All Outputs (19)

The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies (2024)
Journal Article
Cook, R., Brown, N., Rihtman, B., Michniewski, S., Redgwell, T., Clokie, M., …Millard, A. (2024). The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies. Microbial Genomics, 10(2), Article 0.001198. https://doi.org/10.1099/mgen.0.001198

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial... Read More about The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.

Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh (2023)
Journal Article
Williams, A. D., Rousham, E., Neal, A. L., Amin, M. B., Hobman, J. L., Stekel, D., & Islam, M. A. (2023). Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh. Microbiology Spectrum, 11(6), e0176323. https://doi.org/10.1128/spectrum.01763-23

Interactions between humans, animals, and the environment are considered critical foci for addressing antimicrobial resistance (AMR). However, One Health data on AMR in low- and middle-income countries are presently scarce. Using metagenomics, we inv... Read More about Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh.

The adaptability of the ion binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF (2023)
Journal Article
Lithgo, R. M., Hanževački, M., Harris, G., Kamps, J. J. .. G., Holden, E., Gianga, T., …Scott, D. J. (2023). The adaptability of the ion binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF. Journal of Biological Chemistry, 299(11), Article 105331. https://doi.org/10.1016/j.jbc.2023.105331

The periplasmic chaperone SilF has been identified as part of an Ag(I) detoxification system in Gram negative bacteria. Sil proteins also bind Cu(I), but with reported weaker affinity, therefore leading to the designation of a specific detoxification... Read More about The adaptability of the ion binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF.

Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics (2023)
Journal Article
Chio, H., Guest, E. E., Hobman, J. L., Dottorini, T., Hirst, J. D., & Stekel, D. J. (2023). Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics. Journal of Molecular Graphics and Modelling, 123, Article 108508. https://doi.org/10.1016/j.jmgm.2023.108508

Antibiotics enter the environment through waste streams, where they can exert selective pressure for antimicrobial resistance in bacteria. However, many antibiotics are excreted as partly metabolized forms, or can be subject to partial breakdown in w... Read More about Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics.

Laboratory strains of Escherichia coli K-12: not such perfect role models after all (2022)
Preprint / Working Paper
Browning, D. F., Hobman, J. L., & Busby, S. J. Laboratory strains of Escherichia coli K-12: not such perfect role models after all

Escherichia coli K-12 was originally isolated 100 years ago and since then, it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its apparent pedigree, since its initial isolation, E. coli K-12... Read More about Laboratory strains of Escherichia coli K-12: not such perfect role models after all.

Laboratory strains of Escherichia coli K-12: things are seldom what they seem (2022)
Journal Article
F. Browning, D., L. Hobman, J., & Busby, S. J. (2023). Laboratory strains of Escherichia coli K-12: things are seldom what they seem. Microbial Genomics, 9(2), Article 000922. https://doi.org/10.1099/mgen.0.000922

Escherichia coli K-12 was originally isolated 100 years ago and since then it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its pedigree, since its initial isolation E. coli K-12 has been re... Read More about Laboratory strains of Escherichia coli K-12: things are seldom what they seem.

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens (2021)
Journal Article
Cook, R., Hooton, S., Trivedi, U., King, L., Dodd, C. E., Hobman, J. L., …Millard, A. D. (2021). Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens. Microbiome, 9, Article 65. https://doi.org/10.1186/s40168-021-01010-3

Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle... Read More about Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens.

Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids (2021)
Journal Article
Arya, S., Williams, A., Reina, S. V., Knapp, C. W., Kreft, J.-U., Hobman, J. L., & Stekel, D. J. (2021). Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids. Environmental Pollution, 275, Article 116602. https://doi.org/10.1016/j.envpol.2021.116602

© 2021 Elsevier Ltd Many antibiotic resistance genes co-occur with resistance genes for transition metals, such as copper, zinc, or mercury. In some environments, a positive correlation between high metal concentration and high abundance of antibioti... Read More about Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids.

Comparative genomics of bacteriophage of the genus Seuratvirus (2017)
Journal Article
Sazinas, P., Redgwell, T., Rihtman, B., Grigonyte, A., Michniewski, S., Scanlan, D. J., …Millard, A. (in press). Comparative genomics of bacteriophage of the genus Seuratvirus. Genome Biology and Evolution, 10(1), https://doi.org/10.1093/gbe/evx275

Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and performed de novo genome sequencing, assembly... Read More about Comparative genomics of bacteriophage of the genus Seuratvirus.

Bacterial resistance to arsenic protects against protist killing (2017)
Journal Article
Hao, X., Li, X., Pal, C., Hobman, J. L., Larsson, D. J., Saquib, Q., …Rensing, C. (2017). Bacterial resistance to arsenic protects against protist killing. BioMetals, 30(2), 307-311. https://doi.org/10.1007/s10534-017-0003-4

Protists kill their bacterial prey using toxic metals such as copper. Here we hypothesize that the metalloid arsenic has a similar role. To test this hypothesis, we examined intracellular survival of Escherichia coli (E. coli) in the amoeba Dictyoste... Read More about Bacterial resistance to arsenic protects against protist killing.

Draft genome sequence of the bacteriophage vB_Eco_slurp01. (2016)
Journal Article
Sazinas, P., Smith, C., Suhaimi, A., Hobman, J. L., Dodd, C. E., & Millard, A. (2016). Draft genome sequence of the bacteriophage vB_Eco_slurp01. Genome Announcements, 4(6), https://doi.org/10.1128/genomeA.01111-16

Bacteriophage vB_Eco_slurp01 was isolated from porcine feces using Escherichia coli MG1655 as a host. With a genome size of 348 kb, vB_Eco_slurp01 is one of the largest bacteriophages isolated to date.

Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate (2016)
Journal Article
Baker, M., Hobman, J. L., Dodd, C. E., Ramsden, S. J., & Stekel, D. J. (2016). Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate. FEMS Microbiology Ecology, 92(4), Article fiw040. https://doi.org/10.1093/femsec/fiw040

Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobi... Read More about Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate.

Draft genome sequences of 14 Escherichia coli phages isolated from cattle slurry (2015)
Journal Article
Smith, R., O'Hara, M., Hobman, J. L., & Millard, A. (2015). Draft genome sequences of 14 Escherichia coli phages isolated from cattle slurry. Genome Announcements, 3(6), Article e01364-15. https://doi.org/10.1128/genomeA.01364-15

The diversity of bacteriophages in slurry from dairy cows remains largely unknown. Here, we report the draft genome sequences of 14 bacteriophages isolated from dairy cow slurry using Escherichia coli K-12 MG1655 as a host.

Survival in amoeba: a major selection pressure on the presence of bacterial copper and zinc resistance determinants?: identification of a "copper pathogenicity island" (2015)
Journal Article
Hao, X., Luthje, F. L., Qin, Y., McDevitt, S. F., Lutay, N., Hobman, J. L., …Rensing, C. (2015). Survival in amoeba: a major selection pressure on the presence of bacterial copper and zinc resistance determinants?: identification of a "copper pathogenicity island". Applied Microbiology and Biotechnology, 99(14), https://doi.org/10.1007/s00253-015-6749-0

The presence of metal resistance determinants in bacteria usually is attributed to geological or anthropogenic metal contamination in different environments or associated with the use of antimicrobial metals in human healthcare or in agriculture. Whi... Read More about Survival in amoeba: a major selection pressure on the presence of bacterial copper and zinc resistance determinants?: identification of a "copper pathogenicity island".

Bacterial antimicrobial metal ion resistance (2015)
Journal Article
Hobman, J. L., & Crossman, L. (2015). Bacterial antimicrobial metal ion resistance. Journal of Medical Microbiology, 64, https://doi.org/10.1099/jmm.0.023036-0

Metals such as mercury, arsenic, copper and silver have been used in various forms as antimicrobials for thousands of years with until recently, little understanding of their mode of action. The discovery of antibiotics and new organic antimicrobial... Read More about Bacterial antimicrobial metal ion resistance.

The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress (2015)
Journal Article
Takahashi, H., Oshima, T., Hobman, J. L., Doherty, N., Clayton, S. R., Iqbal, M., …Stekel, D. J. (2015). The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress. Interface, 12(106), Article 20150069. https://doi.org/10.1098/rsif.2015.0069

Zinc is essential for life, but toxic in excess. Thus all cells must control their internal zinc concentration. We used a systems approach, alternating rounds of experiments and models, to further elucidate the zinc control systems in Escherichia col... Read More about The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress.

Response of Cupriavidus metallidurans CH34 to metals (2015)
Book Chapter
Monsieurs, P., Hobman, J. L., Vandenbussche, G., Mergeay, M., & Van Hoult, R. (2015). Response of Cupriavidus metallidurans CH34 to metals. In M. Mergay, & R. Van Houdt (Eds.), Metal response in Cupriavidus metallidurans Volume 1: From habitats to genes and proteins. Springer. https://doi.org/10.1007/978-3-319-20594-6

Cupriavidus metallidurans CH34 displays resistance to a plethora of metals. Its response and underlying genetic determinants are dissected and detailed metal by metal (from arsenic to zinc). An important role for its megaplasmids pMOL28 and pMOL30 is... Read More about Response of Cupriavidus metallidurans CH34 to metals.

High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq (2013)
Journal Article
Chumsakul, O., Nakamura, K., Kurata, T., Hobman, J. L., Ogasawara, N., Oshima, T., & Ishikawa, S. (2013). High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq. DNA Research, 20(4), https://doi.org/10.1093/dnares/dst013

Accurate identification of the DNA-binding sites of transcription factors and other DNA-binding proteins on the genome is crucial to understanding their molecular interactions with DNA. Here, we describe a new method: Genome Footprinting by high-thro... Read More about High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.

Laboratory adapted Escherichia coli K-12 becomes a pathogen of Caenorhabditis elegans upon restoration of O antigen biosynthesis (2013)
Journal Article
Browning, D., Wells, T., Franca, F., Morris, F., Sevastyanovich, Y., Bryant, J., …Henderson, I. (2013). Laboratory adapted Escherichia coli K-12 becomes a pathogen of Caenorhabditis elegans upon restoration of O antigen biosynthesis. Molecular Microbiology, 87(5), https://doi.org/10.1111/mmi.12144

Escherichia coli has been the leading model organism for many decades. It is a fundamental player in modern biology, facilitating the molecular biology revolution of the last century. The acceptance of E. coli as model organism is predicated primaril... Read More about Laboratory adapted Escherichia coli K-12 becomes a pathogen of Caenorhabditis elegans upon restoration of O antigen biosynthesis.