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

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

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,

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,

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,

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,

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,

Botté 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 Commun, 3, pp. 53,

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,

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,

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,

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,

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,

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,

Modolon F; Schultz J; Duarte G; Vilela CL; Thomas T; Peixoto RS, 2023, 'In situ devices can culture the microbial dark matter of corals', iScience, pp. 108374 - 108374,

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,

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,

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; Thomas T; 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,

Garritano AN; Song W; Thomas T, 2022, 'Carbon fixation pathways across the bacterial and archaeal tree of life', PNAS Nexus, 1,

Peixoto RS; Voolstra CR; Sweet M; Duarte CM; Carvalho S; Villela H; Lunshof JE; Gram L; Woodhams DC; Walter J; Roik A; Hentschel U; Thurber RV; Daisley B; Ushijima B; Daffonchio D; Costa R; Keller-Costa T; Bowman JS; Rosado AS; Reid G; Mason CE; Walke JB; Thomas T; Berg G, 2022, 'Harnessing the microbiome to prevent global biodiversity loss', Nature Microbiology, 7, pp. 1726 - 1735,

Spindola Vilela CL; Damasceno TL; Thomas T; Peixoto RS, 2022, 'Global qualitative and quantitative distribution of micropollutants in the deep sea', Environmental Pollution, 307,

Song W; Zhang S; Thomas T, 2022, 'MarkerMAG: Linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads', Bioinformatics, 38, pp. 3684 - 3688,

Pettersen AK; Coleman MA; Latombe G; Gonzalez S; Williams NLR; Seymour JR; Campbell AH; Thomas T; Ferrari R; Stuart-Smith RD; Edgar GJ; Steinberg PD; Marzinelli E, 2022, 'Spatial compositional turnover varies with trophic level and body size in marine assemblages of micro- and macroorganisms', Global Ecology and Biogeography, 31, pp. 1556 - 1570,

Taylor JA; Díez-Vives C; Nielsen S; Wemheuer B; Thomas T, 2022, 'Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts', Environmental Microbiology, 24, pp. 2299 - 2314,

Taylor JA; Palladino G; Wemheuer B; Steinert G; Sipkema D; Williams TJ; Thomas T, 2022, 'Correction to: Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts (The ISME Journal, (2021), 15, 2, (503-519), 10.1038/s41396-020-00791-z)', ISME Journal, 16, pp. 1200 - 1200,

Field MA; Yadav S; Dudchenko O; Esvaran M; Rosen BD; Skvortsova K; Edwards RJ; Keilwagen J; Cochran BJ; Manandhar B; Bustamante S; Rasmussen JA; Melvin RG; Chernoff B; Omer A; Colaric Z; Chan EKF; Minoche AE; Smith TPL; Gilbert MTP; Bogdanovic O; Zammit RA; Thomas T; Aiden EL; Ballard JWO, 2022, 'The Australian dingo is an early offshoot of modern breed dogs', Science Advances, 8,

Qi S; Wang J; Wan L; Dai Z; da Silva Matos DM; Du D; Egan S; Bonser SP; Thomas T; Moles AT, 2022, 'Arbuscular Mycorrhizal Fungi Contribute to Phosphorous Uptake and Allocation Strategies of Solidago canadensis in a Phosphorous-Deficient Environment', Frontiers in Plant Science, 13,

Li J; Majzoub ME; Marzinelli EM; Dai Z; Thomas T; Egan S, 2022, 'Bacterial controlled mitigation of dysbiosis in a seaweed disease', ISME Journal, 16, pp. 378 - 387,

Pratap K; Majzoub ME; Taki AC; Miranda Hernandez S; Magnusson M; Glasson CRK; de Nys R; Thomas T; Lopata AL; Kamath SD, 2022, 'The Algal Polysaccharide Ulvan and Carotenoid Astaxanthin Both Positively Modulate Gut Microbiota in Mice', Foods, 11,

Nappi J; Goncalves P; Khan T; Majzoub ME; Grobler AS; Marzinelli EM; Thomas T; Egan S, 2022, 'Differential priority effects impact taxonomy and functionality of host-associated microbiomes', Molecular Ecology,

Mills JG; Selway CA; Weyrich LS; Skelly C; Weinstein P; Thomas T; Young JM; Marczylo E; Yadav S; Yadav V; Lowe AJ; Breed MF, 2022, 'Rare genera differentiate urban green space soil bacterial communities in three cities across the world.', Access Microbiol, 4, pp. 000320,

Vendl C; Nelson T; Ferrari B; Thomas T; Rogers T, 2021, 'Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota', BMC Microbiology, 21,

Bhandarkar NS; Mouatt P; Majzoub ME; Thomas T; Brown L; Panchal SK, 2021, 'Coffee pulp, a by-product of coffee production, modulates gut microbiota and improves metabolic syndrome in high-carbohydrate, high-fat diet-fed rats', Pathogens, 10,

du Preez R; Majzoub ME; Thomas T; Panchal SK; Brown L, 2021, 'Nannochloropsis oceanica as a microalgal food intervention in diet-induced metabolic syndrome in rats', Nutrients, 13,

Dewi DAPR; Thomas T; Mokhtar AMA; Nanyan NSM; Zulfigar SB; Salikin NH, 2021, 'Carbapenem resistance among marine bacteria—an emerging threat to the global health sector', Microorganisms, 9,

Barno AR; Villela HDM; Aranda M; Thomas T; Peixoto RS, 2021, 'Correction referring to: Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals (BioEssays, (2021), 43, 10, (2100068), 10.1002/bies.202100068)', BioEssays, 43,

Barno AR; Villela HDM; Aranda M; Thomas T; Peixoto RS, 2021, 'Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals', BioEssays, 43,

Ferrari J; Goncalves P; Campbell AH; Sudatti DB; Wood GV; Thomas T; Pereira RC; Steinberg PD; Marzinelli EM, 2021, 'Molecular analysis of a fungal disease in the habitat-forming brown macroalga Phyllospora comosa (Fucales) along a latitudinal gradient', Journal of Phycology, 57, pp. 1504 - 1516,

Majzoub ME; McElroy K; Maczka M; Schulz S; Thomas T; Egana S, 2021, 'Genomic Evolution of the Marine Bacterium Phaeobacter inhibens during Biofilm Growth', Applied and Environmental Microbiology, 87, pp. 1 - 14,

Taylor JA; Díez-Vives C; Majzoub ME; Nielsen S; Thomas T, 2021, 'Stress response of the marine sponge Scopalina sp.. Can microbial community composition predict sponge disease?', FEMS Microbiology Ecology, 97,

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