Select Publications

Journal articles

Aw WC; Towarnicki SG; Melvin RG; Youngson NA; Garvin MR; Hu Y; Nielsen S; Thomas T; Pickford R; Bustamante S; Vila-Sanjurjo A; Smyth GK; Ballard JWO, 2018, 'Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness', PLoS Genetics, 14, http://dx.doi.org/10.1371/journal.pgen.1007735

Gribben PE; Thomas T; Pusceddu A; Bonechi L; Bianchelli S; Buschi E; Nielsen S; Ravaglioli C; Bulleri F, 2018, 'Below-ground processes control the success of an invasive seaweed', Journal of Ecology, 106, pp. 2082 - 2095, http://dx.doi.org/10.1111/1365-2745.12966

Dewi DAPR; Thomas T, 2018, 'Detection of carbapenem-resistant bacteria in the public area of a hospital', Journal of Global Antimicrobial Resistance, 14, pp. 166 - 168, http://dx.doi.org/10.1016/j.jgar.2018.07.005

Díez-Vives C; Esteves AIS; Costa R; Nielsen S; Thomas T, 2018, 'Detecting signatures of a sponge-associated lifestyle in bacterial genomes', Environmental Microbiology Reports, 10, pp. 433 - 443, http://dx.doi.org/10.1111/1758-2229.12655

Reynolds A; Joseph SD; Verheyen TV; Chinu K; Taherymoosavi S; Munroe PR; Donne S; Pace B; van Zwieten L; Marjo CE; Thomas T; Rawal A; Hook J, 2018, 'Effect of clay and iron sulphate on volatile and water-extractable organic compounds in bamboo biochars', Journal of Analytical and Applied Pyrolysis, 133, pp. 22 - 29, http://dx.doi.org/10.1016/j.jaap.2018.05.007

Ozkan J; Coroneo M; Willcox M; Wemheuer B; Thomas T, 2018, 'Identification and visualization of a distinct microbiome in ocular surface conjunctival tissue', Investigative Ophthalmology and Visual Science, 59, pp. 4268 - 4276, http://dx.doi.org/10.1167/iovs.18-24651

Roth-Schulze AJ; Pintado J; Zozaya-Valdés E; Cremades J; Ruiz P; Kjelleberg S; Thomas T, 2018, 'Functional biogeography and host specificity of bacterial communities associated with the Marine Green Alga Ulva spp.', Molecular Ecology, 27, pp. 1952 - 1965, http://dx.doi.org/10.1111/mec.14529

Nielsen S; Joseph S; Ye J; Chia C; Munroe P; Zwieten LV; Thomas T, 2018, 'Crop-season and residual effects of sequentially applied mineral enhanced biochar and N fertiliser on crop yield, soil chemistry and microbial communities', Agriculture, Ecosystems and Environment, 255, pp. 52 - 61, http://dx.doi.org/10.1016/j.agee.2017.12.020

Beattie DT; Lachnit T; Dinsdale EA; Thomas T; Steinberg PD, 2018, 'Novel ssDNA viruses detected in the virome of bleached, habitat-forming kelp Ecklonia radiata', Frontiers in Marine Science, 4, http://dx.doi.org/10.3389/fmars.2017.00441

Nguyen MTHD; Thomas T, 2018, 'Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges', PeerJ, 2018, http://dx.doi.org/10.7717/peerj.4965

Ye J; Perez PG; Zhang R; Nielsen S; Huang D; Thomas T, 2018, 'Effects of different C/N ratios on bacterial compositions and processes in an organically managed soil', Biology and Fertility of Soils, 54, pp. 137 - 147, http://dx.doi.org/10.1007/s00374-017-1246-5

Roth-Schulze AJ; Thomas T; Steinberg P; Deveney MR; Tanner JE; Wiltshire KH; Papantoniou S; Runcie JW; Gurgel CFD, 2018, 'The effects of warming and ocean acidification on growth, photosynthesis, and bacterial communities for the marine invasive macroalga Caulerpa taxifolia', Limnology and Oceanography, 63, pp. 459 - 471, http://dx.doi.org/10.1002/lno.10739

Coffey MJ; Low I; Stelzer-Braid S; Rawlinson W; Thomas T; Jaffe A; Ooi CY, 2018, 'EPS4.04 Characterising the intestinal virome in cystic fibrosis', Journal of Cystic Fibrosis, 17, pp. S44 - S44, http://dx.doi.org/10.1016/s1569-1993(18)30256-x

Coffey MJ; Nielsen S; Wemheuer B; Needham B; Jaffe A; Thomas T; Ooi CY, 2018, 'P071 Predicting the functional intestinal profiles in cystic fibrosis', Journal of Cystic Fibrosis, 17, pp. S79 - S79, http://dx.doi.org/10.1016/s1569-1993(18)30368-0

Wemheuer F; Taylor J; Daniel R; Johnston E; Meinicke P; Thomas T; Wemheuer B, 2018, 'Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences', , http://dx.doi.org/10.1101/490037

Meneghine AK; Nielsen S; Varani AM; Thomas T; Alves LMC, 2017, 'Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization', PLoS ONE, 12, http://dx.doi.org/10.1371/journal.pone.0190178

Gribben PE; Nielsen S; Seymour JR; Bradley DJ; West MN; Thomas T, 2017, 'Microbial communities in marine sediments modify success of an invasive macrophyte', Scientific Reports, 7, http://dx.doi.org/10.1038/s41598-017-10231-2

Ozkan J; Nielsen S; Diez-Vives C; Coroneo M; Thomas T; Willcox M, 2017, 'Temporal Stability and Composition of the Ocular Surface Microbiome', Scientific Reports, 7, http://dx.doi.org/10.1038/s41598-017-10494-9

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; Rivera JLA; Al-Moosawi L; Alverdy J; Amato KR; Andras J; Angenent LT; Antonopoulos DA; Apprill A; Armitage D; Ballantine K; Barta 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; Colwell 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; Alexandra Garcia-Amado M; 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; Ibanez-Alamo 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; Martin-Platero AM; Martin-Vivaldi M; Margarita Martinez L; Martinez-Bueno M; Marzinelli EM; Mason OU; Mayer GD; McDevitt-Irwin JM; McDonald JE; 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; Castellano YO; Osuolale O; Oswald W; Parnell J; Peralta-Sanchez 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; Sjoling 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; Thurber RV; Vitaglione P; Walker DA; Walters WA; Wang S; Wang T; Weaver 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, 551, pp. 457 - +, http://dx.doi.org/10.1038/nature24621

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; Vázquez-Baeza Y; González 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 JL; Cary SC; Casper BB; Charles TC; Chu H; Claar DC; Clark RG; Clayton JB; Clemente JC; Cochran A; Coleman ML; Collins G; Colwell 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, 2017, 'A communal catalogue reveals Earth's multiscale microbial diversity', Nature, 551, pp. 457 - 463, http://dx.doi.org/10.1038/nature24621

Moitinho-Silva L; Nielsen S; Amir A; Gonzalez A; Ackermann GL; Cerrano C; Astudillo-Garcia C; Easson C; Sipkema D; Liu F; Steinert G; Kotoulas G; McCormack GP; Feng G; Bell JJ; Vicente J; Bjork JR; Montoya JM; Olson JB; Reveillaud J; Steindler L; Pineda M-C; Marra MV; Ilan M; Taylor MW; Polymenakou P; Erwin PM; Schupp PJ; Simister RL; Knight R; Thacker RW; Costa R; Hill RT; Lopez-Legentil S; Dailianis T; Ravasi T; Hentschel U; Li Z; Webster NS; Thomas T, 2017, 'The sponge microbiome project', GIGASCIENCE, 6, http://dx.doi.org/10.1093/gigascience/gix077

Zozaya-Valdés E; Roth-Schulze AJ; Egan S; Thomas T, 2017, 'Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra', Environmental Microbiology, 19, pp. 3012 - 3024, http://dx.doi.org/10.1111/1462-2920.13758

Moitinho-Silva L; Díez-Vives C; Batani G; Esteves AIS; Jahn MT; Thomas T, 2017, 'Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics', ISME Journal, 11, pp. 1651 - 1666, http://dx.doi.org/10.1038/ismej.2017.25

Song WZ; Thomas T, 2017, 'Binning-refiner: Improving genome bins through the combination of different binning programs', Bioinformatics, 33, pp. 1873 - 1875, http://dx.doi.org/10.1093/bioinformatics/btx086

Moitinho-Silva L; Steinert G; Nielsen S; Hardoim CCP; Wu YC; McCormack GP; López-Legentil S; Marchant R; Webster N; Thomas T; Hentschel U, 2017, 'Predicting the HMA-LMA status in marine sponges by machine learning', Frontiers in Microbiology, 8, http://dx.doi.org/10.3389/fmicb.2017.00752

Ye J; Joseph SD; Ji M; Nielsen S; Mitchell DRG; Donne S; Horvat J; Wang J; Munroe P; Thomas T, 2017, 'Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars', ISME Journal, 11, pp. 1087 - 1101, http://dx.doi.org/10.1038/ismej.2016.187

Esteves AIS; Cullen A; Thomas T, 2017, 'Competitive interactions between sponge-associated bacteria', FEMS Microbiology Ecology, 93, http://dx.doi.org/10.1093/femsec/fix008

Díez-Vives C; Moitinho-Silva L; Nielsen S; Reynolds D; Thomas T, 2017, 'Expression of eukaryotic-like protein in the microbiome of sponges', Molecular Ecology, 26, pp. 1432 - 1451, http://dx.doi.org/10.1111/mec.14003

Song W; Steensen K; Thomas T, 2017, 'HgtSIM: A simulator for horizontal gene transfer (HGT) in microbial communities', PeerJ, 2017, http://dx.doi.org/10.7717/peerj.4015

Nielsen S; Walburn JW; Vergés A; Thomas T; Egan S, 2017, 'Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens', PeerJ, 2017, http://dx.doi.org/10.7717/peerj.3317

Mcgeoch M; Latombe G; Andrew N; Nakagawa S; Nipperess D; Roige M; Marzinelli E; Campbell A; Vergés A; Thomas T; Steinberg P; Selwood K; Hui C, 2017, 'The application of zeta diversity as a continuous measure of compositional change in ecology', , http://dx.doi.org/10.1101/216580

Roth-Schulze AJ; Zozaya-Valdés E; Steinberg PD; Thomas T, 2016, 'Partitioning of functional and taxonomic diversity in surface-associated microbial communities', Environmental Microbiology, 18, pp. 4391 - 4402, http://dx.doi.org/10.1111/1462-2920.13325

Kumar V; Zozaya-Valdes E; Kjelleberg S; Thomas T; Egan S, 2016, 'Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra', Environmental Microbiology, 18, pp. 3962 - 3975, http://dx.doi.org/10.1111/1462-2920.13403

Reynolds D; Thomas T, 2016, 'Evolution and function of eukaryotic-like proteins from sponge symbionts', Molecular ecology, 25, pp. 5242 - 5253, http://dx.doi.org/10.1111/mec.13812

Thomas T; Moitinho-Silva L; Lurgi M; Björk JR; Easson C; Astudillo-García C; Olson JB; Erwin PM; López-Legentil S; Luter H; Chaves-Fonnegra A; Costa R; Schupp PJ; Steindler L; Erpenbeck D; Gilbert J; Knight R; Ackermann G; Victor Lopez J; Taylor MW; Thacker RW; Montoya JM; Hentschel U; Webster NS, 2016, 'Diversity, structure and convergent evolution of the global sponge microbiome', Nature Communications, 7, http://dx.doi.org/10.1038/ncomms11870

Nielsen S; Needham B; Leach ST; Day AS; Jaffe A; Thomas T; Ooi CY, 2016, 'Disrupted progression of the intestinal microbiota with age in children with cystic fibrosis', Scientific Reports, 6, http://dx.doi.org/10.1038/srep24857

Lutz C; Thomas T; Steinberg P; Kjelleberg S; Egan S, 2016, 'Effect of interspecific competition on trait variation in Phaeobacter inhibens biofilms', Environmental Microbiology, 18, pp. 1635 - 1645, http://dx.doi.org/10.1111/1462-2920.13253

Webster NS; Thomas T, 2016, 'The sponge hologenome', mBio, 7, http://dx.doi.org/10.1128/mBio.00135-16

Esteves AIS; Amer N; Nguyen M; Thomas T, 2016, 'Sample processing impacts the viability and cultivability of the sponge microbiome', Frontiers in Microbiology, 7, http://dx.doi.org/10.3389/fmicb.2016.00499

Ye J; Zhang R; Nielsen S; Joseph SD; Huang D; Thomas T, 2016, 'A combination of biochar-mineral complexes and compost improves soil bacterial processes, soil quality, and plant properties', Frontiers in Microbiology, 7, http://dx.doi.org/10.3389/fmicb.2016.00372

Zozaya-Valdés E; Roth-Schulze AJ; Thomas T, 2016, 'Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community', Frontiers in Microbiology, 7, http://dx.doi.org/10.3389/fmicb.2016.00161

Lachnit T; Thomas T; Steinberg P, 2016, 'Expanding our understanding of the seaweed holobiont: RNA Viruses of the Red Alga Delisea pulchra', Frontiers in Microbiology, 6, http://dx.doi.org/10.3389/fmicb.2015.01489

Aslam F; Yasmin A; Thomas T, 2016, 'Genome sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an effective bioremediator', Genome Announcements, 4, http://dx.doi.org/10.1128/genomeA.01068-16

Marzinelli EM; Campbell AH; Zozaya Valdes E; Vergés A; Nielsen S; Wernberg T; de Bettignies T; Bennett S; Caporaso JG; Thomas T; Steinberg PD, 2015, 'Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography', Environmental Microbiology, 17, pp. 4078 - 4088, http://dx.doi.org/10.1111/1462-2920.12972

Joseph S; Husson O; Graber ER; Van Zwieten L; Taherymoosavi S; Thomas T; Nielsen S; Ye J; Pan G; Chia C; Munroe P; Allen J; Lin Y; Fan X; Donne S, 2015, 'The electrochemical properties of biochars and how they affect soil redox properties and processes', Agronomy, 5, pp. 322 - 340, http://dx.doi.org/10.3390/agronomy5030322

Ye J; Nielsen S; Joseph S; Thomas T, 2015, 'High-resolution and specific detection of bacteria on complex surfaces using nanoparticle probes and electron microscopy', PLoS ONE, 10, http://dx.doi.org/10.1371/journal.pone.0126404

Gardiner M; Thomas T; Egan S, 2015, 'A glutathione peroxidase (GpoA) plays a role in the pathogenicity of Nautella italica strain R11 towards the red alga Delisea pulchra', FEMS Microbiology Ecology, 91, http://dx.doi.org/10.1093/femsec/fiv021

Luter HM; Widder S; Botté ES; Wahab MA; Whalan S; Moitinho-Silva L; Thomas T; Webster NS, 2015, 'Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens', PeerJ, 2015, http://dx.doi.org/10.7717/peerj.1435

Gutierrez-Zamora ML; Lee M; Manefield M; Thomas T, 2015, 'Biotransformation of coal linked to nitrification', International Journal of Coal Geology, 137, pp. 136 - 141, http://dx.doi.org/10.1016/j.coal.2014.12.001

Egan S; Thomas T, 2015, 'Editorial for: Microbial symbiosis of marine sessile hosts- diversity and function', Frontiers in Microbiology, 6, http://dx.doi.org/10.3389/fmicb.2015.00585


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