Journal Article

Puxty, Richard J. and Millard, Andrew D. (2023) Functional ecology of bacteriophages in the environment. Current Opinion in Microbiology, 71 . 102245. doi:10.1016/j.mib.2022.102245 ISSN 1369-5274.

Muscatt, George, Hilton, Sally, Raguideau, Sébastien, Teakle, Graham R., Lidbury, Ian, Wellington, Elizabeth M. H., Quince, Christopher, Millard, Andrew D., Bending, Gary D. and Jameson, Eleanor (2022) Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. Microbiome, 10 (1). 181. doi:10.1186/s40168-022-01371-3 ISSN 2049-2618.

Rangel-Pineros, Guillermo, Millard, Andrew D., Michniewski, Slawomir, Scanlan, David J. , Sirén, Kimmo, Reyes, Alejandro, Petersen, Bent, Clokie, Martha R. J. and Sicheritz-Pontén, Thomas (2021) From trees to clouds : PhageClouds for fast comparison of ∼640,000 phage genomic sequences and host-centric visualization using genomic network graphs. PHAGE : Therapy, Applications, and Research, 2 (4). pp. 194-203. doi:10.1089/phage.2021.0008 ISSN 2641-6530.

Rihtman, Branko, Puxty, Richard John, Hapeshi, Alexia, Lee, Yan-Jiun, Zhan, Yuanchao, Michniewski, Slawomir, Waterfield, Nicholas R., Chen, Feng, Weigele, Peter, Millard, Andrew D., Scanlan, David J. and Chen, Yin (2021) A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution. Current Biology, 31 (14). 3199-3206.e4. doi:10.1016/j.cub.2021.05.014 ISSN 0960-9822.

Townsend, Eleanor, Kelly, Lucy, Gannon, Lucy, Muscatt, George, Dunstan, Rhys, Michniewski, Slawomir, Sapkota, Hari, Kiljunen, Saija J., Kolsi, Anna, Skurnik, Mikael, Lithgow, Trevor, Millard, Andrew D. and Jameson, Eleanor (2021) Isolation and chacterisation of Klebsiella phages for phage therapy. PHAGE Therapy, Applications, and Research, 2 (1). pp. 26-42. doi:10.1089/phage.2020.0046 ISSN 2641-6530.

Leungtongkam, Udomluk, Thummeepak, Rapee, Kitti, Thawatchai, Tasanapak, Kannipa, Wongwigkarn, Jintana, Styles, Kathryn, Wellington, Elizabeth M. H., Millard, Andrew D., Sagona, Antonia P. and Sitthisak, Sutthirat (2020) Genomic analysis reveals high virulence and antibiotic resistance amongst phage susceptible Acinetobacter baumannii. Scientific Reports, 10 . 16154. doi:10.1038/s41598-020-73123-y ISSN 2045-2322.

Styles, Kathryn, Thummeepak, Rapee, Leungtongkam, Udomluk, Smith, Sophie, Christie, Gabrielle S., Millard, Andrew D., Moat, John, Dowson, Christopher G., Wellington, Elizabeth M. H., Sitthisak, Sutthirat and Sagona, Antonia P. (2020) Investigating bacteriophages targeting the opportunistic pathogen Acinetobacter baumannii. Antibiotics, 9 (4). 200. doi:10.3390/antibiotics9040200 ISSN 2079-6382.

Grigonyte, Aurelija, Harrison, Christian, Macdonald, Paul R., Montero-Blay, Ariadna, Tridgett, Matthew, Duncan, John, Sagona, Antonia P., Constantinidou, Chrystala, Jaramillo, Alfonso and Millard, Andrew D. (2020) Comparison of CRISPR and marker-based methods for the engineering of Phage T7. Viruses, 12 (2). e193. doi:10.3390/v12020193 ISSN 1999-4915.

Simpson, Daniel H., Hapeshi, Alexia, Rogers, Nicola J., Brabec, Viktor, Clarkson, Guy J., Fox, David J., Hrabina, Ondrej, Kay, Gemma L., King, Andrew, Malina, Jaroslav, Millard, Andrew D., Moat, John, Roper, David I., Song, Hualong, Waterfield, Nicholas R. and Scott, Peter (2019) Metallohelices that kill Gram-negative pathogens using intracellular antimicrobial peptide pathways. Chemical Science, 10 . 9708-9720. doi:10.1039/C9SC03532J ISSN 2041-6520.

Jones, Helen J., Kröber, Eileen, Stephenson, Jason, Mausz, Michaela A., Jameson, Eleanor, Millard, Andrew D., Purdy, Kevin J. and Chen, Yin (2019) A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments. Microbiome, 7 . 120. doi:10.1186/s40168-019-0732-4 ISSN 2049-2618.

Slater, Ross T., Frost, Lucy R., Jossi, Sian E, Millard, Andrew D. and Unnikrishnan, Meera (2019) Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms. Scientific Reports, 9 (1). 9903. doi:10.1038/s41598-019-46143-6 ISSN 2045-2322.

Back, J.J., Blake, Thomas, Brossa Gonzalo, A., Costa Sobral, C. M. , Crocombe, Andrew, Gershon, T. J., Kreps, Michal, Latham, Thomas, Loh, David, Mathad, Abhijit , Millard, Andrew D., Poluektov, Anton and Wicht, Jean (2019) Dalitz plot analysis of the D+ -> K-K+K+ decay. Journal of High Energy Physics (4). 63. doi:10.1007/JHEP04(2019)063 ISSN 1029-8479.

Jameson, Eleanor, Stephenson, Jason, Jones, Helen J., Millard, Andrew D., Kaster, K., Purdy, Kevin J., Airs, R., Murrell, J. C. (J. Colin) and Chen, Yin (2019) Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment. ISME Journal, 13 (2). pp. 277-289. doi:10.1038/s41396-018-0269-8 ISSN 1751-7362.

Back, J. J., Blake, Thomas, Brossa Gonzalo, A., Costa Sobral, C. M. , Crocombe, Andrew, Gershon, T. J., Kreps, Michal, Latham, Thomas, Loh, David, Mathad, Abhijit , Millard, Andrew D. and Vesterinen, M. (2019) Measurement of B + , B 0 and Λ 0 b production in p Pb collisions at √ s NN = 8.16     TeV. Physical Review D (Particles, Fields, Gravitation and Cosmology) . doi:10.1103/PhysRevD.99.052011 ISSN 1550-7998.

Perez-Sepulveda, Blanca, Pitt, Frances Diana, N’Guyen, A. N., Ratin, M., Garczarek, L., Millard, Andrew D. and Scanlan, David J. (2018) Relative stability of ploidy in a marine Synechococcus across various growth conditions. Environmental Microbiology, 10 (4). pp. 428-432. doi:10.1111/1758-2229.12614 ISSN 1462-2912.

Puxty, Richard John, Evans, David J., Millard, Andrew D. and Scanlan, David J. (2018) Energy limitation of cyanophage development : implications for marine carbon cycling. ISME Journal, 12 . 1273-1286 . doi:10.1038/s41396-017-0043-3 ISSN 1751-7362.

Michniewski, Slawomir, Redgwell, Tamsin, Scanlan, David J. and Millard, Andrew D. (2017) Draft genome sequence of Bacteriophage vB_Eco_swan01. Genome Announcements, 5 (28). pp. 1-17. e00501. doi:10.1128/genomeA.00501-17 ISSN 2169-8287.

Guy, Collette S., Tichauer, Esther, Kay, Gemma L., Phillips, Daniel J., Bailey, Trisha L., Harrison, James, Furze, Christopher M., Millard, Andrew D., Gibson, Matthew I., Pallen, Mark J. and Fullam, Elizabeth (2017) Identification of the anti-mycobacterial functional properties of piperidinol derivatives. British Journal of Pharmacology, 174 (14). pp. 2183-2193. doi:10.1111/bph.13744 ISSN 1476-5381.

Sazinas, Pavelas, Smith, Carrie, Suhaimi, Aqilah, Hobman, Jon L., Dodd, Christine and Millard, Andrew D. (2016) Draft genome sequence of the Bacteriophage vB_Eco_slurp01. Genome Announcements, 4 (6). e01111-16. doi:10.1128/genomeA.01111-16 ISSN 2169-8287.

Pitt, Frances Diana, Millard, Andrew D., Ostrowski, Martin, Dervish, Suat, Mazard, Sophie, Paulsen, Ian T., Zubkov, Mikhail V. and Scanlan, David J. (2016) A sample-to-sequence protocol for genus targeted transcriptomic profiling : application to marine Synechococcus. Frontiers in Microbiology, 7 . 1592. doi:10.3389/fmicb.2016.01592 ISSN 1664-302X.

Perez-Sepulveda, Blanca, Redgwell, Tamsin, Rihtman, Branko, Pitt, Frances Diana, Scanlan, David J. , Millard, Andrew D. and Hantke, Klaus (2016) Marine phage genomics : the tip of the iceberg. FEMS Microbiology Letters, 363 (15). doi:10.1093/femsle/fnw158 ISSN 0378-1097.

Puxty, Richard J., Millard, Andrew D., Evans, David J. and Scanlan, David J. (2016) Viruses inhibit CO2 fixation in the most abundant phototrophs on earth. Current Biology, 26 (12). pp. 1585-1589. doi:10.1016/j.cub.2016.04.036 ISSN 0960-9822.

Rihtman, Branko, Meaden, Sean, Clokie, Martha R. J., Koskella, Britt and Millard, Andrew D. (2016) Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes. PeerJ, 4 . pp. 1-21. e2055. doi:10.7717/peerj.2055 ISSN 2167-8359.

Higgins, P. G., Chan, J. Z.-M., Seifert, H., Pallen, Mark J. and Millard, Andrew D. (2016) Draft genome sequences of 11 clinical isolates of Acinetobacter baumannii. Genome Announcements, 4 (2). e00269. doi:10.1128/genomeA.00269-16 ISSN 2169-8287.

Millard, Andrew D., Westblade, Lars, LiPuma, John J., Vavikolanu, Kranthi, Read, Timothy, Pallen, Mark J., Burd, Eileen and Constantinidou, Chrystala (2015) Genome Sequence of the Pandoraea apista LMG 16407 Type Strain. Journal of Bacteriology, 3 (6). e01300-e01315. doi:10.1128/genomeA.01300-15 ISSN 0021-9193.

Chan, Yi-Wah, Millard, Andrew D., Wheatley, Peter J., Holmes, Antony B., Mohr, Remus, Whitworth, Anna L., Mann, Nicholas H., Larkum, Anthony W. D., Hess, Wolfgang R., Scanlan, David J. and Clokie, Martha R. J. (2015) Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacterium Acaryochloris marina. Environmental Microbiology, 17 (11). pp. 4239-4252. doi:10.1111/1462-2920.12735 ISSN 1462-2912.

Puxty, Richard John, Perez-Sepulveda, Blanca, Rihtman, Branko, Evans, David J., Millard, Andrew D. and Scanlan, David J. (2015) Spontaneous deletion of an “ORFanage” region facilitates host adaptation in a “photosynthetic” cyanophage. PLoS One, Volume 10 (Number 7). pp. 1-13. Article number e0132642. doi:10.1371/journal.pone.0132642 ISSN 1932-6203.

Hargreaves, Katherine R., Otieno, James R., Thanki, Anisha, Blades, Matthew J., Millard, Andrew D., Browne, Hilary P., Lawley, Trevor D. and Clokie, Martha R. J. (2015) As clear as mud? Determining the diversity and prevalence of prophages in the draft genomes of estuarine isolates of Clostridium difficile. Genome Biology and Evolution, Volume 7 (Number 7). pp. 1842-1855. doi:10.1093/gbe/evv094 ISSN 1759-6653.

Kay, Gemma L., Millard, Andrew D., Sergeant, Martin J., Midzi, Nicholas, Gwisai, Reggis, Mduluza, Takafira, Ivens, Alasdair, Nausch, Norman, Mutapi, Francisca and Pallen, Mark J. (2015) Differences in the faecal microbiome in Schistosoma haematobium infected children vs. uninfected children. PLoS Neglected Tropical Diseases, 9 (6). e0003861. doi:10.1371/journal.pntd.0003861 ISSN 1935-2727.

Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline, Millard, Andrew D., Quick, Joshua, Szikossy, Ildikó, Pap, Ildikó, Spigelman, Mark, Loman, Nicholas J., Achtman, Mark, Donoghue, Helen D. and Pallen, Mark J. (2015) Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nature Communications, Volume 6 . pp. 1-9. Article number 6717. doi:10.1038/ncomms7717 ISSN 2041-1723.

Chan, Yi-Wah, Millard, Andrew D., Wheatley, Peter J., Holmes, Antony B., Mohr, Remus, Whitworth, Anna L., Mann, Nicholas H., Larkum, Anthony W. D., Hess, Wolfgang R., Scanlan, David J. and Clokie, Martha R. J. (2015) Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacteriumAcaryochloris marina. Environmental Microbiology, 17 (11). pp. 4239-4252. doi:10.1111/1462-2920.12735 ISSN 1462-2912.

Chan, Jacqueline, Millard, Andrew D., Mann, Nicholas H. and Schäfer, Hendrik (2014) Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes. Frontiers in Microbiology, Volume 5 . Article number 506. doi:10.3389/fmicb.2014.00506 ISSN 1664-302X.

Puxty, Richard John, Millard, Andrew D., Evans, David J. and Scanlan, David J. (2014) Shedding new light on viral photosynthesis. Photosynthesis Research, 126 (1). pp. 71-97. doi:10.1007/s11120-014-0057-x ISSN 0166-8595.

Shilova, Irina N., Robidart, Julie C., James Tripp, H., Turk-Kubo, Kendra, Wawrik, Boris, Post, Anton F., Thompson, Anne W., Ward, Bess, Hollibaugh, James T., Millard, Andrew D., Ostrowski, Martin, Scanlan, David J., Paerl, Ryan W., Stuart, Rhona and Zehr, Jonathan P. (2014) A microarray for assessing transcription from pelagic marine microbial taxa. The ISME Journal, Volume 8 . doi:10.1038/ismej.2014.1 ISSN 1751-7362.

Millard, Andrew D., Hands-Portman, Ian and Zwirglmaier, Katrin (2014) Morphotypes of virus-like particles in two hydrothermal vent fields on the East Scotia Ridge, Antarctia. Bacteriophage, Volume 4 (Number 1). Article number e28732 . doi:10.4161/bact.28732 ISSN 2159-7073.

Millard, Andrew D., Scanlan, David J., Gallagher, Connor, Marsh, Andrew and Taylor, Paul C. (2014) Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation. Molecular BioSystems, 10 (3). pp. 380-383. doi:10.1039/c3mb70447e ISSN 1742-206X.

Barnett, James P., Millard, Andrew D., Ksibe, Amira Z., Scanlan, David J., Schmid, Ralf and Blindauer, Claudia A. (2012) Mining genomes of marine cyanobacteria for elements of zinc homeostasis. Frontiers in Microbiology, Volume 3 . Article number 142. doi:10.3389/fmicb.2012.00142 ISSN 1664-302X.

Chan, Yi-Wah, Mohr, Remus, Millard, Andrew D., Holmes, Antony B., Larkum, Anthony W. D., Whitworth, Anna L., Mann, Nicholas H., Scanlan, David J., Hess, Wolfgang R. and Clokie, Martha R. J. (2011) Discovery of cyanophage genomes which contain mitochondrial DNA polymerase. Molecular Biology and Evolution, Vol.28 (No.8). pp. 2269-2274. doi:10.1093/molbev/msr041 ISSN 0737-4038.

Clokie, Martha R. J., Millard, Andrew D. and Mann, Nicholas H. (2010) T4 genes in the marine ecosystem: studies of the T4-like cyanophages and their role in marine ecology. Virology Journal, Volume 7 . Article number 291. doi:10.1186/1743-422X-7-291 ISSN 1743-422X.

Jia, Ying, Shan, Jinyu, Millard, Andrew D., Clokie, Martha R. J. and Mann, Nicholas H. (2010) Light-dependent adsorption of photosynthetic cyanophages to Synechococcus sp. WH7803. FEMS Microbiology Letters, 310 (2). pp. 120-126. doi:10.1111/j.1574-6968.2010.02054.x ISSN 0378-1097.

Millard, Andrew D., Gierga, G., Clokie, Martha R. J., Evans, David J., Hess, Wolfgang R. and Scanlan, David J. (2010) An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease. ISME Journal, The, Vol.2010 (No.4). pp. 1121-1135. doi:10.1038/ismej.2010.43 ISSN 1751-7362.

Sánchez-Romero, María Antonia, Busby, S. (Stephen), Dyer, Nigel, Ott, Sascha, Millard, Andrew D. and Grainger, David C. (2010) Dynamic distribution of SeqA protein across the chromosome of Escherichia coli K-12. mBio, Vol.1 (No.1). Article number e00012-10. doi:10.1128/mBio.00012-10 ISSN 2150-7511.

Millard, Andrew D., Zwirglmaier, Katrin, Downey, Mike J., Mann, Nicholas H. and Scanlan, David J. (2009) Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region : implications for mechanisms of cyanophage evolution. Environmental Microbiology, Volume 11 (Number 9). pp. 2370-2387. doi:10.1111/j.1462-2920.2009.01966.x ISSN 1462-2912.

Whitworth, David E., Millard, Andrew D., Hodgson, D. A. and Hawkins, Peter F. (2008) Protein-protein interactions between two-component system transmitter and receiver domains of Myxococcus xanthus. Proteomics, Vol.8 (No.9). pp. 1839-1842. doi:10.1002/pmic.200700544 ISSN 1615-9853.

Clokie, Martha R. J., Millard, Andrew D., Mehta, Jaytry Y. and Mann, Nicholas H. (2006) Virus isolation studies suggest short-term variations in abundance in natural cyanophage populations of the Indian Ocean. Journal of the Marine Biological Association of the United Kingdom, Vol.86 (No.3). pp. 499-505. doi:10.1017/S0025315406013415 ISSN 0025-3154.

Millard, Andrew D. and Mann, Nicholas H. (2006) A temporal and spatial investigation of cyanophage abundance in the Gulf of Aqaba Red Sea. Journal of the Marine Biological Association of the United Kingdom, Vol.86 (No.3). pp. 507-515. doi:10.1017/S0025315406013415 ISSN 0025-3154.

Mann, Nicholas H., Clokie, Martha R. J., Millard, Andrew D., Cook, A. (Annabel), Wilson, W. H. (William H.), Wheatley, P. J., Letarov, Andrey and Krish, H. M (2005) The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains. Journal of Bacteriology, Volume 187 (Number 9). pp. 3188-3200. doi:10.1128/JB.187.9.3188-3200.2005 ISSN 0021-9193.

Somerfield, Paul J., Muhling, Martin, Fuller, Nicholas J., Millard, Andrew D., Dominique, Marie, Wilson, W. H., Scanlan, David J., Post, Anton F., Joint, Ian and Mann, Nicholas H. (2005) Genetic diversity of marine Synechococcus and co-occurring cyanophage communities : evidence for viral control of phytoplankton. Environmental Microbiology, Volume 7 (Number 4). pp. 499-508. doi:10.1111/j.1462-2920.2005.00713.x ISSN 1462-2912.

Millard, Andrew D., Clokie, Martha R. J., Shub, David A. and Mann, Nicholas H. (2004) Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proceedings of the National Academy of Sciences of the United States of America, Volume 101 (Number 30). pp. 11007-11012. doi:10.1073/pnas.0401478101 ISSN 0027-8424.

Conference Item

Tacke, D., Gillis, M., Higgins, P. G., Millard, Andrew D., Chan, J. Z. M., Pallen, Mark J., Faetkenheuer, G., Cornely, O. A., Seifert, H. and Vehreschild, M. J. G. T. (2014) Use of whole-genome sequencing to investigate the epidemiology of vancomycin-resistant enterococci on an intensive care unit. In: 24th European Society of Clinical Microbiology and Infectious Diseases (ECCMID) Conference 2014, Barcelona, Spain, 10-14 May 2014

Clokie, Martha R. J., Millard, Andrew D., Wilson, William H. and Mann, Nicholas H. (2003) Encapsidation of host DNA by bacteriophages infecting marine Synechococcus strains. In: 8th Symposium on Aquatic Microbial Ecology (SAME-8), Sicily, Italy, 25-29 Oct 2002. Published in: FEMS Microbiology Ecology, Volume 46 (Number 3). pp. 349-352. doi:10.1016/S0168-6496(03)00247-2 ISSN 0168-6496.

Journal Item

Bailey, Shaun, Clokie, Martha R. J., Millard, Andrew D. and Mann, Nicholas H. (2004) Cyanophage infection and photoinhibition in marine cyanobacteria. Research in Microbiology, Volume 155 (Number 9). pp. 720-725. doi:10.1016/j.resmic.2004.06.002

Mann, Nicholas H., Cook, A. (Annabel), Millard, Andrew D., Bailey, S. (Shaun) and Clokie, Martha R. J. (2003) Marine ecosystems : bacterial photosynthesis genes in a virus. Nature, Volume 424 (Number 6950). Article number 741. doi:10.1038/424741a