By Professor Torsten Thomas

Books

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

, 2008, Protein Adaptation in Extremophiles, Siddiqui KS; Thomas T, (ed.), Nova Biomedical Books, New York, https://www.novapublishers.com/catalog/product_info.php?cPath=23_29&products_id=6238&osCsid=523411be245aa875dc809b66c2ebf54b

Book Chapters

Thomas T; Gilbert J; Meyer F, 2015, 'A 123 of Metagenomics', in Encyclopedia of Metagenomics, Springer US, pp. 1 - 9, http://dx.doi.org/10.1007/978-1-4899-7478-5_728

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, http://dx.doi.org/10.1201/b16568

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, http://au.wiley.com/WileyCDA/WileyTitle/productCd-3527334653.html

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, http://dx.doi.org/10.1201/b14585

, 2013, 'The Potential of Biochar Amendments to Remediate Contaminated Soils', in Biochar and Soil Biota, CRC Press, pp. 108 - 141, http://dx.doi.org/10.1201/b14585-6

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, 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, Nova Biomedical Books, New York, pp. 167 - 192

Cavicchioli R; Curmi PMG; Siddiqui KS; Thomas T, 2006, '17 Proteins from Psychrophiles', in , Elsevier, 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

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

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

Journal articles

Santoro EP; Cárdenas A; Villela HDM; Vilela CLS; Ghizelini AM; Duarte GAS; Perna G; Saraiva JP; Thomas T; Voolstra CR; Peixoto RS, 2025, 'Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes', Science Advances, 11, http://dx.doi.org/10.1126/sciadv.adq2583

Araujo G; Montoya JM; Thomas T; Webster NS; Lurgi M, 2025, 'A mechanistic framework for complex microbe-host symbioses', Trends in Microbiology, 33, pp. 96 - 111, http://dx.doi.org/10.1016/j.tim.2024.08.002

Del Olmo G; Ruiz P; Nappi J; Thomas T; Egan S; Cremades J; Pintado J, 2025, 'Optimizing Ulva-Phaeobacter co-culture: A two-phase light intensity approach for integrated multi-trophic aquaculture applications', Journal of Applied Phycology, http://dx.doi.org/10.1007/s10811-025-03461-9

Villela LB; da Silva-Lima AW; Moreira APB; Aiube YRA; Ribeiro FDV; Villela HDM; Majzoub ME; Amario M; de Moura RL; Thomas T; Peixoto RS; Salomon PS, 2024, 'Bacterial and Symbiodiniaceae communities’ variation in corals with distinct traits and geographical distribution', Scientific Reports, 14, http://dx.doi.org/10.1038/s41598-024-70121-2

Wang W; Song W; Majzoub ME; Feng X; Xu B; Tao J; Zhu Y; Li Z; Qian PY; Webster NS; Thomas T; Fan L, 2024, 'Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-52464-6

Zhang S; Song W; Marinos G; Waschina S; Zimmermann J; Kaleta C; Thomas T, 2024, 'Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-55222-w

Ribeiro B; N. Garritano A; Raimundo I; Delgadillo-Ordoñez N; Nappi J; Garcias-Bonet N; Villela H; Thomas T; Klautau M; Peixoto RS, 2024, 'Not only for corals: exploring the uptake of beneficial microorganisms for corals by sponges', npj Biofilms and Microbiomes, 10, http://dx.doi.org/10.1038/s41522-024-00584-8

Ozkan J; Majzoub ME; Khan M; Coroneo M; Thomas T; Willcox M, 2024, 'The Effect of Face Mask Wear on the Ocular Surface and Contact Lens Microbiome', Eye and Contact Lens, 50, pp. 467 - 474, http://dx.doi.org/10.1097/ICL.0000000000001122

Majzoub ME; Luu LDW; Haifer C; Paramsothy S; Borody TJ; Leong RW; Thomas T; Kaakoush NO, 2024, 'Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling', mSystems, 9, http://dx.doi.org/10.1128/msystems.00746-24

Bell JJ; Micaroni V; Strano F; Ryan KG; Mitchell K; Mitchell P; Wilkinson S; Thomas T; Batchiar R; Smith RO, 2024, 'Marine heatwave-driven mass mortality and microbial community reorganisation in an ecologically important temperate sponge', Global Change Biology, 30, http://dx.doi.org/10.1111/gcb.17417

Marzinelli EM; Thomas T; Vadillo Gonzalez S; Egan S; Steinberg PD, 2024, 'Seaweeds as holobionts: Current state, challenges, and potential applications', Journal of Phycology, 60, pp. 785 - 796, http://dx.doi.org/10.1111/jpy.13485

Li J; Saha M; Majzoub ME; Yang T; Chu H; Thomas T; Weinberger F; Egan S, 2024, 'Non-selective microbiota reduction after the elicitation of a seaweed's immune response', Environmental Microbiology Reports, 16, http://dx.doi.org/10.1111/1758-2229.13268

Cardoso PM; Hill LJ; Villela HDM; Vilela CLS; Assis JM; Rosado PM; Rosado JG; Chacon MA; Majzoub ME; Duarte GAS; Thomas T; Peixoto RS, 2024, 'Localization and symbiotic status of probiotics in the coral holobiont', mSystems, 9, http://dx.doi.org/10.1128/msystems.00261-24

Hill LJ; Messias CSMDA; Vilela CLS; Garritano AN; Villela HDM; do Carmo FL; Thomas T; Peixoto RS, 2024, 'Bacteria associated with the in hospite Symbiodiniaceae's phycosphere', iScience, 27, http://dx.doi.org/10.1016/j.isci.2024.109531

Rahman Z; McLaws ML; Thomas T, 2024, 'Genomic characterization of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli from urban wastewater in Australia', MicrobiologyOpen, 13, http://dx.doi.org/10.1002/mbo3.1403

Castro LC; Vergés A; Straub SC; Campbell AH; Coleman MA; Wernberg T; Steinberg P; Thomas T; Dworjanyn S; Cetina-Heredia P; Roughan M; Marzinelli EM, 2024, 'Effect of marine heatwaves and warming on kelp microbiota influence trophic interactions', Molecular Ecology, 33, http://dx.doi.org/10.1111/mec.17267

Khan T; Song W; Nappi J; Marzinelli EM; Egan S; Thomas T, 2024, 'Functional guilds and drivers of diversity in seaweed-associated bacteria', FEMS Microbes, 5, http://dx.doi.org/10.1093/femsmc/xtad023

Syukur S; Richmond J; Majzoub ME; Nappi J; Egan S; Thomas T, 2024, 'Not all parents are the same: Diverse strategies of symbiont transmission in seaweeds', Environmental Microbiology, 26, http://dx.doi.org/10.1111/1462-2920.16564

Garritano AN; Zhang Z; Jia Y; Allen MA; Hill LJ; Kuzhiumparambil U; Hinkley C; Raina JB; Peixoto RS; Thomas T, 2024, 'Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage', ISME Journal, 18, http://dx.doi.org/10.1093/ismejo/wrae197

Song W; Zhang S; Majzoub ME; Egan S; Kjelleberg S; Thomas T, 2024, 'The impact of interspecific competition on the genomic evolution of Phaeobacter inhibens and Pseudoalteromonas tunicata during biofilm growth', Environmental Microbiology, 26, http://dx.doi.org/10.1111/1462-2920.16553

Modolon F; Schultz J; Duarte G; Vilela CLS; Thomas T; Peixoto RS, 2023, 'In situ devices can culture the microbial dark matter of corals', iScience, 26, http://dx.doi.org/10.1016/j.isci.2023.108374

Nappi J; Goncalves P; Khan T; Majzoub ME; Grobler AS; Marzinelli EM; Thomas T; Egan S, 2023, 'Differential priority effects impact taxonomy and functionality of host-associated microbiomes', Molecular Ecology, 32, pp. 6278 - 6293, http://dx.doi.org/10.1111/mec.16336

Pintado J; Del Olmo G; Guinebert T; Ruiz P; Nappi J; Thomas T; Egan S; Masaló I; Cremades J, 2023, 'Manipulating the Ulva holobiont: Co-culturing Ulva ohnoi with Phaeobacter bacteria as a strategy for disease control in fish-macroalgae IMTA-RAS aquaculture', Journal of Applied Phycology, 35, pp. 2017 - 2029, http://dx.doi.org/10.1007/s10811-023-02986-1

Ozkan J; Majzoub ME; Coroneo M; Thomas T; Willcox M, 2023, 'Ocular microbiome changes in dry eye disease and meibomian gland dysfunction', Experimental Eye Research, 235, http://dx.doi.org/10.1016/j.exer.2023.109615

Garritano AN; Majzoub ME; Ribeiro B; Damasceno T; Modolon F; Messias C; Vilela C; Duarte G; Hill L; Peixoto R; Thomas T, 2023, 'Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae', ISME Journal, 17, pp. 1517 - 1519, http://dx.doi.org/10.1038/s41396-023-01439-4

Nguyen VH; Wemheuer B; Song W; Bennett H; Webster N; Thomas T, 2023, 'Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species', Systematic and Applied Microbiology, 46, http://dx.doi.org/10.1016/j.syapm.2023.126426

Mills JG; Selway CA; Thomas T; Weyrich LS; Lowe AJ, 2023, 'Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children', Microbial Ecology, 86, pp. 658 - 669, http://dx.doi.org/10.1007/s00248-022-02052-2

Botte ES; Bennett H; Engelberts JP; Thomas T; Bell JJ; Webster NS; Luter HM, 2023, 'Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis', ISME COMMUNICATIONS, 3, http://dx.doi.org/10.1038/s43705-023-00247-3

Strano F; Micaroni V; Thomas T; Woods L; Davy SK; Bell JJ, 2023, 'Marine heatwave conditions drive carryover effects in a temperate sponge microbiome and developmental performance', Proceedings of the Royal Society B: Biological Sciences, 290, http://dx.doi.org/10.1098/rspb.2022.2539

Rahman Z; Liu W; Stapleton L; Kenters N; Rasmika Dewi DAP; Gudes O; Ziochos H; Khan SJ; Power K; McLaws ML; Thomas T, 2023, 'Wastewater-based monitoring reveals geospatial-temporal trends for antibiotic-resistant pathogens in a large urban community', Environmental Pollution, 325, http://dx.doi.org/10.1016/j.envpol.2023.121403

Li J; Weinberger F; de Nys R; Thomas T; Egan S, 2023, 'A pathway to improve seaweed aquaculture through microbiota manipulation', Trends in Biotechnology, 41, pp. 545 - 556, http://dx.doi.org/10.1016/j.tibtech.2022.08.003

Nguyen VH; Wemheuer B; Song W; Bennett H; Palladino G; Burgsdorf I; Sizikov S; Steindler L; Webster NS; Thomas T, 2023, 'Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges', Systematic and Applied Microbiology, 46, http://dx.doi.org/10.1016/j.syapm.2023.126401

McKay I; van Dorst J; Katz T; Doumit M; Prentice B; Owens L; Belessis Y; Chuang S; Jaffe A; Thomas T; Coffey M; Ooi CY, 2023, 'Diet and the gut-lung axis in cystic fibrosis–direct & indirect links', Gut Microbes, 15, http://dx.doi.org/10.1080/19490976.2022.2156254

Hardoim CCP; Hardoim PR; Lôbo-Hajdu G; Custódio MR; Thomas T, 2023, 'The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact', FEMS Microbiology Letters, 370, http://dx.doi.org/10.1093/femsle/fnad064

Zhang S; Song W; Nothias LF; Couvillion SP; Webster N; Thomas T, 2022, 'Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts', Microbiome, 10, http://dx.doi.org/10.1186/s40168-021-01220-9

Liu R; Wei X; Song W; Wang L; Cao J; Wu J; Thomas T; Jin T; Wang Z; Wei W; Wei Y; Zhai H; Yao C; Shen Z; Du J; Fang J, 2022, 'Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats', Microbiome, 10, http://dx.doi.org/10.1186/s40168-022-01263-6

Shaffer JP; Nothias LF; Thompson LR; Sanders JG; Salido RA; Couvillion SP; Brejnrod AD; Lejzerowicz F; Haiminen N; Huang S; Lutz HL; Zhu Q; Martino C; Morton JT; Karthikeyan S; Nothias-Esposito M; Dührkop K; Böcker S; Kim HW; Aksenov AA; Bittremieux W; Minich JJ; Marotz C; Bryant MKM; Sanders K; Schwartz T; Humphrey G; Vásquez-Baeza Y; Tripathi A; Parida L; Carrieri AP; Beck KL; Das P; González A; McDonald D; Ladau J; Karst SM; Albertsen M; Ackermann G; DeReus J; Thomas T; Petras D; Shade A; Stegen J; Song SJ; Metz TO; Swafford AD; Dorrestein PC; Jansson JK; Gilbert JA; Knight R; Angenant LT; Berry AM; Bittleston LS; Bowen JL; Chavarría M; Cowan DA; Distel D; Girguis PR; Huerta-Cepas J; Jensen PR; Jiang L; King GM; Lavrinienko A; MacRae-Crerar A; Makhalanyane TP; Mappes T; Marzinelli EM; Mayer G; McMahon KD; Metcalf JL; Miyake S; Mousseau TA; Murillo-Cruz C; Myrold D; Palenik B; Pinto-Tomás AA; Porazinska DL; Ramond JB; Rowher F; RoyChowdhury T; Sandin SA; Schmidt SK; Seedorf H; Shipway JR; Smith JE; Stewart FJ; Tait K; Tucker Y; U’Ren JM; Watts PC; Webster NS; Zaneveld JR; Zhang S, 2022, 'Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity', Nature Microbiology, 7, pp. 2128 - 2150, http://dx.doi.org/10.1038/s41564-022-01266-x

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