Select Publications


Thomas T, 2010, Proteins from Archaea, 1, Lambert Publishing Group, Saarbrücken, Germany

2008, Protein Adaptation in Extremophiles, Siddiqui KS; Thomas T, (ed.), Original, Nova Biomedical Books, New York,

Book Chapters

Thomas T; Gilbert J; Meyer F, 2015, 'A 123 of Metagenomics', in Encyclopedia of Metagenomics, Springer US, pp. 1 - 9,

Thomas T; Gilbert J; Meyer F, 2014, 'Metagenomics: A guide from sampling to data analysis', in The Role of Bioinformatics in Agriculture, pp. 357 - 383,

Harder T; Rice SA; Dobretsov S; Thomas T; Carré-Mlouka A; Kjelleberg S; Steinberg PD; McDougald D, 2014, 'Bacterial communication systems', in Le Barre S; Kornprobst J-M (ed.), Outstanding Marine Molecules, Wiley-Blackwell, pp. 173 - 187,

Joseph S; van Zwieten L; Chia C; Kimber S; Munroe PR; Lin Y; Marjo C; Hook J; Thomas T; Nielsen S; Donne S; Taylor P, 2013, 'Designing Specific Biochars to Address Soil Constrains: A Developing Industry', in Ladygina N; Rineau F (ed.), Biochar and Soil Biota, CRC Press, pp. 165 - 201,

Thomas T; Yung PY; Kjelleberg S, 2011, 'Phylogenetic screening of metagenomic libraries using homing endonuclease restriction and marker insertion', in de Bruijn FJ (ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, edn. 21, Wiley-Blackwell, Hoboken, New Jersey, pp. 245 - 250,

Kato C; Sato T; Abe F; Ohmae E; Tamegai H; Nakasone K; Siddiqui KS; Thomas T, 2008, 'Protein Adaptation to High-Pressure Environments', in Protein Adaptation in Extremophiles, edn. Original, Nova Biomedical Books, New York, pp. 167 - 192

Cavicchioli R; Curmi PMG; Siddiqui KS; Thomas T, 2006, '17 Proteins from Psychrophiles', in Methods in Microbiology, edn. Original, Elsevier, London, England, pp. 395 - 436,

Webb JS; Taylor M; Rice SA; Thomas T; Rao D; McDougald D; Kjelleberg S, 2006, 'Biofilms on living surfaces', in Hurst CJ; Crawford RL; Garland JL; Lipson DA; Mills AL; Stetzenbach LD (ed.), Manual of Environmental Microbiology, ASM Press, Washington, DC, pp. 563 - 574,

Cavicchioli R; Thomas T, 2004, 'Extremophiles', in Schaechter M (ed.), The Desk Encyclopedia of Microbiology, edn. Original, Academic Press, San Diego, California, pp. 434 - 451

Cavicchioli R; Torsten T, 2000, 'Extremophiles', in Encyclopedia of Microbiology, Volume 2, second edition, edn. Revised, Academic Press Inc, San Diego, California, pp. 317 - 337

Journal articles

Vendl C; Slavich E; Wemheuer B; Nelson T; Ferrari B; Thomas T; Rogers T, 2020, 'Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast', Scientific Reports, vol. 10,

Yadav S; Dudchenko O; Esvaran M; Rosen B; Field M; Skvortsova K; Gopalakrishnan S; Keilwagen J; Cockran B; Manandhar B; Bucknall M; Bustamante S; Rasmussen J; Melvin R; Omer A; Colaric, Z; Chan E; Minoche A; Smith T; Gilbert T; Bogdanovic O; Zammit R; Thomas T; Aiden E; Ballard B, 2020, 'Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem', bioRix,

Mangott A; Nappi J; Delli Paoli Carini A; Goncalves P; Hua K; Domingos JA; de Nys R; Thomas T, 2020, 'Ulva lactuca as a functional ingredient and water bioremediator positively influences the hepatopancreas and water microbiota in the rearing of Litopenaeus vannamei', Algal Research, vol. 51,

Astudillo-García C; Bell JJ; Montoya JM; Moitinho-Silva L; Thomas T; Webster NS; Taylor MW, 2020, 'Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef', Environmental Microbiology, vol. 22, pp. 3985 - 3999,

Mills JG; Bissett A; Gellie NJC; Lowe AJ; Selway CA; Thomas T; Weinstein P; Weyrich LS; Breed MF, 2020, 'Revegetation of urban green space rewilds soil microbiotas with implications for human health and urban design', Restoration Ecology, vol. 28, pp. S322 - S334,

Vendl C; Slavich E; Nelson T; Acevedo-Whitehouse K; Montgomery K; Ferrari B; Thomas T; Rogers T, 2020, 'Does sociality drive diversity and composition of airway microbiota in cetaceans?', Environmental Microbiology Reports, vol. 12, pp. 324 - 333,

Wemheuer F; Taylor JA; Daniel R; Johnston E; Meinicke P; Thomas T; Wemheuer B, 2020, 'Tax4Fun2: Prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences', Environmental Microbiomes, vol. 15,

Dewi DAPR; Götz B; Thomasa T, 2020, 'Diversity and genetic basis for carbapenem resistance in a coastal marine environment', Applied and Environmental Microbiology, vol. 86,

Chew J; Zhu L; Nielsen S; Graber E; Mitchell DRG; Horvat J; Mohammed M; Liu M; van Zwieten L; Donne S; Munroe P; Taherymoosavi S; Pace B; Rawal A; Hook J; Marjo C; Thomas DS; Pan G; Li L; Bian R; McBeath A; Bird M; Thomas T; Husson O; Solaiman Z; Joseph S; Fan X, 2020, 'Biochar-based fertilizer: Supercharging root membrane potential and biomass yield of rice', Science of the Total Environment, vol. 713,

Coffey MJ; Mckay IR; Doumit M; Chuang S; Adams S; Stelzer-Braid S; Waters SA; Kasparian NA; Thomas T; Jaffe A; Katz T; Ooi CY, 2020, 'Evaluating the Alimentary and Respiratory Tracts in Health and disease (EARTH) research programme: a protocol for prospective, longitudinal, controlled, observational studies in children with chronic disease at an Australian tertiary paediatric hospital', BMJ Open, vol. 10, pp. e033916,

Zhang HY; Goncalves P; Copeland E; Qi SS; Dai ZC; Li GL; Wang CY; Du DL; Thomas T, 2020, 'Invasion by the weed Conyza canadensis alters soil nutrient supply and shifts microbiota structure', Soil Biology and Biochemistry, vol. 143,

Bhandarkar NS; Mouatt P; Goncalves P; Thomas T; Brown L; Panchal SK, 2020, 'Modulation of gut microbiota by spent coffee grounds attenuates diet-induced metabolic syndrome in rats', FASEB Journal, vol. 34, pp. 4783 - 4797,

Parata L; Nielsen S; Xing X; Thomas T; Egan S; Vergés A, 2020, 'Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish', FEMS Microbiology Ecology, vol. 96,

du Preez R; Paul N; Mouatt P; Majzoub ME; Thomas T; Panchal SK; Brown L, 2020, 'Carrageenans from the Red Seaweed Sarconema filiforme Attenuate Symptoms of Diet-Induced Metabolic Syndrome in Rats', Marine Drugs, vol. 18, pp. 97 - 97,

Nayfach S; Roux S; Seshadri R; Udwary D; Varghese N; Schulz F; Wu D; Paez-Espino D; Chen IM; Huntemann M; Palaniappan K; Ladau J; Mukherjee S; Reddy TBK; Nielsen T; Kirton E; Faria JP; Edirisinghe JN; Henry CS; Jungbluth SP; Chivian D; Dehal P; Wood-Charlson EM; Arkin AP; Tringe SG; Visel A; Abreu H; Acinas SG; Allen E; Allen MA; Andersen G; Anesio AM; Attwood G; Avila-Magaña V; Badis Y; Bailey J; Baker B; Baldrian P; Barton HA; Beck DAC; Becraft ED; Beller HR; Beman JM; Bernier-Latmani R; Berry TD; Bertagnolli A; Bertilsson S; Bhatnagar JM; Bird JT; Blumer-Schuette SE; Bohannan B; Borton MA; Brady A; Brawley SH; Brodie J; Brown S; Brum JR; Brune A; Bryant DA; Buchan A; Buckley DH; Buongiorno J; Cadillo-Quiroz H; Caffrey SM; Campbell AN; Campbell B; Carr S; Carroll JL; Cary SC; Cates AM; Cattolico RA; Cavicchioli R; Chistoserdova L; Coleman ML; Constant P; Conway JM; Mac Cormack WP; Crowe S; Crump B; Currie C; Daly R; Denef V; Denman SE; Desta A; Dionisi H; Dodsworth J; Dombrowski N; Donohue T; Dopson M; Driscoll T; Dunfield P; Dupont CL; Dynarski KA; Edgcomb V; Edwards EA; Elshahed MS; Figueroa I; Flood B; Fortney N; Fortunato CS, 2020, 'A genomic catalog of Earth’s microbiomes', Nature Biotechnology,

Ozkan J; Coroneo M; Sandbach J; Subedi D; Willcox M; Thomas T, 2020, 'Bacterial contamination of intravitreal needles by the ocular surface microbiome', Ocular Surface,

Taylor JA; Palladino G; Wemheuer B; Steinert G; Sipkema D; Williams TJ; Thomas T, 2020, 'Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts', ISME Journal,

John OD; Mouatt P; Majzoub ME; Thomas T; Panchal SK; Brown L, 2020, 'Physiological and metabolic effects of yellow mangosteen (Garcinia dulcis) rind in rats with dietinduced metabolic syndrome', International Journal of Molecular Sciences, vol. 21, pp. 272 - 272,

Coffey MJ; Low I; Stelzer-Braid S; Wemheuer B; Garg M; Thomas T; Jaffe A; Rawlinson WD; Ooi CY, 2020, 'The intestinal virome in children with cystic fibrosis differs from healthy controls.', PLoS One, vol. 15, pp. e0233557,

Ozkan J; Coroneo M; Thomas T; Willcox M, 2019, 'Biogeography of the human ocular microbiota', The Ocular Surface, vol. 17,

Botté ES; Nielsen S; Abdul Wahab MA; Webster J; Robbins S; Thomas T; Webster NS, 2019, 'Changes in the metabolic potential of the sponge microbiome under ocean acidification', Nature Communications, vol. 10, pp. 4134,

Song W; Thomas T; Edwards RJ, 2019, 'Complete genome sequences of pooled genomic DNA from 10 marine bacteria using PacBio long-read sequencing', Marine Genomics, vol. 48,

Batani G; Bayer K; Böge J; Hentschel U; Thomas T, 2019, 'Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria', Scientific Reports, vol. 9, pp. 18618,

Coffey MJ; Nielsen S; Wemheuer B; Kaakoush NO; Garg M; Needham B; Pickford R; Jaffe A; Thomas T; Ooi CY, 2019, 'Gut Microbiota in Children With Cystic Fibrosis: A Taxonomic and Functional Dysbiosis', Scientific Reports, vol. 9, pp. 18593,

Lurgi M; Thomas T; Wemheuer B; Webster NS; Montoya JM, 2019, 'Modularity and predicted functions of the global sponge-microbiome network', Nature Communications, vol. 10, pp. 992,

Santini NS; Lovelock CE; Hua Q; Zawadzki A; Mazumder D; Mercer TR; Muñoz-Rojas M; Hardwick SA; Madala BS; Cornwell W; Thomas T; Marzinelli EM; Adam P; Paul S; Vergés A, 2019, 'Natural and Regenerated Saltmarshes Exhibit Similar Soil and Belowground Organic Carbon Stocks, Root Production and Soil Respiration', Ecosystems, vol. 22, pp. 1803 - 1822,

Webster J; Lee M; Gurba LW; Manefield M; Thomas T, 2019, 'The effect of oxidative treatment on soluble compounds from Australian coal', Fuel, vol. 257, pp. 116071 - 116071,

Trevathan-Tackett SM; Sherman CDH; Huggett MJ; Campbell AH; Laverock B; Hurtado-McCormick V; Seymour JR; Firl A; Messer LF; Ainsworth TD; Negandhi KL; Daffonchio D; Egan S; Engelen AH; Fusi M; Thomas T; Vann L; Hernandez-Agreda A; Gan HM; Marzinelli EM; Steinberg PD; Hardtke L; Macreadie PI, 2019, 'A horizon scan of priorities for coastal marine microbiome research', Nature Ecology and Evolution, vol. 3, pp. 1509 - 1520,

McGeoch MA; Latombe G; Andrew NR; Nakagawa S; Nipperess DA; Roigé M; Marzinelli EM; Campbell AH; Vergés A; Thomas T; Steinberg PD; Selwood KE; Henriksen MV; Hui C, 2019, 'Measuring continuous compositional change using decline and decay in zeta diversity', Ecology, vol. 100,

Breider S; Sehar S; Berger M; Thomas T; Brinkhoff T; Egan S, 2019, 'Genome sequence of Epibacterium ulvae strain DSM 24752T, an indigoidine-producing, macroalga-associated member of the marine Roseobacter group', Environmental Microbiomes, vol. 14,

Glasl B; Bourne DG; Frade PR; Thomas T; Schaffelke B; Webster NS, 2019, 'Microbial indicators of environmental perturbations in coral reef ecosystems', Microbiome, vol. 7,

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, vol. 95,

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, vol. 7, pp. 36,

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, vol. 12, pp. 275 - 288,

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, vol. 13, pp. 632 - 650,

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, vol. 286,

Wemheuer B; Thomas T; Wemheuer F, 2019, 'Fungal endophyte communities of three agricultural important grass species differ in their response towards management regimes', Microorganisms, vol. 7,

Chen Q; Wu WW; Qi SS; Cheng H; Li Q; Ran Q; Dai ZC; Du DL; Egan S; Thomas T, 2019, 'Arbuscular mycorrhizal fungi improve the growth and disease resistance of the invasive plant Wedelia trilobata', Journal of Applied Microbiology,

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