Prof James McDonald

Professor in Biology (Biotechnology)

Contact info

James McDonald is a microbiologist and Senior Lecturer at Bangor University.

Current research themes include microbiome analysis of biomass-degrading microorganisms for biofuels and biotechnology, high-throughput methods for the detection of human pathogens in aquatic environments, and microbiome analysis of the complex tree disease, Acute Oak Decline.

His group applies a combination of microbiological culture techniques and contemporary ‘omics’ technologies (e.g. genomics, metagenomics, metatranscriptomics and metaproteomics) to address these research themes.

Location: F6 Memorial Building

Tel: +44 (0)1248 383492

Personal webpage: http://jamesmcdonaldlab.com/jamesmcdonaldlab.com/Welcome.html

  1. Article › Research › Peer-reviewed
  2. 454-pyrosequencing: a molecular battiscope for freshwater viral ecology

    Rooks, D. J., Smith, D. L., McDonald, J. E., Woodward, M. J., McCarthy, A. J. & Allison, H. E., 21 Jul 2010, In : Genes. 1, 2, p. 210-26 17 p.

    Research output: Contribution to journalArticle

  3. Published

    A communal catalogue reveals Earth's multiscale microbial diversity

    Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vazquez-Baeza, Y., Gonzalez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., Haroon, M. F., Kanbar, J., Zhu, Q., Song, S. J., Kosciolek, T., Bokulich, N. A., Lefler, J., Brislawn, C. J., Humphrey, G., Owens, S. M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J. A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D., Jansson, J. K., Gilbert, J. A., Knight, R., Agosto Rivera, J. L., Al-Moosawi, L., Alverdy, J., Amato, K. R., Andras, J., Angenent, L. T., Antonopoulos, D. A., Apprill, A., Armitage, D., Ballantine, K., Bárta, J., Baum, J. K., Berry, A., Bhatnagar, A., Bhatnagar, M., Biddle, J. F., Bittner, L., Boldgiv, B., Bottos, E., Boyer, D. M., Braun, J., Brazelton, W., Brearley, F. Q., Campbell, A. H., Caporaso, J. G., Cardona, C., Carroll, J., Cary, S. C., Casper, B. B., Charles, T. C., Chu, H., Claar, D. C., Clark, R. G., Clayton, J. B., Clemente, J. C., Cochran, A., Coleman, M. L., Collins, G., Colwel, R. R., Contreras, M., Crary, B. B., Creer, S., Cristol, D. A., Crump, B. C., Cui, D., Daly, S. E., Davalos, L., Dawson, R. D., Defazio, J., Delsuc, F., Dionisi, H. M., Dominguez-Bello, M. G., Dowell, R., Dubinsky, E. A., Dunn, P. O., Ercolini, D., Espinoza, R. E., Ezenwa, V., Fenner, N., Findlay, H. S., Fleming, I. D., Fogliano, V., Forsman, A., Freeman, C., Friedman, E. S., Galindo, G., Garcia, L., Garcia-Amado, M. A., Garshelis, D., Gasser, R. B., Gerdts, G., Gibson, M. K., Gifford, I., Gill, R. T., Giray, T., Gittel, A., Golyshin, P., Gong, D., Grossart, H-P., Guyton, K., Haig, S-J., Hale, V., Hall, R. S., Hallam, S. J., Handley, K. M., Hasan, N. A., Haydon, S. R., Hickman, J. E., Hidalgo, G., Hofmockel, K. S., Hooker, J., Hulth, S., Hultman, J., Hyde, E., Ibáñez-Álamo, J. D., Jastrow, J. D., Jex, A. R., Johnson, L. S., Johnston, E. R., Joseph, S., Jurburg, S. D., Jurelevicius, D., Karlsson, A., Karlsson, R., Kauppinen, S., Kellogg, C. T. E., Kennedy, S. J., Kerkhof, L. J., King, G. M., Kling, G. W., Koehler, A. V., Krezalek, M., Kueneman, J., Lamendella, R., Landon, E. M., Lane-deGraaf, K., LaRoche, J., Larsen, P., Laverock, B., Lax, S., Lentino, M., Levin, I. I., Liancourt, P., Liang, W., Linz, A. M., Lipson, D. A., Liu, Y., Lladser, M. E., Lozada, M., Spirito, C. M., MacCormack, W. P., MacRae-Crerar, A., Magris, M., Martín-Platero, A. M., Martín-Vivaldi, M., Martínez, L. M., Martínez-Bueno, M., Marzinelli, E. M., Mason, O. U., Mayer, G. D., McDevitt-Irwin, J. M., McDonald, J., McGuire, K. L., McMahon, K. D., McMinds, R., Medina, M., Mendelson, J. R., Metcalf, J. L., Meyer, F., Michelangeli, F., Miller, K., Mills, D. A., Minich, J., Mocali, S., Moitinho-Silva, L., Moore, A., Morgan-Kiss, R. M., Munroe, P., Myrold, D., Neufeld, J. D., Ni, Y., Nicol, G. W., Nielsen, S., Nissimov, J. I., Niu, K., Nolan, M. J., Noyce, K., O’Brien, S. L., Okamoto, N., Orlando, L., Ortiz Castellano, Y., Osuolale, O., Oswald, W., Parnell, J., Peralta-Sánchez, J. M., Petraitis, P., Pfister, C., Pilon-Smits, E., Piombino, P., Pointing, S. B., Pollock, F. J., Potter, C., Prithiviraj, B., Quince, C., Rani, A., Ranjan, R., Rao, S., Rees, A. P., Richardson, M., Riebesell, U., Robinson, C., Rockne, K. J., Rodriguezl, S. M., Rohwer, F., Roundstone, W., Safran, R. J., Sangwan, N., Sanz, V., Schrenk, M., Schrenzel, M. D., Scott, N. M., Seger, R. L., Seguin-Orlando, A., Seldin, L., Seyler, L. M., Shakhsheer, B., Sheets, G. M., Shen, C., Shi, Y., Shin, H., Shogan, B. D., Shutler, D., Siegel, J., Simmons, S., Sjöling, S., Smith, D. P., Soler, J. J., Sperling, M., Steinberg, P. D., Stephens, B., Stevens, M. A., Taghavi, S., Tai, V., Tait, K., Tan, C. L., Tas, N., Taylor, D. L., Thomas, T., Timling, I., Turner, B. L., Urich, T., Ursell, L. K., van der Lelie, D., Van Treuren, W., van Zwieten, L., Vargas-Robles, D., Vega Thurber, R., Vitaglione, P., Walker, D. A., Walters, W. A., Wang, S., Wang, T., Weave, T., Webster, N. S., Wehrle, B., Weisenhorn, P., Weiss, S., Werner, J. J., West, K., Whitehead, A., Whitehead, S. R., Whittingham, L. A., Willerslev, E., Williams, A. E., Wood, S. A., Woodhams, D. C., Yang, Y., Zaneveld, J., Zarraonaindia, I., Zhang, Q. & Zhao, H., 23 Nov 2017, In : Nature. 551, 7681, p. 457-+

    Research output: Contribution to journalArticle

  4. Published

    Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

    Hassard, F., Gwyther, C. L., Farkas, K., Andrews, A., Jones, V., Cox, B., Brett, H., Jones, D., McDonald, J. & Malham, S., 1 Nov 2016, In : Frontiers in Microbiology.

    Research output: Contribution to journalArticle

  5. Published

    Bioreduction of Sheep Carcasses Effectively Contains and Reduces Pathogen Levels under Operational and Simulated Breakdown Conditions

    Golyshin, P., Gwyther, C. L., Jones, D. L., Golyshin, P. N., Edwards-Jones, G., McKillen, J., McNair, I., McDonald, J. E. & Williams, A. P., 21 May 2013, In : Environmental Science and Technology. 47, 10, p. 5267–5275

    Research output: Contribution to journalArticle

  6. Published

    Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules

    McDonald, J., Larsen, N., Pennington, A., Connolly, J., Wallis, C., Rooks, D. J., Hall, N., McCarthy, A. J. & Allison, H. E., 8 Jun 2016, In : PLoS ONE. 11, 6, e0157046.

    Research output: Contribution to journalArticle

  7. Published

    Composition of the landfill microbial community as determined by application of domian- and group-specific 16s and 18s rRNA-targeted oligonucleotide probes.

    McDonald, J. E., Allison, H. E. & McCarthy, A. J., 1 Feb 2010, In : Applied and Environmental Microbiology. 76, 4, p. 1301-1306

    Research output: Contribution to journalArticle

  8. Published

    Critical Evaluation of CrAssphage as a Molecular Marker for Human-Derived Wastewater Contamination in the Aquatic Environment

    Farkas, K., Adriaenssens, E. M., Walker, D. I., McDonald, J., Malham, S. & Jones, D. L., 1 Jun 2019, In : Food and Environmental Virology. 11, 2, p. 113-119

    Research output: Contribution to journalArticle

  9. Published

    Critical Review on the Public Health Impact of Norovirus Contamination in Shellfish and the Environment: A UK Perspective

    Hassard, F., Sharp, J., Taft, H., Le Vay, L., Harris, J., McDonald, J., Tuson, K., Wilson, J., Jones, D. & Malham, S., Jun 2017, In : Food and Environmental Virology. 9, 2, p. 123-141

    Research output: Contribution to journalArticle

  10. Published

    Decay rates of faecal indicator bacteria from sewage and ovine faeces in brackish and freshwater microcosms with contrasting suspended particulate matter concentrations

    Perkins, T. L., Perrow, K. A., Rajko-Nenow, P., Jago, C. F., Jones, D. L., Malham, S. K. & McDonald, J. E., 1 Dec 2016, In : Science of the Total Environment. 572, p. 1645-1652

    Research output: Contribution to journalArticle

  11. Published

    Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR.

    McDonald, J. E., Lockhart, R. J., Cox, M. J., Allison, H. E. & McCarthy, A. J., 1 May 2008, In : Environmental Microbiology. 10, 5, p. 2360-2365

    Research output: Contribution to journalArticle

  12. Published

    Developing Skills in Second Year Biological Science Undergraduates

    Robinson, R. L. & McDonald, J. E., 1 Jul 2014, In : Bioscience Education. 22, 1, p. 42-53

    Research output: Contribution to journalArticle

  13. Published

    Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages.

    Rooks, D. J., Yan, Y., McDonald, J. E., Woodward, M. J., McCarthy, A. J. & Allison, H. E., 1 May 2010, In : Environmental Microbiology. 12, 5, p. 1194-1204

    Research output: Contribution to journalArticle

  14. Published

    Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs

    Ransom-Jones, E., Jones, D. L., Edwards, A. & McDonald, J. E., 17 Jul 2014, In : Systematic and Applied Microbiology. 37, 7, p. 502-509

    Research output: Contribution to journalArticle

  15. Published

    Draft Genome Sequence of Clostridium sp. strain W14A isolated from a cellulose-degrading biofilm in a landfill leachate microcosm

    Ransom-Jones, E. & McDonald, J., 22 Sep 2016, In : Genome Announcements. 4, 5, e0098516.

    Research output: Contribution to journalArticle

  16. Published

    Enhancing first year undergraduate student engagement via the School of Biological Sciences tutorials module

    McDonald, J. E. & Robinson, R. L., 1 Jul 2014, In : Bioscience Education. 22, 1, p. 54-69

    Research output: Contribution to journalArticle

  17. Published

    Evaluation of Molecular Methods for the Detection and Quantification of Pathogen-Derived Nucleic Acids in Sediment

    Farkas, K., Hassard, F., McDonald, J., Malham, S. & Jones, D., 24 Jan 2017, In : Frontiers in Microbiology. 6, p. 1-12 53.

    Research output: Contribution to journalArticle

  18. Published

    Evaluation of Two Triplex One-Step qRT-PCR Assays for the Quantification of Human Enteric Viruses in Environmental Samples

    Farkas, K., Peters, D. E., McDonald, J., de Rougemont, A., Malham, S. & Jones, D., Sep 2017, In : Food and Environmental Virology. 9, 3, p. 342-349

    Research output: Contribution to journalArticle

  19. Published

    Extraction of Microbial and Host DNA, RNA, and Proteins from Oak Bark Tissue

    Broberg, M. & McDonald, J., 5 Feb 2019, In : Methods and Protocols. 2, 1, 15.

    Research output: Contribution to journalArticle

  20. Published

    Fifty important research questions in microbial ecology

    Antwis, R. E., Griffiths, S. M., Harrison, X. A., Aranega-Bou, P., Arce, A., Bettridge, A. S., Brailsford, F., de Menezes, A., Devaynes, A., Forbes, K. M., Fry, E. L., Goodhead, I., Haskell, E., Heys, C., James, C., Johnston, S. R., Lewis, G. R., Lewis, Z., Macey, M. C., McCarthy, A., McDonald, J., Mejia-Florez, N. L., O'Brien, D., Orland, C., Pautasso, M., Reid, W. D. K., Robinson, H. A., Wilson, K. & Sutherland, W. J., May 2017, In : Fems Microbiology Ecology. 93, 5, fix044.

    Research output: Contribution to journalArticle

  21. Published

    Genomic analysis of bacteria in the Acute Oak Decline pathobiome

    Doonan, J., Denman, S., Pachebat, J. A. & McDonald, J., 8 Jan 2019, In : Microbial Genomics. 5, 1, 15 p.

    Research output: Contribution to journalArticle

  22. Published

    High-Throughput Method for Rapid Induction of Prophages from Lysogens and Its Application in the Study of Shiga Toxin-Encoding Escherichia coli Strains

    McDonald, J. E., Smith, D. L., Fogg, P. C., McCarthy, A. J. & Allison, H. E., 1 Apr 2010, In : Applied and Environmental Microbiology. 76, 7, p. 2360-2365

    Research output: Contribution to journalArticle

  23. Published

    Identification of Armillaria species on declined oak in Britain: implications for oak health

    Denman, S., Barrett, G., Kirk, S. A., McDonald, J. & Coetzee, M. P. A., 7 Jan 2017, In : Forestry. 90, 1, p. 148-161

    Research output: Contribution to journalArticle

  24. Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by gammaproteobacteria and bacteroidetes

    Edwards, J. L., Smith, D. L., Connolly, J., McDonald, J. E., Cox, M. J., Joint, I., Edwards, C. & McCarthy, A. J., 26 Oct 2010, In : Genes. 1, 3, p. 371-84 14 p.

    Research output: Contribution to journalArticle

  25. Published
  26. Published

    Importance of Micromonospora spp. as colonizers of cellulose in freshwater lakes as demonstrated by quantitative reverse transcriptase PCR of 16S rRNA

    de Menezes, A. B., McDonald, J. E., Allison, H. E. & McCarthy, A. J., May 2012, In : Applied and Environmental Microbiology. 78, 9, p. 3495-9 5 p.

    Research output: Contribution to journalArticle

  27. Published

    Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

    Broberg, M., Doonan, J., Mundt, F. & McDonald, J., 30 Jan 2018, In : Microbiome. 6, 21.

    Research output: Contribution to journalArticle

  28. Published

    Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline

    Denman, S., Plummer, S., Peace, A. & McDonald, J., 1 Oct 2016, In : Systematic and Applied Microbiology. 39, 7, p. 484-490

    Research output: Contribution to journalArticle

  29. Published

    Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass- Degrading Diversity Emma

    Ransom-Jones, E., McCarthy, AJ., Haldenby, S., Doonan, J. & McDonald, JE., Aug 2017, In : mSphere. 2, 4, e00300.

    Research output: Contribution to journalArticle

  30. Published

    Metagenomic approaches to the discovery of cellulases

    Rooks, D. J., McDonald, J. E. & McCarthy, A. J., 2012, In : Methods in Enzymology. 510, p. 375-94 20 p.

    Research output: Contribution to journalArticle

  31. Published

    Methods for the isolation of cellulose-degrading microorganisms

    McDonald, J. E., Rooks, D. J. & McCarthy, A. J., 2012, In : Methods in Enzymology. 510, p. 349-74 26 p.

    Research output: Contribution to journalArticle

  32. Published

    Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline

    Denman, S., Doonan, J., Ransom-Jones, E., Broberg, M., Plummer, S., Kirk, S. A., Scarlett, K., Griffiths, A., Kaczmarek, M., Foster, J., Peace, A., Golyshin, P., Hassard, F., Brown, N., Kenny, J. G. & McDonald, J., 2018, In : The ISME Journal. 12, p. 386-399

    Research output: Contribution to journalArticle

  33. Published

    Molecular biological detection and quantification of novel Fibrobacter populations in freshwater lakes.

    McDonald, J. E., De Menezes, A. B., Allison, H. E. & McCarthy, A. J., 1 Aug 2009, In : Applied and Environmental Microbiology. 75, 15, p. 5148-5152

    Research output: Contribution to journalArticle

  34. Published

    Multilocus sequence typing provides insights into the population structure and evolutionary potential of Brenneria goodwinii, associated with acute oak decline

    Kaczmarek, M., Mullett, M. S., McDonald, J. & Denman, S., 1 Jun 2017, In : PLoS ONE. 12, 6, e0178390.

    Research output: Contribution to journalArticle

  35. Published

    Physicochemical Factors Influence the Abundance and Culturability of Human Enteric Pathogens and Fecal Indicator Organisms in Estuarine Water and Sediment

    Hassard, F., Andrews, A., Jones, D. L., Parsons, L., Jones, V., Cox, B. A., Daldorph, P., Brett, H., McDonald, J. & Malham, S., Oct 2017, In : Frontiers in Microbiology. 8, 1996.

    Research output: Contribution to journalArticle

  36. Published

    Seasonal and diurnal surveillance of treated and untreated wastewater for human enteric viruses

    Farkas, K., Marshall, M., Cooper, D., McDonald, J., Malham, S., Peters, D. E., Maloney, J. & Jones, D. L., 1 Nov 2018, In : Environmental Science and Pollution Research. 25, 33, p. 33391-33401

    Research output: Contribution to journalArticle

  37. Published

    Seasonal and spatial dynamics of enteric viruses in wastewater and in riverine and estuarine receiving waters

    Malham, S., Farkas, K., McDonald, J., Jones, D. L., Cooper, D. & de Rougemont, A., 1 Sep 2018, In : Science of the Total Environment. 634, p. 1174 1183 p.

    Research output: Contribution to journalArticle

  38. Published
  39. Published

    Spatial patterns and environmental constraints on ecosystem services at a catchment scale

    Emmett, B., Cooper, D., Smart, S., Jackson, B., Thomas, A., Cosby, B., Evans, C., Glanville, H., McDonald, J., Malham, S., Marshall, M., Jarvis, S., Rajko-Nenow, P., Webb, G. P., Ward, S., Rowe, E., Jones, L., Vanbergen, E. J., Keith, A., Carter, H., Pereira, M. G., Hughes, S., Lebron, I., Wade, A. & Jones, D., 1 Dec 2016, In : Science of the Total Environment. 572, p. 1586-1600

    Research output: Contribution to journalArticle

  40. Published

    Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems

    Potter, C., Freeman, C., Golyshin, P., Ackerman, G., Fenner, N., McDonald, J., Ehbair, A., Jones, T., Murphy, L. & Creer, S., Sep 2017, In : Scientific Reports. 7, 11314.

    Research output: Contribution to journalArticle

  41. Published

    The Fibrobacteres: an Important Phylum of Cellulose-Degrading Bacteria

    Ransom-Jones, E., Jones, D., McCarthy, A. J. & McDonald, J. E., Feb 2012, In : Microbial Ecology. 63, 2, p. 267-281

    Research output: Contribution to journalArticle

  42. Published

    The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters

    Malham, S. K., Rajko-Nenow, P., Howlett, E., Tuson, K. E., Perkins, T. L., Pallett, D. W., Wang, H., Jago, C. F., Jones, D. L. & McDonald, J. E., 7 Jul 2014, In : Environmental Science: Processes and Impacts. 16, p. 2145-2155

    Research output: Contribution to journalArticle

  43. Published

    The intergenic transcribed spacer region 1 as a molecular marker for identification and discrimination of Enterobacteriaceae associated with acute oak decline

    Doonan, J., Denman, S., Gertler, C., Pachebat, J. A., Golyshin, P. N. & McDonald, J. E., 1 Jan 2015, In : Journal of Applied Microbiology. 118, 1, p. 193-201 9 p.

    Research output: Contribution to journalArticle

  44. Published

    The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters

    McDonald, J. E., Houghton, J. N., Rooks, D. J., Allison, H. E. & McCarthy, A. J., 1 Apr 2012, In : Environmental Microbiology. 14, 4, p. 1077-1087

    Research output: Contribution to journalArticle

  45. Published

    Two-Step Concentration of Complex Water Samples for the Detection of Viruses

    Farkas, K., McDonald, J., Malham, S. & Jones, D. L., 10 Sep 2018, In : Methods and Protocols. 1, 3, 35.

    Research output: Contribution to journalArticle

  46. Published

    Use of Mytilus edulis biosentinels to investigate spatial patterns of norovirus and faecal indicator organism contamination around coastal sewage discharges

    Winterbourn, J., Clements, K., Lowther, J. A., Malham, S., McDonald, J. & Jones, D., 15 Nov 2016, In : Water Research. 105, November, p. 241-250

    Research output: Contribution to journalArticle

  47. Published

    Using chemical, microbial and fluorescence techniques to understand contaminant sources and pathways to wetlands in a conservation site

    Rhymes, J. M., Rhymes, J., Jones, L., Lapworth, D. J., White, D., Fenner, N., McDonald, J. E. & Perkins, T. L., 20 Jan 2015, In : Science of the Total Environment. 511, p. 703-710

    Research output: Contribution to journalArticle

  48. Chapter › Research › Not peer-reviewed
  49. Published

    Shotgun Metagenomic Sequencing Analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities

    Doonan, J., Denman, S., McDonald, J. & Golyshin, P., 30 Nov 2016, Metagenomics. Streit, W. R. & Daniel, R. (eds.). Springer New York, Vol. 1539. p. 85-97 (Methods in Molecular Biology; vol. 1539).

    Research output: Chapter in Book/Report/Conference proceedingChapter

  50. Review article › Research › Peer-reviewed
  51. Taxonomy and identification of bacteria associated with acute oak decline

    Brady, C., Arnold, D., McDonald, J. & Denman, S., Jul 2017, In : World Journal of Microbiology and Biotechnology. 33, 7, p. 143

    Research output: Contribution to journalReview article