Research outputs
Selected research outputs
- Introduction: the secret lives of microbial mobile genetic elements (Journal article - 2022)
- Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation (Journal article - 2021)
- Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways (Journal article - 2020)
- Competitive species interactions constrain abiotic adaptation in a bacterial soil community (Journal article - 2018)
- Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities (Journal article - 2016)
2026
Revealing Functional Traits of Insect Pest Suppressive Rhizobacterial Strains Through Comparative Genomics
Cairns, E. C., Del Carratore, F., Hall, J. P. J., & Zytynska, S. E. (2026). Revealing Functional Traits of Insect Pest Suppressive Rhizobacterial Strains Through Comparative Genomics. ENVIRONMENTAL MICROBIOLOGY, 28(9), 19 pages. doi:10.1111/1462-2920.70409
Invasive plasmids as ecosystem engineers-from mechanism to application
Garland, S., Orr, V. T., Hall, J. P. J., & Harrison, E. (2026). Invasive plasmids as ecosystem engineers-from mechanism to application. ESSAYS IN BIOCHEMISTRY, 70(3), 461-472. doi:10.1042/EBC20250040
Distinct bacterial hosts, shared blaOXA-48 plasmid backbones: longitudinal comparative genomics of carbapenemase-producing Enterobacterales from hospital wastewater, biofilms and patients
Fungicide Drives De Novo Evolution of Multidrug Resistance in the Plant Growth Promoting Rhizobacterium, Pseudomonas fluorescens
Kelbrick, M., Hall, J. P. J., & O'Brien, S. (2026). Fungicide Drives De Novo Evolution of Multidrug Resistance in the Plant Growth Promoting Rhizobacterium, Pseudomonas fluorescens. EVOLUTIONARY APPLICATIONS, 19(8), 11 pages. doi:10.1111/eva.70307
The interplay between ecological networks drives host-plasmid community dynamics
Wang, Y. -J., Schaal, K. A., Nauta, J., Liaghat, A., De Domenico, M., Hall, J. P. J., & Pilosof, S. (2026). The interplay between ecological networks drives host-plasmid community dynamics. PLOS COMPUTATIONAL BIOLOGY, 22(5), 24 pages. doi:10.1371/journal.pcbi.1014339
Fungicide drives <i>de novo</i> evolution of multidrug resistance in the plant growth promoting rhizobacterium, <i>Pseudomonas fluorescens</i>
The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements
Fungicide and warming interact to reduce soil ecosystem functioning
Kelbrick, M., McEntagart, J., McCartney, J., Cairns, E., Paterson, S., Zytynska, S. E., . . . O’Brien, S. (2026). Fungicide and warming interact to reduce soil ecosystem functioning. Isme Journal, 20(1). doi:10.1093/ismejo/wrag196
The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements
Orr, V. T., Harrison, E., Rivett, D. W., Wright, R. C. T., & Hall, J. P. J. (2026). The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements. Microbial Genomics, 12(7). doi:10.1099/mgen.0.001789
2025
The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens
McCallum, G. E., & Hall, J. P. J. (2025). The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens. NPJ ANTIMICROBIALS AND RESISTANCE, 3(1), 8 pages. doi:10.1038/s44259-025-00137-9
Species interactions determine plasmid persistence in a 3-member bacterial community
2024
Nutrient-rich spatial refuges buffer against extinction and promote evolutionary rescue in evolving microbial populations
Kelbrick, M., Fenton, A., Parratt, S., Hall, J. P. J., & O'Brien, S. (2024). Nutrient-rich spatial refuges buffer against extinction and promote evolutionary rescue in evolving microbial populations. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 291(2036), 10 pages. doi:10.1098/rspb.2024.2197
A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation.
Wright, R. C. T., Wood, A. J., Bottery, M. J., Muddiman, K. J., Paterson, S., Harrison, E., . . . Hall, J. P. J. (2024). A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation.. PLoS biology, 22(12), e3002926. doi:10.1371/journal.pbio.3002926
Loading and unloading plasmid cargoes
Hall, J. P. J. (2024). Loading and unloading plasmid cargoes. TRENDS IN MICROBIOLOGY, 32(12), 1150-1152. doi:10.1016/j.tim.2024.09.012
Exploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo
Fothergill, J., Kadioglu, A., & Hall, J. (2024). Exploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo. Nature Communications.
Multi-layered genome defences in bacteria.
Agapov, A., Baker, K. S., Bedekar, P., Bhatia, R. P., Blower, T. R., Brockhurst, M. A., . . . Wright, R. (2024). Multi-layered genome defences in bacteria.. Current opinion in microbiology, 78, 102436. doi:10.1016/j.mib.2024.102436
Data associated with the manuscript Superiority of chromosomal compared to plasmid-encoded compensatory mutations.
Wright, R. C. T., Wood, A. J., Bottery, M. J., Muddiman, K. J., Paterson, S., Harrison, E., . . . Hall, J. P. J. (n.d.). Data associated with the manuscript Superiority of chromosomal compared to plasmid-encoded compensatory mutations.. N/A. doi:10.17638/datacat.liverpool.ac.uk/2585
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.
Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., . . . Kyrpides, N. C. (2024). IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. NUCLEIC ACIDS RESEARCH, 52(D1), D164-D173. doi:10.1093/nar/gkad964
Plasmids manipulate bacterial behaviour through translational regulatory crosstalk (vol 21, e3001988, 2023)
Thompson, C. M. A., Hall, J. P. J., Chandra, G., Martins, C., Saalbach, G., Panturat, S., . . . Malone, J. G. (2024). Plasmids manipulate bacterial behaviour through translational regulatory crosstalk (vol 21, e3001988, 2023). PLOS BIOLOGY, 22(2), 2 pages. doi:10.1371/journal.pbio.3002531
2023
How do interactions between mobile genetic elements affect horizontal gene transfer?
Horne, T., Orr, V. T., & Hall, J. P. J. (2023). How do interactions between mobile genetic elements affect horizontal gene transfer?. CURRENT OPINION IN MICROBIOLOGY, 73, 8 pages. doi:10.1016/j.mib.2023.102282
Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities
Bird, S. M., Ford, S., Thompson, C. M. A., Little, R., Hall, J. P. J., Jackson, R. W., . . . Brockhurst, M. A. (2023). Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities. FEMS MICROBIOLOGY ECOLOGY, 99(4), 8 pages. doi:10.1093/femsec/fiad027
Plasmids manipulate bacterial behaviour through translational regulatory crosstalk.
Thompson, C. M. A., Hall, J. P. J., Chandra, G., Martins, C., Saalbach, G., Panturat, S., . . . Malone, J. G. (2023). Plasmids manipulate bacterial behaviour through translational regulatory crosstalk.. PLoS Biol, 21(2), e3001988. doi:10.1371/journal.pbio.3001988
Microbial Musings: Spring 2023
Hall, J. P. J. (2023). Microbial Musings: Spring 2023. MICROBIOLOGY-SGM, 169(7), 3 pages. doi:10.1099/mic.0.001379
2022
Horizontal gene transfer and ecological interactions jointly control microbiome stability.
Coyte, K. Z., Stevenson, C., Knight, C. G., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2022). Horizontal gene transfer and ecological interactions jointly control microbiome stability.. PLoS biology, 20(11), e3001847. doi:10.1371/journal.pbio.3001847
A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella.
Malaka De Silva, P., Stenhouse, G. E., Blackwell, G. A., Bengtsson, R. J., Jenkins, C., Hall, J. P. J., & Baker, K. S. (2022). A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella.. Proceedings. Biological sciences, 289(1980), 20220581. doi:10.1098/rspb.2022.0581
Horizontal gene transfer increases microbiome stability
Introduction: the secret lives of microbial mobile genetic elements
Hall, J. P. J., Harrison, E., & Baltrus, D. A. (2022). Introduction: the secret lives of microbial mobile genetic elements. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 377(1842), 7 pages. doi:10.1098/rstb.2020.0460
What makes a megaplasmid?
Hall, J. P. J., Botelho, J., Cazares, A., & Baltrus, D. A. (2022). What makes a megaplasmid?. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 377(1842), 13 pages. doi:10.1098/rstb.2020.0472
2021
A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among <i>Shigella</i>
De Silva, M., Stenhouse, G., Blackwell, G., Bengtsson, R., Jenkins, C., Hall, J. P. J., & Baker, K. (2021). A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among <i>Shigella</i>. doi:10.1101/2021.12.17.473221
Is the bacterial chromosome a mobile genetic element?
Hall, J. P. J. (2021). Is the bacterial chromosome a mobile genetic element?. NATURE COMMUNICATIONS, 12(1), 4 pages. doi:10.1038/s41467-021-26758-y
Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation
Hall, J. P. J., Wright, R. C. T., Harrison, E., Muddiman, K. J., Wood, A. J., Paterson, S., & Brockhurst, M. A. (2021). Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLOS Biology, 19(10), e3001225. doi:10.1371/journal.pbio.3001225
Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation
Hall, J. (n.d.). Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. doi:10.17638/datacat.liverpool.ac.uk/1275
The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities
Positive Selection Inhibits Plasmid Coexistence in Bacterial Genomes
Carrilero, L., Kottara, A., Guymer, D., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2021). Positive Selection Inhibits Plasmid Coexistence in Bacterial Genomes. MBIO, 12(3), 12 pages. doi:10.1128/mBio.00558-21
The proficiency of the original host species determines community-level plasmid dynamics.
Kottara, A., Hall, J. P. J., & Brockhurst, M. Α. (2021). The proficiency of the original host species determines community-level plasmid dynamics.. FEMS Microbiology Ecology. doi:10.1093/femsec/fiab026
The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities.
Kottara, A., Carrilero, L., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2021). The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities. Microbiology United Kingdom, 167(9). doi:10.1099/MIC.0.001086
2020
The proficiency of the original host species determines community-level plasmid dynamics
Positive selection inhibits plasmid coexistence in bacterial genomes
The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer
Hall, J. P. J., Harrison, E., Parnanen, K., Virta, M., & Brockhurst, M. A. (2020). The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer. FRONTIERS IN MICROBIOLOGY, 11, 14 pages. doi:10.3389/fmicb.2020.01846
Data files associated with "The impact of mercury selection and conjugative genetic elements on community structure and resistance gene transfer" by Hall, Pärnänen, Harrison, Virta, and Brockhurst.
Hall, J. (n.d.). Data files associated with "The impact of mercury selection and conjugative genetic elements on community structure and resistance gene transfer" by Hall, Pärnänen, Harrison, Virta, and Brockhurst.. doi:10.17638/datacat.liverpool.ac.uk/1076
A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas.
Cazares, A., Moore, M. P., Hall, J. P. J., Wright, L. L., Grimes, M., Emond-Rhéault, J. -G., . . . Winstanley, C. (2020). A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas.. Nature communications, 11(1). doi:10.1038/s41467-020-15081-7
Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways
Hall, J. P. J., Wright, R., Guymer, D., Harrison, E., & Brockhurst, M. (2020). Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways. Microbiology, 166(1), 56-62. doi:10.1099/mic.0.000862
2019
The Ecology and Evolution of Pangenomes.
Brockhurst, M. A., Harrison, E., Hall, J. P. J., Richards, T., McNally, A., & MacLean, C. (2019). The Ecology and Evolution of Pangenomes.. Current biology : CB, 29(20), R1094-R1103. doi:10.1016/j.cub.2019.08.012
Data files associated with "Extremely fast amelioration of plasmid fitness costs by multiple functionally-diverse pathways" by Hall, Wright, Guymer, Harrison, and Brockhurst.
Hall, J. (n.d.). Data files associated with "Extremely fast amelioration of plasmid fitness costs by multiple functionally-diverse pathways" by Hall, Wright, Guymer, Harrison, and Brockhurst.. doi:10.17638/datacat.liverpool.ac.uk/953
Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections
Jayaraman, S., Harris, C., Paxton, E., Donachie, A. -M., Vaikkinen, H., McCulloch, R., . . . Morrison, L. (2019). Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Neglected Tropical Diseases. doi:10.1371/journal.pntd.0007262
Coinfection promotes plasmid stability
Aguado, L. C., Hall, J. P. J., & Brockhurst, M. (2019). Coinfection promotes plasmid stability. Access Microbiology, 1(1A). doi:10.1099/acmi.ac2019.po0455
Mobile Compensatory Mutations Promote Plasmid Survival
Zwanzig, M., Harrison, E., Brockhurst, M. A., Hall, J. P. J., Berendonk, T. U., & Berger, U. (2019). Mobile Compensatory Mutations Promote Plasmid Survival. MSYSTEMS, 4(1), 11 pages. doi:10.1128/mSystems.00186-18
2018
Competitive species interactions constrain abiotic adaptation in a bacterial soil community
Hall, J. P. J., Harrison, E., & Brockhurst, M. (2018). Competitive species interactions constrain abiotic adaptation in a bacterial soil community. Evolution Letters, 2(6), 580-589. doi:10.1002/evl3.83
Migration promotes plasmid stability under spatially heterogeneous positive selection
Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2018). Migration promotes plasmid stability under spatially heterogeneous positive selection. Proceedings of the Royal Society B: Biological Sciences, 285(1879), 20180324. doi:10.1098/rspb.2018.0324
Plasmid stability is enhanced by higher-frequency pulses of positive selection
Stevenson, C., Hall, J. P. J., Brockhurst, M. A., & Harrison, E. (2018). Plasmid stability is enhanced by higher-frequency pulses of positive selection. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 285(1870), 8 pages. doi:10.1098/rspb.2017.2497
Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species
Kottara, A., Hall, J. P. J., Harrison, E., & Brockhurst, M. A. (2018). Variable plasmid fitness effects and mobile genetic element dynamics across <i>Pseudomonas</i> species. FEMS MICROBIOLOGY ECOLOGY, 94(1), 7 pages. doi:10.1093/femsec/fix172
2017
Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria
Hall, J. P. J., Brockhurst, M. A., & Harrison, E. (2017). Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 372(1735), 10 pages. doi:10.1098/rstb.2016.0424
Positive selection inhibits gene mobilization and transfer in soil bacterial communities
Hall, J. P. J., Williams, D., Paterson, S., Harrison, E., & Brockhurst, M. A. (2017). Positive selection inhibits gene mobilization and transfer in soil bacterial communities. Nature Ecology and Evolution, 1, 1348-1353. doi:10.1038/s41559-017-0250-3
Gene mobility promotes the spread of resistance in bacterial populations
Stevenson, C., Hall, J. P. J., Harrison, E., Wood, A. J., & Brockhurst, M. A. (2017). Gene mobility promotes the spread of resistance in bacterial populations. ISME JOURNAL, 11(8), 1930-1932. doi:10.1038/ismej.2017.42
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). Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction. MOLECULAR ECOLOGY, 26(10), 2757-2764. doi:10.1111/mec.14080
The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories?
Hall, J. P. J., Brockhurst, M. A., Dytham, C., & Harrison, E. (2017). The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories?. PLASMID, 91, 90-95. doi:10.1016/j.plasmid.2017.04.003
2016
Resistance is a numbers game
Hall, J. P. J., & Harrison, E. (2016). Resistance is a numbers game. NATURE MICROBIOLOGY, 1(12), 2 pages. doi:10.1038/NMICROBIOL.2016.235
Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
Hall, J. P. J., Wood, A. J., Harrison, E., & Brockhurst, M. A. (2016). Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 113(29), 8260-8265. doi:10.1073/pnas.1600974113
Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses
Harvey, W. T., Benton, D. J., Gregory, V., Hall, J. P. J., Daniels, R. S., Bedford, T., . . . Reeve, R. (2016). Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses. PLoS Pathogens, 12(4). doi:10.1371/journal.ppat.1005526
Multi-host environments select for hostgeneralist conjugative plasmids
Kottara, A., Hall, J. P. J., Harrison, E., & Brockhurst, M. A. (2016). Multi-host environments select for hostgeneralist conjugative plasmids. BMC EVOLUTIONARY BIOLOGY, 16, 4 pages. doi:10.1186/s12862-016-0642-z
Rapid compensatory evolution promotes the survival of conjugative plasmids
Harrison, E., Dytham, C., Hall, J. P. J., Guymer, D., Spiers, A. J., Paterson, S., & Brockhurst, M. A. (2016). Rapid compensatory evolution promotes the survival of conjugative plasmids. Mobile Genetic Elements, 6(3). doi:10.1080/2159256X.2016.1179074
2015
Environmentally co‐occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context‐dependent fitness effects
Hall, J. P. J., Harrison, E., Lilley, A. K., Paterson, S., Spiers, A. J., & Brockhurst, M. A. (2015). Environmentally co‐occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context‐dependent fitness effects. Environmental Microbiology, 17(12), 5008-5022. doi:10.1111/1462-2920.12901
DNA recombination strategies during antigenic variation in the African trypanosome
McCulloch, R., Morrison, L. J., & Hall, J. P. J. (2015). DNA recombination strategies during antigenic variation in the African trypanosome. In Mobile DNA III (pp. 409-435). doi:10.1128/9781555819217.ch19
DNA Recombination Strategies During Antigenic Variation in the African Trypanosome
McCulloch, R., Morrison, L. J., & Hall, J. P. J. (2015). DNA Recombination Strategies During Antigenic Variation in the African Trypanosome. MICROBIOLOGY SPECTRUM, 3(2). doi:10.1128/microbiolspec.MDNA3-0016-2014
2014
Withstanding the challenges of host immunity: Antigenic variation and the trypanosome surface coat
Hall, J. P. J., & Plenderleith, L. (2014). Withstanding the challenges of host immunity: Antigenic variation and the trypanosome surface coat. In Trypanosomes and Trypanosomiasis (pp. 61-87). doi:10.1007/978-3-7091-1556-5_3
2013
Viral host-adaptation: insights from evolution experiments with phages
Hall, J. P. J., Harrison, E., & Brockhurst, M. A. (2013). Viral host-adaptation: insights from evolution experiments with phages. CURRENT OPINION IN VIROLOGY, 3(5), 572-577. doi:10.1016/j.coviro.2013.07.001
Mosaic <i>VSGs</i> and the Scale of <i>Trypanosoma brucei</i> Antigenic Variation
Hall, J. P. J., Wang, H., & Barry, J. D. (2013). Mosaic <i>VSGs</i> and the Scale of <i>Trypanosoma brucei</i> Antigenic Variation. PLOS PATHOGENS, 9(7), 13 pages. doi:10.1371/journal.ppat.1003502
2012
Genome hyperevolution and the success of a parasite
Barry, J. D., Hall, J. P. J., & Plenderleith, L. (2012). Genome hyperevolution and the success of a parasite. In EFFECTS OF GENOME STRUCTURE AND SEQUENCE ON VARIATION AND EVOLUTION (Vol. 1267, pp. 11-17). doi:10.1111/j.1749-6632.2012.06654.x
2006
Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa
Lin, L. -H., Hall, J., Onstott, T. C., Gihring, T., Lollar, B. S., Boice, E., . . . Bellamy, R. E. S. (2006). Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa. In GEOMICROBIOLOGY JOURNAL Vol. 23 (pp. 475-497). doi:10.1080/01490450600875829