PUBLICATIONS

2019

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

  Farkas, K, Adriaenssens, EM, Walker, DI, McDonald, J, Malham, S & Jones, DL 2019, 'Critical Evaluation of CrAssphage as a Molecular Marker for Human-Derived Wastewater Contamination in the Aquatic Environment', Food and Environmental Virology, vol. 11, no. 2, pp. 113-119. https://doi.org/10.1007/s12560-019-09369-1.

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

  Broberg, M & McDonald, J 2019, 'Extraction of Microbial and Host DNA, RNA, and Proteins from Oak Bark Tissue', Methods and Protocols, vol. 2, no. 1, 15. https://doi.org/10.3390/mps2010015

• Genomic analysis of bacteria in the Acute Oak Decline pathobiome

  Doonan, J, Denman, S, Pachebat, JA & McDonald, J 2019, 'Genomic analysis of bacteria in the Acute Oak Decline pathobiome', Microbial Genomics, vol. 5, no. 1. https://doi.org/10.1099/mgen.0.000240

2018

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

  Farkas, K, Marshall, M, Cooper, D, McDonald, J, Malham, S, Peters, DE, Maloney, J & Jones, DL 2018, 'Seasonal and diurnal surveillance of treated and untreated wastewater for human enteric viruses', Environmental Science and Pollution Research, vol. 25, no. 33, pp. 33391-33401. https://doi.org/10.1007/s11356-018-3261-y

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

  Farkas, K, McDonald, J, Malham, S & Jones, DL 2018, 'Two-Step Concentration of Complex Water Samples for the Detection of Viruses', Methods and Protocols, vol. 1, no. 3, 35. https://doi.org/10.3390/mps1030035

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

  Malham, S, Farkas, K, McDonald, J, Jones, DL, Cooper, D & de Rougemont, A 2018, 'Seasonal and spatial dynamics of enteric viruses in wastewater and in riverine and estuarine receiving waters', Science of the Total Environment, vol. 634, pp. 1174. https://doi.org/10.1016/j.scitotenv.2018.04.038

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

  Broberg, M, Doonan, J, Mundt, F & McDonald, J 2018, 'Integrated multi-omic analysis of host-microbiota interactions in acute oak decline', Microbiome, vol. 6, 21. https://doi.org/10.1186/s40168-018-0408-5

• 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, SA, Scarlett, K, Griffiths, A, Kaczmarek, M, Foster, J, Peace, A, Golyshin, P, Hassard, F, Brown, N, Kenny, JG & McDonald, J 2018, 'Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline', The ISME Journal, vol. 12, pp. 386-399. https://doi.org/10.1038/ismej.2017.170

2017

• A communal catalogue reveals Earth's multiscale microbial diversity

  Thompson, LR, Sanders, JG, McDonald, D, Amir, A, Ladau, J, Locey, KJ, Prill, RJ, Tripathi, A, Gibbons, SM, Ackermann, G, Navas-Molina, JA, Janssen, S, Kopylova, E, Vazquez-Baeza, Y, Gonzalez, A, Morton, JT, Mirarab, S, Xu, ZZ, Jiang, L, Haroon, MF, Kanbar, J, Zhu, Q, Song, SJ, Kosciolek, T, Bokulich, NA, Lefler, J, Brislawn, CJ, Humphrey, G, Owens, SM, Hampton-Marcell, J, Berg-Lyons, D, McKenzie, V, Fierer, N, Fuhrman, JA, Clauset, A, Stevens, RL, Shade, A, Pollard, KS, Goodwin, KD, Jansson, JK, Gilbert, JA, Knight, R, Agosto Rivera, JL, Al-Moosawi, L, Alverdy, J, Amato, KR, Andras, J, Angenent, LT, Antonopoulos, DA, Apprill, A, Armitage, D, Ballantine, K, Bárta, J, Baum, JK, Berry, A, Bhatnagar, A, Bhatnagar, M, Biddle, JF, Bittner, L, Boldgiv, B, Bottos, E, Boyer, DM, Braun, J, Brazelton, W, Brearley, FQ, Campbell, AH, Caporaso, JG, Cardona, C, Carroll, J, Cary, SC, Casper, BB, Charles, TC, Chu, H, Claar, DC, Clark, RG, Clayton, JB, Clemente, JC, Cochran, A, Coleman, ML, Collins, G, Colwel, RR, Contreras, M, Crary, BB, Creer, S, Cristol, DA, Crump, BC, Cui, D, Daly, SE, Davalos, L, Dawson, RD, Defazio, J, Delsuc, F, Dionisi, HM, Dominguez-Bello, MG, Dowell, R, Dubinsky, EA, Dunn, PO, Ercolini, D, Espinoza, RE, Ezenwa, V, Fenner, N, Findlay, HS, Fleming, ID, Fogliano, V, Forsman, A, Freeman, C, Friedman, ES, Galindo, G, Garcia, L, Garcia-Amado, MA, Garshelis, D, Gasser, RB, Gerdts, G, Gibson, MK, Gifford, I, Gill, RT, Giray, T, Gittel, A, Golyshin, P, Gong, D, Grossart, H-P, Guyton, K, Haig, S-J, Hale, V, Hall, RS, Hallam, SJ, Handley, KM, Hasan, NA, Haydon, SR, Hickman, JE, Hidalgo, G, Hofmockel, KS, Hooker, J, Hulth, S, Hultman, J, Hyde, E, Ibáñez-Álamo, JD, Jastrow, JD, Jex, AR, Johnson, LS, Johnston, ER, Joseph, S, Jurburg, SD, Jurelevicius, D, Karlsson, A, Karlsson, R, Kauppinen, S, Kellogg, CTE, Kennedy, SJ, Kerkhof, LJ, King, GM, Kling, GW, Koehler, AV, Krezalek, M, Kueneman, J, Lamendella, R, Landon, EM, Lane-deGraaf, K, LaRoche, J, Larsen, P, Laverock, B, Lax, S, Lentino, M, Levin, II, Liancourt, P, Liang, W, Linz, AM, Lipson, DA, Liu, Y, Lladser, ME, Lozada, M, Spirito, CM, MacCormack, WP, MacRae-Crerar, A, Magris, M, Martín-Platero, AM, Martín-Vivaldi, M, Martínez, LM, Martínez-Bueno, M, Marzinelli, EM, Mason, OU, Mayer, GD, McDevitt-Irwin, JM, McDonald, J, McGuire, KL, McMahon, KD, McMinds, R, Medina, M, Mendelson, JR, Metcalf, JL, Meyer, F, Michelangeli, F, Miller, K, Mills, DA, Minich, J, Mocali, S, Moitinho-Silva, L, Moore, A, Morgan-Kiss, RM, Munroe, P, Myrold, D, Neufeld, JD, Ni, Y, Nicol, GW, Nielsen, S, Nissimov, JI, Niu, K, Nolan, MJ, Noyce, K, O’Brien, SL, Okamoto, N, Orlando, L, Ortiz Castellano, Y, Osuolale, O, Oswald, W, Parnell, J, Peralta-Sánchez, JM, Petraitis, P, Pfister, C, Pilon-Smits, E, Piombino, P, Pointing, SB, Pollock, FJ, Potter, C, Prithiviraj, B, Quince, C, Rani, A, Ranjan, R, Rao, S, Rees, AP, Richardson, M, Riebesell, U, Robinson, C, Rockne, KJ, Rodriguezl, SM, Rohwer, F, Roundstone, W, Safran, RJ, Sangwan, N, Sanz, V, Schrenk, M, Schrenzel, MD, Scott, NM, Seger, RL, Seguin-Orlando, A, Seldin, L, Seyler, LM, Shakhsheer, B, Sheets, GM, Shen, C, Shi, Y, Shin, H, Shogan, BD, Shutler, D, Siegel, J, Simmons, S, Sjöling, S, Smith, DP, Soler, JJ, Sperling, M, Steinberg, PD, Stephens, B, Stevens, MA, Taghavi, S, Tai, V, Tait, K, Tan, CL, Tas, N, Taylor, DL, Thomas, T, Timling, I, Turner, BL, Urich, T, Ursell, LK, van der Lelie, D, Van Treuren, W, van Zwieten, L, Vargas-Robles, D, Vega Thurber, R, Vitaglione, P, Walker, DA, Walters, WA, Wang, S, Wang, T, Weave, T, Webster, NS, Wehrle, B, Weisenhorn, P, Weiss, S, Werner, JJ, West, K, Whitehead, A, Whitehead, SR, Whittingham, LA, Willerslev, E, Williams, AE, Wood, SA, Woodhams, DC, Yang, Y, Zaneveld, J, Zarraonaindia, I, Zhang, Q & Zhao, H 2017, 'A communal catalogue reveals Earth's multiscale microbial diversity', Nature, vol. 551, no. 7681, pp. 457-+. https://doi.org/10.1038/nature24621

• 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, DL, Parsons, L, Jones, V, Cox, BA, Daldorph, P, Brett, H, McDonald, J & Malham, S 2017, 'Physicochemical Factors Influence the Abundance and Culturability of Human Enteric Pathogens and Fecal Indicator Organisms in Estuarine Water and Sediment', Frontiers in Microbiology, vol. 8, 1996. https://doi.org/10.3389/fmicb.2017.01996

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

  Farkas, K, Peters, DE, McDonald, J, de Rougemont, A, Malham, S & Jones, D 2017, 'Evaluation of Two Triplex One-Step qRT-PCR Assays for the Quantification of Human Enteric Viruses in Environmental Samples', Food and Environmental Virology, vol. 9, no. 3, pp. 342-349. https://doi.org/10.1007/s12560-017-9293-5

• 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 2017, 'Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems', Scientific Reports, vol. 7, 11314. https://doi.org/10.1038/s41598-017-11546-w

• 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 2017, 'Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass- Degrading Diversity Emma', mSphere, vol. 2, no. 4, e00300. https://doi.org/10.1128/mSphere.00300-17

• Taxonomy and identification of bacteria associated with acute oak decline

  Brady, C, Arnold, D, McDonald, J & Denman, S 2017, 'Taxonomy and identification of bacteria associated with acute oak decline', World Journal of Microbiology and Biotechnology, vol. 33, no. 7, pp. 143. https://doi.org/10.1007/s11274-017-2296-4

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

  Kaczmarek, M, Mullett, MS, McDonald, J & Denman, S 2017, 'Multilocus sequence typing provides insights into the population structure and evolutionary potential of Brenneria goodwinii, associated with acute oak decline', PLoS ONE, vol. 12, no. 6, e0178390. https://doi.org/10.1371/journal.pone.0178390

• Critical Review on the Public Health Impact of Norovirus Contamination in Shellfish and the Environment

  Hassard, F, Sharp, J, Taft, H, Le Vay, L, Harris, J, McDonald, J, Tuson, K, Wilson, J, Jones, D & Malham, S 2017, 'Critical Review on the Public Health Impact of Norovirus Contamination in Shellfish and the Environment: A UK Perspective', Food and Environmental Virology, vol. 9, no. 2, pp. 123-141. https://doi.org/10.1007/s12560-017-9279-3

• Fifty important research questions in microbial ecology

  Antwis, RE, Griffiths, SM, Harrison, XA, Aranega-Bou, P, Arce, A, Bettridge, AS, Brailsford, F, de Menezes, A, Devaynes, A, Forbes, KM, Fry, EL, Goodhead, I, Haskell, E, Heys, C, James, C, Johnston, SR, Lewis, GR, Lewis, Z, Macey, MC, McCarthy, A, McDonald, J, Mejia-Florez, NL, O'Brien, D, Orland, C, Pautasso, M, Reid, WDK, Robinson, HA, Wilson, K & Sutherland, WJ 2017, 'Fifty important research questions in microbial ecology', Fems Microbiology Ecology, vol. 93, no. 5, fix044. https://doi.org/10.1093/femsec/fix044

• 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 2017, 'Evaluation of Molecular Methods for the Detection and Quantification of Pathogen-Derived Nucleic Acids in Sediment', Frontiers in Microbiology, vol. 6, 53, pp. 1-12. https://doi.org/10.3389/fmicb.2017.00053

• Identification of Armillaria species on declined oak in Britain

  Denman, S, Barrett, G, Kirk, SA, McDonald, J & Coetzee, MPA 2017, 'Identification of Armillaria species on declined oak in Britain: implications for oak health', Forestry, vol. 90, no. 1, pp. 148-161. https://doi.org/10.1093/forestry/cpw054

2016

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

  Perkins, TL, Perrow, KA, Rajko-Nenow, P, Jago, CF, Jones, DL, Malham, SK & McDonald, JE 2016, 'Decay rates of faecal indicator bacteria from sewage and ovine faeces in brackish and freshwater microcosms with contrasting suspended particulate matter concentrations', Science of the Total Environment, vol. 572, pp. 1645-1652. https://doi.org/10.1016/j.scitotenv.2016.03.076

• 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, GP, Ward, S, Rowe, E, Jones, L, Vanbergen, EJ, Keith, A, Carter, H, Pereira, MG, Hughes, S, Lebron, I, Wade, A & Jones, D 2016, 'Spatial patterns and environmental constraints on ecosystem services at a catchment scale', Science of the Total Environment, vol. 572, pp. 1586-1600. https://doi.org/10.1016/j.scitotenv.2016.04.004

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

  Doonan, J, Denman, S, McDonald, J & Golyshin, P 2016, Shotgun Metagenomic Sequencing Analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities. in WR Streit & R Daniel (eds), Metagenomics. vol. 1539, Methods in Molecular Biology, vol. 1539, Springer New York, pp. 85-97. https://doi.org/10.1007/978-1-4939-6691-2_7

• 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, JA, Malham, S, McDonald, J & Jones, D 2016, 'Use of Mytilus edulis biosentinels to investigate spatial patterns of norovirus and faecal indicator organism contamination around coastal sewage discharges', Water Research, vol. 105, no. November, pp. 241-250. https://doi.org/10.1016/j.watres.2016.09.002

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

  Hassard, F, Gwyther, CL, Farkas, K, Andrews, A, Jones, V, Cox, B, Brett, H, Jones, D, McDonald, J & Malham, S 2016, 'Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review', Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2016.01692

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

  Denman, S, Plummer, S, Peace, A & McDonald, J 2016, 'Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline', Systematic and Applied Microbiology, vol. 39, no. 7, pp. 484-490.

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

  Ransom-Jones, E & McDonald, J 2016, 'Draft Genome Sequence of Clostridium sp. strain W14A isolated from a cellulose-degrading biofilm in a landfill leachate microcosm', Genome Announcements, vol. 4, no. 5, e0098516. https://doi.org/10.1128/genomeA.00985-16

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

  McDonald, J, Larsen, N, Pennington, A, Connolly, J, Wallis, C, Rooks, DJ, Hall, N, McCarthy, AJ & Allison, HE 2016, 'Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules', PLoS ONE, vol. 11, no. 6, e0157046. https://doi.org/10.1371/ journal.pone.0157046

2015

• Impact of climate change on UK estuaries: A review of past trends and potential projections

  Robins, PE, Skov, MW, Lewis, MJ, Gimenez, L, Davies, AG, Malham, SK, Neill, SP, McDonald, JE, Whitton, TA, Jackson, SE & Jago, CF 2015, 'Impact of climate change on UK estuaries: A review of past trends and potential projections', Estuarine, Coastal and Shelf Science, vol. 169, pp. 119-135. https://doi.org/10.1016/j.ecss.2015.12.016

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

  Rhymes, JM, Rhymes, J, Jones, L, Lapworth, DJ, White, D, Fenner, N, McDonald, JE & Perkins, TL 2015, 'Using chemical, microbial and fluorescence techniques to understand contaminant sources and pathways to wetlands in a conservation site', Science of the Total Environment, vol. 511, pp. 703-710. https://doi.org/10.1016/j.scitotenv.2014.12.085

• 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, JA, Golyshin, PN & McDonald, JE 2015, 'The intergenic transcribed spacer region 1 as a molecular marker for identification and discrimination of Enterobacteriaceae associated with acute oak decline', Journal of Applied Microbiology, vol. 118, no. 1, pp. 193-201. https://doi.org/10.1111/jam.12677

2014

• Sediment Composition Influences Spatial Variation in the Abundance of Human Pathogen Indicator Bacteria within an Estuarine Environment

  Perkins, TL, Clements, K, Baas, JH, Jago, CF, Jones, DL, Malham, SK & McDonald, JE 2014, 'Sediment Composition Influences Spatial Variation in the Abundance of Human Pathogen Indicator Bacteria within an Estuarine Environment', PLoS ONE, vol. 9, no. 11. https://doi.org/10.1371/journal.pone.0112951

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

  Ransom-Jones, E, Jones, DL, Edwards, A & McDonald, JE 2014, 'Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs', Systematic and Applied Microbiology, vol. 37, no. 7, pp. 502-509. https://doi.org/10.1016/j.syapm.2014.06.001

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

  Malham, SK, Rajko-Nenow, P, Howlett, E, Tuson, KE, Perkins, TL, Pallett, DW, Wang, H, Jago, CF, Jones, DL & McDonald, JE 2014, 'The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters', Environmental Science: Processes and Impacts, vol. 16, pp. 2145-2155. https://doi.org/10.1039/C4EM00031E

• Developing Skills in Second Year Biological Science Undergraduates

  Robinson, RL & McDonald, JE 2014, 'Developing Skills in Second Year Biological Science Undergraduates', Bioscience Education, vol. 22, no. 1, pp. 42-53. https://doi.org/10.11120/beej.2014.00026

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

  McDonald, JE & Robinson, RL 2014, 'Enhancing first year undergraduate student engagement via the School of Biological Sciences tutorials module', Bioscience Education, vol. 22, no. 1, pp. 54-69. https://doi.org/10.11120/beej.2014.00025

2013

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

  Golyshin, P, Gwyther, CL, Jones, DL, Golyshin, PN, Edwards-Jones, G, McKillen, J, McNair, I, McDonald, JE & Williams, AP 2013, 'Bioreduction of Sheep Carcasses Effectively Contains and Reduces Pathogen Levels under Operational and Simulated Breakdown Conditions', Environmental Science and Technology, vol. 47, no. 10, pp. 5267–5275. https://doi.org/10.1021/es400183z

2012

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

  de Menezes, AB, McDonald, JE, Allison, HE & McCarthy, AJ 2012, 'Importance of Micromonospora spp. as colonizers of cellulose in freshwater lakes as demonstrated by quantitative reverse transcriptase PCR of 16S rRNA', Applied and Environmental Microbiology, vol. 78, no. 9, pp. 3495-9. https://doi.org/10.1128/AEM.07314-11

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

  McDonald, JE, Houghton, JN, Rooks, DJ, Allison, HE & McCarthy, AJ 2012, 'The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters', Environmental Microbiology, vol. 14, no. 4, pp. 1077-1087. https://doi.org/10.1111/j.1462-2920.2011.02688.x

• The Fibrobacteres: an Important Phylum of Cellulose-Degrading Bacteria

  Ransom-Jones, E, Jones, D, McCarthy, AJ & McDonald, JE 2012, 'The Fibrobacteres: an Important Phylum of Cellulose-Degrading Bacteria', Microbial Ecology, vol. 63, no. 2, pp. 267-281. https://doi.org/10.1007/s00248-011-9998-1

• Metagenomic approaches to the discovery of cellulases

  Rooks, DJ, McDonald, JE & McCarthy, AJ 2012, 'Metagenomic approaches to the discovery of cellulases', Methods in Enzymology, vol. 510, pp. 375-94. https://doi.org/10.1016/B978-0-12-415931-0.00020-3

• Methods for the isolation of cellulose-degrading microorganisms

  McDonald, JE, Rooks, DJ & McCarthy, AJ 2012, 'Methods for the isolation of cellulose-degrading microorganisms', Methods in Enzymology, vol. 510, pp. 349-74. https://doi.org/10.1016/B978-0-12-415931-0.00019-7

2010

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

  Edwards, JL, Smith, DL, Connolly, J, McDonald, JE, Cox, MJ, Joint, I, Edwards, C & McCarthy, AJ 2010, 'Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by gammaproteobacteria and bacteroidetes', Genes, vol. 1, no. 3, pp. 371-84. https://doi.org/10.3390/genes1030371

• 454-pyrosequencing

  Rooks, DJ, Smith, DL, McDonald, JE, Woodward, MJ, McCarthy, AJ & Allison, HE 2010, '454-pyrosequencing: a molecular battiscope for freshwater viral ecology', Genes, vol. 1, no. 2, pp. 210-26. https://doi.org/10.3390/genes1020210

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

  Rooks, DJ, Yan, Y, McDonald, JE, Woodward, MJ, McCarthy, AJ & Allison, HE 2010, 'Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages.', Environmental Microbiology, vol. 12, no. 5, pp. 1194-1204. https://doi.org/10.1111/j.1462-2920.2010.02162.x

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

  McDonald, JE, Smith, DL, Fogg, PC, McCarthy, AJ & Allison, HE 2010, 'High-Throughput Method for Rapid Induction of Prophages from Lysogens and Its Application in the Study of Shiga Toxin-Encoding Escherichia coli Strains', Applied and Environmental Microbiology, vol. 76, no. 7, pp. 2360-2365. https://doi.org/10.1128/​AEM.02923-09

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

  McDonald, JE, Allison, HE & McCarthy, AJ 2010, 'Composition of the landfill microbial community as determined by application of domian- and group-specific 16s and 18s rRNA-targeted oligonucleotide probes.', Applied and Environmental Microbiology, vol. 76, no. 4, pp. 1301-1306. https://doi.org/10.1128/AEM.01783-09

2009

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

  McDonald, JE, De Menezes, AB, Allison, HE & McCarthy, AJ 2009, 'Molecular biological detection and quantification of novel Fibrobacter populations in freshwater lakes.', Applied and Environmental Microbiology, vol. 75, no. 15, pp. 5148-5152. https://doi.org/10.1128/AEM.00701-09

2008

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

  McDonald, JE, Lockhart, RJ, Cox, MJ, Allison, HE & McCarthy, AJ 2008, 'Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR.', Environmental Microbiology, vol. 10, no. 5, pp. 2360-2365. https://doi.org/10.1111/j.1462-2920.2007.01544.x