By Professor Torsten Thomas

Journal articles

Majzoub ME; Beyersmann PG; Simon M; Thomas T; Brinkhoff T; Egan S, 2019, 'Phaeobacter inhibens controls bacterial community assembly on a marine diatom', FEMS Microbiology Ecology, 95, http://dx.doi.org/10.1093/femsec/fiz060

Song W; Wemheuer B; Zhang S; Steensen K; Thomas T, 2019, 'MetaCHIP: Community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches', Microbiome, 7, http://dx.doi.org/10.1186/s40168-019-0649-y

Wilkes Walburn J; Wemheuer B; Thomas T; Copeland E; O'Connor W; Booth M; Fielder S; Egan S, 2019, 'Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi)', Microbial Biotechnology, 12, pp. 275 - 288, http://dx.doi.org/10.1111/1751-7915.13323

Beckmann S; Luk AWS; Gutierrez-Zamora ML; Chong NHH; Thomas T; Lee M; Manefield M, 2019, 'Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation', ISME Journal, 13, pp. 632 - 650, http://dx.doi.org/10.1038/s41396-018-0296-5

Qiu Z; Coleman MA; Provost E; Campbell AH; Kelaher BP; Dalton SJ; Thomas T; Steinberg PD; Marzinelli EM, 2019, 'Future climate change is predicted to affect the microbiome and condition of habitat-forming kelp', Proceedings of the Royal Society B: Biological Sciences, 286, http://dx.doi.org/10.1098/rspb.2018.1887

Wemheuer B; Thomas T; Wemheuer F, 2019, 'Fungal endophyte communities of three agricultural important grass species differ in their response towards management regimes', Microorganisms, 7, http://dx.doi.org/10.3390/microorganisms7020037

Zhang S; Song W; Wemheuer B; Reveillaud J; Webster N; Thomas T, 2019, 'Comparative genomics reveals ecological and evolutionary insights into sponge-associated Thaumarchaeota', mSystems, 4, http://dx.doi.org/10.1128/mSystems.00288-19

Mills JG; Brookes JD; Gellie NJC; Liddicoat C; Lowe AJ; Sydnor HR; Thomas T; Weinstein P; Weyrich LS; Breed MF, 2019, 'Relating urban biodiversity to human health with the 'Holobiont' concept', Frontiers in Microbiology, 10, http://dx.doi.org/10.3389/fmicb.2019.00550

Coffey MJ; Low I; Stelzer-Braid S; Rawlinson W; Thomas T; Jaffe A; Ooi CY, 2019, '1139 – The Intestinal Virome in Children with Cystic Fibrosis: A Pilot Study', Gastroenterology, 156, pp. S - 241, http://dx.doi.org/10.1016/s0016-5085(19)37406-2

Coffey MJ; Nielsen S; Wemheuer B; Garg M; Needham B; Jaffe A; Thomas T; Ooi CY, 2019, 'Mo1947 – Taxonomic and Functional Intestinal Dysbiosis in Children with Cystic Fibrosis', Gastroenterology, 156, pp. S - 895, http://dx.doi.org/10.1016/s0016-5085(19)39210-8

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; Björk JR; Montoya JM; Olson JB; Reveillaud J; Steindler L; Pineda MC; 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, 2018, 'Erratum: The sponge microbiome project (GigaScience (2017) 6 DOI: 10.1093/gigascience/gix077)', GigaScience, 7, http://dx.doi.org/10.1093/gigascience/giy145

Ozkan J; Willcox M; Wemheuer B; Wilcsek G; Coroneo M; Thomas T, 2018, 'Biogeography of the human ocular microbiota', The Ocular Surface, 17, pp. 111 - 118, http://dx.doi.org/10.1016/j.jtos.2018.11.005

Majzoub ME; McElroy K; Maczka M; Thomas T; Egan S, 2018, 'Causes and consequences of a variant strain of Phaeobacter inhibens with reduced competition', Frontiers in Microbiology, 9, pp. 2601, http://dx.doi.org/10.3389/fmicb.2018.02601

Aslam F; Yasmin A; Thomas T, 2018, 'Essential Gene Clusters Identified in Stenotrophomonas MB339 for Multiple Metal/Antibiotic Resistance and Xenobiotic Degradation', Current Microbiology, 75, pp. 1484 - 1492, http://dx.doi.org/10.1007/s00284-018-1549-2

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, pp. 9845, 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, pp. 9880, 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; 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; Thomas T; Munroe P; Steinberg P; Marzinelli E; Nielsen S; Moitinho e Silva L, 2017, 'A communal catalogue reveals Earth's multiscale microbial diversity', Nature, 551, pp. 457 - 463, 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; Zech Xu Z; Jiang L; Haroon MF; Kanbar J; Zhu Q; Jin Song S; 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; Thomas T; Marzinelli E; Nielsen S; Steinberg P; Campbell A; Moitinho e Silva L; Munroe P, 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, pp. 752, 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, pp. e4015, 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, pp. e3317, 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, pp. 24857, http://dx.doi.org/10.1038/srep24857

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