.1046/j.1461-0248.2000.00161.x · Cited by 560 · see citing works

Antagonistic coevolution accelerates molecular evolution

Paterson, S., Vogwill, T., Buckling, A. G. J., Benmayor, R., Spiers, A. J., Thomson, N. R., Quail, M. A., Smith, F., Walker, D., Libberton, B., et al. (2010) · Nature · doi:10.1038/nature08798 · Cited by 547 · see citing works

The fate of competing beneficial mutations in an asexual population.

Gerrish, P. J., & Lenski, R. E. (1998) · PubMed · Cited by 520 · see citing works

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

Chou, H.-H. D., Chiu, H.-C., Delaney, N. F., Segrè, D., & Marx, C. J. (2011) · Science · doi:10.1126/science.1203799 · Cited by 510 · see citing works

Determining Mutation Rates in Bacterial Populations

Rosche, W. A., & Foster, P. L. (2000) · Methods · doi:10.1006/meth.1999.0901 · Cited by 482 · see citing works

Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex

Morran, L. T., Schmidt, O. G., Gelarden, I. A., Parrish, R. C., & Lively, C. M. (2011) · Science · doi:10.1126/science.1206360 · Cited by 434 · see citing works

Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria–Delbrück fluctuation analysis

Hall, B. M., Ma, C.-X., Liang, P., & Singh, K. K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp253 · Cited by 375 · cited 2× · see citing works

The role of parasites in sympatric and allopatric host diversification

Buckling, A. G. J., & Rainey, P. B. (2002) · Nature · doi:10.1038/nature01164 · Cited by 351 · see citing works

Coevolution with viruses drives the evolution of bacterial mutation rates

Pál, C., Macia, M. D., Oliver, A., Schachar, I. H., & Buckling, A. G. J. (2007) · Nature · doi:10.1038/nature06350 · Cited by 324 · see citing works

Natural Selection Drives Extremely Rapid Evolution in Antiviral RNAi Genes

Obbard, D. J., Jiggins, F. M., Halligan, D. L., & Little, T. J. (2006) · Current Biology · doi:10.1016/j.cub.2006.01.065 · Cited by 311 · see citing works

Host-parasite coevolutionary arms races give way to fluctuating selection

Hall, A. R., Scanlan, P. D., Morgan, A. D., & Buckling, A. G. J. (2011) · Ecology Letters · doi:10.1111/j.1461-0248.2011.01624.x · Cited by 307 · see citing works

The Phage Therapy Paradigm: Prêt-à-Porter or Sur-mesure?

Pirnay, J., Vos, D. D., Verbeken, G., Merabishvili, M., Чанішвілі, Н., Vaneechoutte, M., Zizi, M., Laire, G., Lavigne, R., Huys, I., et al. (2010) · Pharmaceutical Research · doi:10.1007/s11095-010-0313-5 · Cited by 298 · see citing works

Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables

Zapala, M. A., & Schork, N. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609333103 · Cited by 292 · see citing works

Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution

Maisnier‐Patin, S., & Andersson, D. I. (2004) · Research in Microbiology · doi:10.1016/j.resmic.2004.01.019 · Cited by 259 · see citing works

EXPERIMENTAL STUDIES OF PLEIOTROPY AND EPISTASIS INESCHERICHIA COLI. I. VARIATION IN COMPETITIVE FITNESS AMONG MUTANTS RESISTANT TO VIRUS T4

Lenski, R. E. (1988) · Evolution · doi:10.1111/j.1558-5646.1988.tb04149.x · Cited by 258 · see citing works

Evolutionary Genetics of the Major Histocompatibility Complex

Hedrick, P. W. (1994) · The American Naturalist · doi:10.1086/285643 · Cited by 247 · see citing works

Diverse virulence traits underlying different clinical outcomes of Salmonella infection

Fierer, J., & Guiney, D. G. (2001) · Journal of Clinical Investigation · doi:10.1172/jci12561 · Cited by 245 · see citing works

Role of Lipopolysaccharides in Antibiotic Resistance and Bacteriophage Adsorption of Escherichia coli K-12

Tamaki, S., Sato, T., & Matsuhashi, M. (1971) · Journal of Bacteriology · doi:10.1128/jb.105.3.968-975.1971 · Cited by 230 · see citing works

Coevolution: The Geographic Mosaic of Coevolutionary Arms Races

Thompson, J. N. (2005) · Current Biology · doi:10.1016/j.cub.2005.11.046 · Cited by 218 · see citing works

Rapid diversification of coevolving marine Synechococcus and a virus

Marston, M. F., Pierciey, F. J., Shepard, A., Gearin, G., Qi, J., Yandava, C., Schuster, S. C., Henn, M. R., & Martiny, J. B. H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120310109 · Cited by 204 · see citing works

Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage

Qimron, U., Marintcheva, B., Tabor, S., & Richardson, C. C. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609428103 · Cited by 201 · see citing works

Molecular evolution as predicted by natural selection

Valen, L. M. V. (1974) · Journal of Molecular Evolution · doi:10.1007/bf01796554 · Cited by 165 · see citing works

Purification and Visualization of Lipopolysaccharide from Gram-negative Bacteria by Hot Aqueous-phenol Extraction

Michael R. Davis, Jr., & Goldberg, J. B. (2012) · Journal of Visualized Experiments · doi:10.3791/3916 · Cited by 163 · see citing works

Experimental Studies of Pleiotropy and Epistasis in Escherichia coli. I. Variation in Competitive Fitness Among Mutants Resistant to Virus T4

Lenski, R. E. (1988) · Evolution · doi:10.2307/2409028 · Cited by 153 · see citing works

The effect of spatial heterogeneity and parasites on the evolution of host diversity

Brockhurst, M. A., Rainey, P. B., & Buckling, A. G. J. (2004) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2003.2556 · Cited by 151 · see citing works

Negative Control of Flagellum Synthesis in Pseudomonas aeruginosa Is Modulated by the Alternative Sigma Factor AlgT (AlgU)

Garrett, E. S., Perlegas, D., & Wozniak, D. J. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.23.7401-7404.1999 · Cited by 144 · see citing works

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli

Plucain, J., Hindré, T., Gac, M. L., Tenaillon, O., Cruveiller, S., Médigue, C., Leiby, N., Harcombe, W. R., Marx, C. J., Lenski, R. E., et al. (2014) · Science · doi:10.1126/science.1248688 · Cited by 128 · see citing works

Bacteria‐Phage Coevolution and the Emergence of Generalist Pathogens

Hall, A. R., Scanlan, P. D., & Buckling, A. (2010) · The American Naturalist · doi:10.1086/657441 · Cited by 126 · see citing works

Septal Localization of FtsQ, an Essential Cell Division Protein in Escherichia coli

Chen Joseph, C., Weiss, D. S., Ghigo, J., & Beckwith, J. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.2.521-530.1999 · Cited by 126 · see citing works

Chromosomal DNA deletion confers phage resistance to Pseudomonas aeruginosa

Le, S., Yao, X., Lu, S., Tan, Y., Rao, X., Li, M., Jin, X., Wang, J., Zhao, Y., Wu, N. C., et al. (2014) · Scientific Reports · doi:10.1038/srep04738 · Cited by 115 · see citing works

Co-evolution with lytic phage selects for the mucoid phenotype of Pseudomonas fluorescens SBW25

Scanlan, P. D., & Buckling, A. G. J. (2011) · The ISME Journal · doi:10.1038/ismej.2011.174 · Cited by 114 · see citing works

Quantifying Fitness and Gene Stability in Microorganisms

Lenski, R. E. (1991) · Elsevier eBooks · doi:10.1016/b978-0-409-90199-3.50015-2 · Cited by 112 · see citing works

Genetic basis of infectivity evolution in a bacteriophage

Scanlan, P. D., Hall, A. R., LOPEZ‐PASCUA, L. D. C., & Buckling, A. G. J. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04903.x · Cited by 107 · see citing works

Antagonistic coevolution with parasites increases the cost of host deleterious mutations

Buckling, A. G. J., Wei, Y., Massey, R. C., Brockhurst, M. A., & Hochberg, M. (2005) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2005.3279 · Cited by 107 · see citing works

Multiple promoters and induction by heat shock of the gene encoding the alternative sigma factor AlgU (sigma E) which controls mucoidy in cystic fibrosis isolates of Pseudomonas aeruginosa

Schurr, M. J., Yu, H. D., Boucher, J. C., Hibler, N. S., & Deretic, V. P. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.19.5670-5679.1995 · Cited by 105 · see citing works

The Coupon Collector and the Suppressor Mutation

Poon, A. F. Y., Davis, B., & Chao, L. (2005) · Genetics · doi:10.1534/genetics.104.037259 · Cited by 99 · see citing works

The Lipopolysaccharide of Bordetella bronchiseptica Acts as a Protective Shield against Antimicrobial Peptides

Banemann, A., Deppisch, H., & Gross, R. (1998) · Infection and Immunity · doi:10.1128/iai.66.12.5607-5612.1998 · Cited by 97 · see citing works

The Wzz (Cld) Protein in Escherichia coli : Amino Acid Sequence Variation Determines O-Antigen Chain Length Specificity

Franco, A. V., Liu, D., & Reeves, P. R. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.10.2670-2675.1998 · Cited by 96 · see citing works

Evolution of Pseudomonas aeruginosa Virulence as a Result of Phage Predation

Hosseinidoust, Z., van de Ven, T. G. M., & Tufenkji, N. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01421-13 · Cited by 71 · see citing works

PARALLEL CHANGES IN HOST RESISTANCE TO VIRAL INFECTION DURING 45,000 GENERATIONS OF RELAXED SELECTION

Meyer, J. R., Agrawal, A. A., Quick, R. T., Dobias, D. T., Schneider, D., & Lenski, R. E. (2010) · Evolution · doi:10.1111/j.1558-5646.2010.01049.x · Cited by 63 · see citing works

Antagonistic coevolution limits population persistence of a virus in a thermally deteriorating environment

Zhang, Q., & Buckling, A. (2011) · Ecology Letters · doi:10.1111/j.1461-0248.2010.01586.x · Cited by 60 · see citing works

Deletion of theparA(soj) Homologue inPseudomonas aeruginosaCauses ParB Instability and Affects Growth Rate, Chromosome Segregation, and Motility

Lasocki, K., Bartosik, A. A., Mierzejewska, J., Thomas, C. M., & Jagura‐Burdzy, G. (2007) · Journal of Bacteriology · doi:10.1128/jb.00371-07 · Cited by 60 · see citing works

Selection on non‐social traits limits the invasion of social cheats

Morgan, A. D., Quigley, B. J. Z., Brown, S. P., & Buckling, A. G. J. (2012) · Ecology Letters · doi:10.1111/j.1461-0248.2012.01805.x · Cited by 59 · see citing works

Ongoing Phenotypic and Genomic Changes in Experimental Coevolution of RNA Bacteriophage Qβ and Escherichia coli

Kashiwagi, A., & Yomo, T. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002188 · Cited by 54 · see citing works

GGDEF and EAL proteins play different roles in the control of Sinorhizobium meliloti growth, motility, exopolysaccharide production, and competitive nodulation on host alfalfa

Wang, Y., Xu, J., Chen, A., Wang, Y., Zhu, J., Yu, G., Xu, L., & Luo, L. (2010) · Acta Biochimica et Biophysica Sinica · doi:10.1093/abbs/gmq034 · Cited by 33 · see citing works

Purification and Visualization of Lipopolysaccharide from Gram-negative Bacteria by Hot Aqueous-phenol Extraction

Davis, M. R., & Goldberg, J. B. (2012) · Journal of Visualized Experiments · doi:10.3791/3916-v · Cited by 31 · see citing works

Rapid degradation of bacteriophage λ O protein by ClpP/ClpX protease influences the lysis-versus-lysogenization decision of the phage under certain growth conditions of the host cells

Czyż, A., Zielke, R. A., & Węgrzyn, G. (2001) · Archives of Virology · doi:10.1007/s007050170073 · Cited by 10 · see citing works

Synergistic interaction between phage therapy and antibiotics clears Pseudomonas aeruginosa infection in endocarditis and reduces virulence

Oechslin, F., Piccardi, P., Mancini, S., Gabard, J., Moreillon, P., Entenza, J. M., Resch, G., & Que, Y. (2016) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiw632 · Cited by 327 · see citing works

Pleiotropy complicates a trade-off between phage resistance and antibiotic resistance

Burmeister, A. R., Fortier, A. V., Roush, C., Lessing, A. J., Bender, R. G., Barahman, R., Grant, R. S., Chan, B. K., & Turner, P. E. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1919888117 · Cited by 288 · see citing works

The Human Gut Phage Community and Its Implications for Health and Disease

Manrique, P., Dills, M., & Young, M. (2017) · Viruses · doi:10.3390/v9060141 · Cited by 253 · see citing works

Framing the Future with Bacteriophages in Agriculture

Svircev, A. M., Roach, D. R., & Castle, A. J. (2018) · Viruses · doi:10.3390/v10050218 · Cited by 252 · see citing works

Evolutionary Ecology of Prokaryotic Immune Mechanisms

van Houte, S., Buckling, A., & Westra, E. R. (2016) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00011-16 · Cited by 243 · see citing works

The Significance of Mutualistic Phages for Bacterial Ecology and Evolution

Obeng, N., Pratama, A. A., & van Elsas, J. D. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2015.12.009 · Cited by 209 · see citing works

Pseudomonas predators: understanding and exploiting phage–host interactions

Smet, J. D., Hendrix, H., Blasdel, B. G., Danis-Wlodarczyk, K. M., & Lavigne, R. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.61 · Cited by 202 · see citing works

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

den Bergh, B. V., Swings, T., Fauvart, M., & Michiels, J. J. (2018) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00008-18 · Cited by 180 · see citing works

Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery

McDonald, M. J. (2019) · EMBO Reports · doi:10.15252/embr.201846992 · Cited by 165 · see citing works

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

Huang, D., Yu, P., Ye, M., Schwarz, C., Jiang, X., & Alvarez, P. J. J. (2021) · Microbiome · doi:10.1186/s40168-021-01074-1 · Cited by 167 · see citing works

Resistance Evolution against Phage Combinations Depends on the Timing and Order of Exposure

Wright, R. C. T., Friman, V., Smith, M. C. M., & Brockhurst, M. A. (2019) · mBio · doi:10.1128/mbio.01652-19 · Cited by 152 · see citing works

Evolutionary Dynamics between Phages and Bacteria as a Possible Approach for Designing Effective Phage Therapies against Antibiotic-Resistant Bacteria

Hasan, M., & Ahn, J. (2022) · Antibiotics · doi:10.3390/antibiotics11070915 · Cited by 144 · see citing works

Cross-resistance is modular in bacteria–phage interactions

Wright, R. C. T., Friman, V., Smith, M. C. M., & Brockhurst, M. A. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2006057 · Cited by 139 · see citing works

rSalvador: An R Package for the Fluctuation Experiment

Zheng, Q. (2017) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.117.300120 · Cited by 98 · see citing works

Bacteria–Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality

Scanlan, P. D. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.02.012 · Cited by 115 · see citing works

Phage Therapy in the Twenty-First Century: Facing the Decline of the Antibiotic Era; Is It Finally Time for the Age of the Phage?

Hesse, S. E., & Adhya, S. L. (2019) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090817-062535 · Cited by 110 · see citing works

Pre‐adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates

Friman, V., Soanes‐Brown, D., Sierocinski, P., Molin, S., Johansen, H. K., Merabishvili, M., Pirnay, J., Vos, D. D., & Buckling, A. G. J. (2015) · Journal of Evolutionary Biology · doi:10.1111/jeb.12774 · Cited by 106 · see citing works

Effects of single and combined use of bacteriophages and antibiotics to inactivate Escherichia coli

Valério, N., Oliveira, C., Jesus, V. I. R., Branco, T. M., Pereira, C., Moreirinha, C., & Almeida, A. (2017) · Virus Research · doi:10.1016/j.virusres.2017.07.015 · Cited by 105 · see citing works

The evolutionary trade‐offs in phage‐resistant Klebsiella pneumoniae entail cross‐phage sensitization and loss of multidrug resistance

Majkowska-Skrobek, G., Markwitz, P., Sosnowska, E., Lood, C., Lavigne, R., & Drulis‐Kawa, Z. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15476 · Cited by 92 · see citing works

Functions of the Microbiota for the Physiology of Animal Metaorganisms

Esser, D., Lange, J., Μαρίνος, Γ., Sieber, M., Best, L., Prasse, D., Bathia, J., Rühlemann, M. C., Boersch, K., Jaspers, C., et al. (2018) · Journal of Innate Immunity · doi:10.1159/000495115 · Cited by 90 · see citing works

Recent progress toward the implementation of phage therapy in Western medicine

Pirnay, J., Ferry, T., & Resch, G. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab040 · Cited by 87 · see citing works

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

Gómez, P., Paterson, S., Meester, L. D., Liu, X., Lenzi, L., Sharma, M. D., McElroy, K., & Buckling, A. G. J. (2016) · Nature Communications · doi:10.1038/ncomms12453 · Cited by 82 · see citing works

Sequential Combined Effect of Phages and Antibiotics on the Inactivation of Escherichia coli

Lopes, A. S., Pereira, C., & Almeida, A. (2018) · Microorganisms · doi:10.3390/microorganisms6040125 · Cited by 81 · see citing works

Competitive species interactions constrain abiotic adaptation in a bacterial soil community

Hall, J. P. J., Harrison, E., & Brockhurst, M. A. (2018) · Evolution Letters · doi:10.1002/evl3.83 · Cited by 79 · see citing works

Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP

Yoshimura, D., Kajitani, R., Gotoh, Y., Katahira, K., Okuno, M., Ogura, Y., Hayashi, T., & Itoh, T. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000261 · Cited by 71 · see citing works

Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota

Bonilla‐Rosso, G., Steiner, T., Wichmann, F., Bexkens, E., & Engel, P. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2000228117 · Cited by 68 · see citing works

The interaction of phages and bacteria: the co-evolutionary arms race

Safari, F., Sharifi, M., Farajnia, S., Akbari, B., Ahmadi, M. K. B., Negahdaripour, M., & Ghasemi, Y. (2019) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2019.1674774 · Cited by 69 · see citing works

Multistep diversification in spatiotemporal bacterial-phage coevolution

Tamar, E. S., & Kishony, R. (2022) · Nature Communications · doi:10.1038/s41467-022-35351-w · Cited by 68 · see citing works

Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa

Latino, L., Midoux, C., Hauck, Y., Vergnaud, G., & Pourcel, C. (2016) · Microbiology · doi:10.1099/mic.0.000263 · Cited by 68 · see citing works

Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs

Wang, X., Wei, Z., Li, M., Wang, X., Shan, A., Mei, X., Jousset, A., Shen, Q., Xu, Y., & Friman, V. (2016) · Evolution · doi:10.1111/evo.13143 · Cited by 56 · see citing works

Microbial evolution and ecological opportunity in the gut environment

Scanlan, P. D. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.1964 · Cited by 54 · see citing works

A role for bacterial experimental evolution in coral bleaching mitigation?

Maire, J., & van Oppen, M. J. H. (2021) · Trends in Microbiology · doi:10.1016/j.tim.2021.07.006 · Cited by 54 · see citing works

Experimental evolution and bacterial resistance: (co)evolutionary costs and trade-offs as opportunities in phage therapy research

Scanlan, P. D., Buckling, A. G. J., & Hall, A. R. (2015) · Bacteriophage · doi:10.1080/21597081.2015.1050153 · Cited by 54 · see citing works

Long‐term effects of single and combined introductions of antibiotics and bacteriophages on populations of Pseudomonas aeruginosa

Barceló, C. T., Franzon, B., Vasse, M., & Hochberg, M. (2016) · Evolutionary Applications · doi:10.1111/eva.12364 · Cited by 54 · see citing works

Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli

Maddamsetti, R., Hatcher, P. J., Green, A. G., Williams, B. L., Marks, D. S., & Lenski, R. E. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx064 · Cited by 53 · see citing works

Coevolutionary dynamics shape the structure of bacteria‐phage infection networks

Fortuna, M. A., Barbour, M. A., Zaman, L., Hall, A. R., Buckling, A. G. J., & Bascompte, J. (2019) · Evolution · doi:10.1111/evo.13731 · Cited by 52 · see citing works

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

Braga, L. P. P., Soucy, S. M., Amgarten, D., da Silva, A. M., & Setúbal, J. C. (2018) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2018.00006 · Cited by 49 · see citing works

A phage tail–like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria

Backman, T., Latorre, S. M., Symeonidi, E., Muszyński, A., Bleak, E., Eads, L., Martinez-Koury, P. I., Som, S., Hawks, A., Gloss, A. D., et al. (2024) · Science · doi:10.1126/science.ado0713 · Cited by 48 · see citing works

Dissecting the genetic architecture of a stepwise infection process

Hall, M. D., Routtu, J., & Ebert, D. (2019) · Molecular Ecology · doi:10.1111/mec.15166 · Cited by 46 · see citing works

Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution

Cairns, J., Becks, L., Jalasvuori, M., & Hiltunen, T. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2016.0040 · Cited by 46 · see citing works

Network structure and local adaptation in co‐evolving bacteria–phage interactions

Gurney, J., Aldakak, L., Betts, A., Gougat‐Barbera, C., Poisot, T., Kaltz, O., & Hochberg, M. (2017) · Molecular Ecology · doi:10.1111/mec.14008 · Cited by 43 · see citing works

Genetic hurdles limit the arms race betweenProchlorococcusand the T7-like podoviruses infecting them

Schwartz, D. A., & Lindell, D. (2017) · The ISME Journal · doi:10.1038/ismej.2017.47 · Cited by 42 · see citing works

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Näpflin, K., O'Connor, E., Becks, L., Bensch, S., Ellis, V. A., Hafer-Hahmann, N., Harding, K., Lindén, S. K., Olsen, M. T., Roved, J., et al. (2019) · PeerJ · doi:10.7717/peerj.8013 · Cited by 30 · see citing works

How to Train Your Phage: The Recent Efforts in Phage Training

Abdelsattar, A. S., Dawoud, A., Rezk, N., Makky, S., Safwat, A., Richards, P., & El‐Shibiny, A. (2021) · Biologics · doi:10.3390/biologics1020005 · Cited by 42 · see citing works

Ecological conditions determine extinction risk in co-evolving bacteria-phage populations

Wright, R. C. T., Brockhurst, M. A., & Harrison, E. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0808-8 · Cited by 41 · see citing works

Specific adaptation to strong competitors can offset the negative effects of population size reductions

Zhao, X., Buckling, A. G. J., Zhang, Q., & Hesse, E. (2018) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.0007 · Cited by 36 · see citing works

Bacteriocins and the assembly of natural Pseudomonas fluorescens populations

Bruce, J. B., West, S. A., & Griffin, A. S. (2016) · Journal of Evolutionary Biology · doi:10.1111/jeb.13010 · Cited by 35 · see citing works

A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens

Mutalik, V. K., & Arkin, A. P. (2022) · iScience · doi:10.1016/j.isci.2022.104121 · Cited by 32 · see citing works

A new practical guide to the Luria–Delbrück protocol

Zheng, Q. (2015) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2015.08.005 · Cited by 34 · see citing works

Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria

Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv270 · Cited by 33 · see citing works

Resistance gained, resistance lost: An explanation for host–parasite coexistence

Koskella, B. L. (2018) · PLoS Biology · doi:10.1371/journal.pbio.3000013 · Cited by 31 · see citing works

Evolutionary contribution to coexistence of competitors in microbial food webs

Hiltunen, T., Kaitala, V., Laakso, J., & Becks, L. (2017) · Proceedings of the Royal Society of London. Biological Sciences · doi:10.1098/rspb.2017.0415 · Cited by 32 · see citing works

Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae)

Smith, C. H., Pfeiffer, J. M., & Johnson, N. A. (2020) · Cladistics · doi:10.1111/cla.12423 · Cited by 26 · see citing works

Host Resistance, Genomics and Population Dynamics in a Salmonella Enteritidis and Phage System

Holguín, A. V., Cárdenas, P., Prada-Peñaranda, C., Leite, L. R., Buitrago, C. A., Clavijo, V., Oliveira, G., Leekitcharoenphon, P., Aarestrup, F. M., & Vives, M. J. (2019) · Viruses · doi:10.3390/v11020188 · Cited by 26 · see citing works

Experimental evolution can unravel the complex causes of natural selection in clinical infections

Brockhurst, M. A. (2015) · Microbiology · doi:10.1099/mic.0.000107 · Cited by 25 · see citing works

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction

Harrison, E., Hall, J. P. J., Paterson, S., Spiers, A. J., & Brockhurst, M. A. (2017) · Molecular Ecology · doi:10.1111/mec.14080 · Cited by 25 · see citing works

Impact of bile salts on coevolutionary dynamics between the gut bacterium Escherichia coli and its lytic phage PP01

Scanlan, J., Hall, A. R., & Scanlan, P. D. (2019) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2019.05.021 · Cited by 25 · see citing works

Genomic evolution of bacterial populations under coselection by antibiotics and phage

Cairns, J., Frickel, J., Jalasvuori, M., Hiltunen, T., & Becks, L. (2016) · Molecular Ecology · doi:10.1111/mec.13950 · Cited by 25 · see citing works

Coping with multiple enemies: pairwise interactions do not predict evolutionary change in complex multitrophic communities

McClean, D., Friman, V., Finn, A., Salzberg, L. I., & Donohue, I. (2019) · Oikos · doi:10.1111/oik.06586 · Cited by 24 · see citing works

Resistance evolution can disrupt antibiotic exposure protection through competitive exclusion of the protective species

Quinn, A., Bottery, M. J., Thompson, H., & Friman, V. (2022) · The ISME Journal · doi:10.1038/s41396-022-01285-w · Cited by 25 · see citing works

Plasmid carriage can limit bacteria–phage coevolution

Harrison, E., Truman, J., Wright, R. C. T., Spiers, A. J., Paterson, S., & Brockhurst, M. A. (2015) · Biology Letters · doi:10.1098/rsbl.2015.0361 · Cited by 23 · see citing works

Phage resistance-mediated trade-offs with antibiotic resistance in Salmonella Typhimurium

Laure, N. N., & Ahn, J. (2022) · Microbial Pathogenesis · doi:10.1016/j.micpath.2022.105732 · Cited by 22 · see citing works

Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

Klimenko, A. I., Matushkin, Y. G., Kolchanov, N. A., & Lashin, S. A. (2016) · BMC Microbiology · doi:10.1186/s12866-015-0620-4 · Cited by 22 · see citing works

Genotype‐by‐genotype interactions between an insect and its pathogen

Hudson, A. I., Fleming-Davies, A. E., Páez, D. J., & Dwyer, G. (2016) · Journal of Evolutionary Biology · doi:10.1111/jeb.12977 · Cited by 22 · see citing works

Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness

Xu, Z., Ding, Z., Shi, L., Xie, Y., Zhang, Y., Wang, Z., & Liu, Q. (2023) · The ISME Journal · doi:10.1038/s41396-023-01529-3 · Cited by 21 · see citing works

Phage-driven coevolution reveals trade-off between antibiotic and phage resistance in Salmonella anatum

Zhao, Y., Shu, M., Zhang, L., Zhong, C., Liao, N., & Wu, G. (2024) · ISME Communications · doi:10.1093/ismeco/ycae039 · Cited by 20 · see citing works

Challenges of bacteriophages application in controlling bacterial plant diseases and how to overcome them

Halawa, E. M. (2023) · Journal of Genetic Engineering and Biotechnology · doi:10.1186/s43141-023-00549-y · Cited by 19 · see citing works

Multiyear Time-Shift Study of Bacteria and Phage Dynamics in the Phyllosphere

Dewald-Wang, E. A., Parr, N., Tiley, K., Lee, A., & Koskella, B. L. (2021) · The American Naturalist · doi:10.1086/717181 · Cited by 19 · see citing works

Evolution of honey resistance in experimental populations of bacteria depends on the type of honey and has no major side effects for antibiotic susceptibility

Bischofberger, A. M., Pfrunder‐Cardozo, K. R., Baumgartner, M., & Hall, A. R. (2021) · Evolutionary Applications · doi:10.1111/eva.13200 · Cited by 17 · see citing works

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

Warwick-Dugdale, J., Tian, F., Michelsen, M. L., Cronin, D. R., Moore, K., Farbos, A., Chittick, L., Bell, A. G., Zayed, A. A., Buchholz, H. H., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48300-6 · Cited by 15 · see citing works

Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment

Baumgartner, M., Roffler, S., Wicker, T., & Pernthaler, J. (2017) · The ISME Journal · doi:10.1038/ismej.2017.87 · Cited by 15 · see citing works

Parasite host range and the evolution of host resistance

Gorter, F. A., Hall, A. R., Buckling, A. G. J., & Scanlan, P. D. (2015) · Journal of Evolutionary Biology · doi:10.1111/jeb.12639 · Cited by 13 · see citing works

Resource‐dependent antagonistic coevolution leads to a new paradox of enrichment

Zhang, Q., & Buckling, A. G. J. (2016) · Ecology · doi:10.1890/15-1408.1 · Cited by 12 · see citing works

Protistan predation interferes with bacterial long‐term adaptation to substrate restriction by selecting for defence morphotypes

Baumgartner, M., Neu, T. R., Blom, J. F., & Pernthaler, J. (2016) · Journal of Evolutionary Biology · doi:10.1111/jeb.12957 · Cited by 11 · see citing works

Parasite genetic distance and local adaptation in co‐evolving bacteria–bacteriophage populations

Scanlan, P. D., Hall, A. R., & Buckling, A. G. J. (2016) · Molecular Ecology · doi:10.1111/mec.13897 · Cited by 9 · see citing works

Microbiota in drug resistance

Jia, R. F., Xiao, C., Zhang, Y., Hu, L.-Y., Jun-jun, Y., Zuo, R., Hu, Y., Xie, Y.-H., Ma, X., Li, Q., et al. (2025) · Drug Resistance Updates · doi:10.1016/j.drup.2025.101311 · Cited by 8 · see citing works

Hidden paths to endless forms most wonderful: parasite-blind diversification of host quality

Freund, L., Vasse, M., & Velicer, G. J. (2021) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2021.0456 · Cited by 7 · see citing works

Ecological partitioning enables phage–antibiotic cooperation in a human Pseudomonas infection

Luong, T., Kharrat, L., Champagne-Jorgensen, K. P., Melendez, J. A., Pride, D. T., Conrad, D. J., & Roach, D. R. (2026) · Nature Communications · doi:10.1038/s41467-026-69247-w · Cited by 9 · see citing works

Dip-a-Dee-Doo-Dah: Bacteriophage-Mediated Rescoring of a Harmoniously Orchestrated RNA Metabolism

Dendooven, T., & Lavigne, R. (2019) · Annual Review of Virology · doi:10.1146/annurev-virology-092818-015644 · Cited by 7 · see citing works

Localised genetic heterogeneity provides a novel mode of evolution in dsDNA phages

Magill, D., Kucher, P. A., Krylov, V. N., Pleteneva, E. A., Quinn, J. P., & Kulakov, L. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-14285-0 · Cited by 7 · see citing works

Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing

Zhou, W., Li, Y., Li, Z., Ma, B., Jiang, X., Hu, C., Ai, Y., & Luo, P. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.710262 · Cited by 5 · see citing works

Fight Not Flight: Parasites Drive the Bacterial Evolution of Resistance, Not Escape

Blazanin, M., Moore, J. P., Olsen, S., & Travisano, M. (2024) · The American Naturalist · doi:10.1086/733414 · Cited by 5 · see citing works

Two Lytic Bacteriophages That Depend on the Escherichia coli Multi-Drug Efflux Gene tolC and Differentially Affect Bacterial Growth and SelectionPreprint

Burmeister, A. R., Bender, R. G., Fortier, A. V., Lessing, A. J., Chan, B. K., & Turner, P. E. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/397695 · Cited by 5 · see citing works

Synergistic coevolution accelerates genome evolutionPreprint

Preußger, D., Herbig, A., & Kost, C. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.19.444833 · Cited by 5 · see citing works

Phylogeny-agnostic strain-level prediction of phage-host interactions from genomesPreprint

Noonan, A. J. C., Morinière, L., Rivera-Lopez, E. O., Patel, K., Pena, M., Svab, M., Kazakov, A. E., Deutschbauer, A. M., Dudley, E. G., Mutalik, V. K., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.15.688630 · Cited by 5 · see citing works

Comparative genomic analysis of gene clusters of Pseudomonas aeruginosa that define specific biofilm formation in deciphering target regions for novel treatment options

Ambutsi, M., Reva, O., & OKOTH, P. K. (2021) · Scientific African · doi:10.1016/j.sciaf.2021.e00910 · Cited by 4 · see citing works

Molecular Detection and Identification of Pathogens, Pathotypes, and Genes

Saharan, G. S., Mehta, N. K., & Meena, P. D. (2023) · Springer eBooks · doi:10.1007/978-981-19-3812-2_4 · Cited by 4 · see citing works

Source-sink migration of natural enemies drives maladaptation of victim populations in sink habitats

Chu, X., Buckling, A. G. J., & Zhang, Q. (2023) · Evolution · doi:10.1093/evolut/qpad099 · Cited by 2 · see citing works

Comparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogen Pseudomonas aeruginosa

Deery, J., Carmody, M., Flavin, R., Tomanek, M., O'Keeffe, M., McGlacken, G. P., & Reen, F. J. (2024) · Microbial Genomics · doi:10.1099/mgen.0.001205 · Cited by 2 · see citing works

Phage therapy for One Health approach: current status, challenges and opportunities

Wei, Z., Wang, X., Ma, Y., Mao, Y. E., Xu, Y., Shen, Q., & Zhu, Y. (2022) · Scientia Sinica Vitae · doi:10.1360/ssv-2021-0402 · Cited by 2 · see citing works

Enhanced Antibacterial Activity of a Novel Phage-Antibiotic Combination Against Klebsiella pneumoniae Isolates

Lew, B. Y. X., Njondimackal, N. L., Ravisankar, V., & Ayuni, N. N. (2023) · Springer eBooks · doi:10.1007/978-981-99-8369-8_24 · Cited by 2 · see citing works

Pleiotropic Costs of Phage Resistance

Abedon, S. T. (2022) · Springer eBooks · doi:10.1007/978-3-030-94309-7_22 · Cited by 2 · see citing works

Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development in Vibrio anguillarumPreprint

Chen, L., Middelboe, M., & Svenningsen, S. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.28.630609 · Cited by 2 · see citing works

Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning

Noonan, A. J. C., Morinière, L., Rivera-Lopez, E. O., Patel, K., Pena, M., Svab, M., Kazakov, A. E., Deutschbauer, A. M., Dudley, E. G., Mutalik, V. K., et al. (2026) · Nature Microbiology · doi:10.1038/s41564-026-02482-5 · Cited by 1 · see citing works

Biofilm and Chronic Typhoid Carriers with Special Reference to Bacteriophage Therapy

Nath, G., Yadav, V. B., & Singh, S. K. (2022) · JOURNAL OF GASTROINTESTINAL INFECTIONS · doi:10.5005/jp-journals-10068-3053 · Cited by 1 · see citing works

Prokaryotic Viruses: Intriguing Players in the Aquatic Realm

Schweichhart, J. S. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-819166-8.00106-7 · Cited by 1 · see citing works

Source-sink migration of natural enemies drives local maladaptation of victim populations in edge habitatsPreprint

Chu, X., Buckling, A. G. J., & Zhang, Q. (2022) · doi:10.22541/au.165123938.89441744/v1 · Cited by 1 · see citing works

Environment-dependent evolution drives divergent adaptive strategies balancing parasite costs and competitive benefitsPreprint

Lungu, T. S., Badruna, L., & Rendueles, O. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.17.694638 · Cited by 1 · see citing works

Molecular basis of cyanphage resistance in marine Synechococcus

Perez-Sepulveda, B. M. (2015)

Understanding the structure and dynamics of bacteria-phage infection networks

Wright, R. C. T. (2018) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)

Genomic and phenotypic signatures of bacteriophage coevolution with the phytopathogen Pseudomonas syringae

Hernandez, C. A., Delesalle, V. A., Krukonis, G. P., DeCurzio, J. M., & Koskella, B. L. (2023) · Molecular Ecology · doi:10.1111/mec.16850 · Cited by 7 · see citing works

Greater Phage Genotypic Diversity Constrains Arms-Race Coevolution

Castledine, M., Sierocinski, P., Inglis, M., Kay, S., Hayward, A., Buckling, A. G. J., & Padfield, D. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.834406 · Cited by 17 · see citing works

Antagonistic coevolution with parasites increases the cost of host deleterious mutations

Buckling, A. G. J., Wei, Y., Massey, R. C., Brockhurst, M. A., & Hochberg, M. (2005) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2005.3279 · Cited by 107 · see citing works

IMPACT OF BACTERIAL MUTATION RATE ON COEVOLUTIONARY DYNAMICS BETWEEN BACTERIA AND PHAGES

Morgan, A. D., Bonsall, M. B., & Buckling, A. G. J. (2010) · Evolution · doi:10.1111/j.1558-5646.2010.01037.x · Cited by 35 · see citing works

Phage-induced diversification improves host evolvability

Williams, H. T. P. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-17 · Cited by 77 · see citing works