Select Publications

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, http://dx.doi.org/10.1038/s41598-020-69602-x

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, http://dx.doi.org/10.1101/2020.11.15.384057

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, http://dx.doi.org/10.1016/j.algal.2020.102040

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, http://dx.doi.org/10.1111/1462-2920.15185

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, http://dx.doi.org/10.1111/rec.13175

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, http://dx.doi.org/10.1111/1758-2229.12835

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, http://dx.doi.org/10.1186/s40793-020-00358-7

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, http://dx.doi.org/10.1128/AEM.02939-19

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, http://dx.doi.org/10.1016/j.scitotenv.2019.136431

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, http://dx.doi.org/10.1136/bmjopen-2019-033916

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, http://dx.doi.org/10.1016/j.soilbio.2020.107739

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, http://dx.doi.org/10.1096/fj.201902416RR

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, http://dx.doi.org/10.1093/femsec/fiz179

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, http://dx.doi.org/10.3390/md18020097

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, http://dx.doi.org/10.1038/s41587-020-0718-6

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, http://dx.doi.org/10.1016/j.jtos.2020.05.010

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, http://dx.doi.org/10.1038/s41396-020-00791-z

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, http://dx.doi.org/10.3390/ijms21010272

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, http://dx.doi.org/10.1371/journal.pone.0233557

Ozkan J; Coroneo M; Thomas T; Willcox M, 2019, 'Biogeography of the human ocular microbiota', The Ocular Surface, vol. 17, http://dx.doi.org/10.1016/j.jtos.2018.11.005

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, http://dx.doi.org/10.1038/s41467-019-12156-y

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, http://dx.doi.org/10.1016/j.margen.2019.05.002

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, http://dx.doi.org/10.1038/s41598-019-55049-2

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, http://dx.doi.org/10.1038/s41598-019-55028-7

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, http://dx.doi.org/10.1038/s41467-019-08925-4

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, http://dx.doi.org/10.1007/s10021-019-00373-x

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, http://dx.doi.org/10.1016/j.fuel.2019.116071

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, http://dx.doi.org/10.1038/s41559-019-0999-7

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, http://dx.doi.org/10.1002/ecy.2832

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, http://dx.doi.org/10.1186/s40793-019-0343-5

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, http://dx.doi.org/10.1186/s40168-019-0705-7

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, 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, vol. 7, pp. 36, 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, vol. 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, vol. 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, vol. 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, vol. 7, http://dx.doi.org/10.3390/microorganisms7020037

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, http://dx.doi.org/10.1111/jam.14415

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, vol. 4, http://dx.doi.org/10.1128/mSystems.00288-19

Vendl C; Ferrari BC; Thomas T; Slavich E; Zhang E; Nelson T; Rogers T, 2019, 'Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales', FEMS Microbiology Ecology, vol. 95, http://dx.doi.org/10.1093/femsec/fiz102

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, vol. 10, pp. 550, http://dx.doi.org/10.3389/fmicb.2019.00550

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, vol. 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, vol. 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, 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, vol. 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, vol. 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, vol. 14, pp. e1007735, 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, vol. 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, vol. 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, vol. 10, pp. 433 - 443, http://dx.doi.org/10.1111/1758-2229.12655


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