Torsten Thomas

Areas of Expertise

Microbiology; Genomics; Marine Ecology

I hold a Masters degree from the Rheinische Friedrich Wilhelms University in Bonn, Germany (1996) and obtained a PhD from University of New South Wales (2001). From 2001-2004 I worked as a Senior Scientist at the biotech company Nucleics Pty Ltd. In 2004 I returned to academia as a Senior Research Associate within the Centre for Marine Bio-Innovation (CMB) at UNSW and received a fellowship from the American Australian Association in 2005. I went on to become a Senior Research Fellow after being awarded a fellowship from the Australian Research Council (ARC) (2006-2009). In December 2009, I took on a Senior Lecturer position at the School of Biotechnology and Biomolecular Sciences (BABS) at UNSW, was appointed an Associate Professor in 2013 and awarded an ARC Future Fellowship in 2014. In 2016, I became the Director of the CMB and moved to the School of Biological, Earth and Environmental Sciences (BEES) at UNSW, where I was promoted to Professor in 2017. During 2018-2020 I formed the Centre for Marine Science and Innovation (CMSI) and directed it during this period.

I have been the Chair for Division 3 and the Special Interest Group "Microbial Informatics" of the Australian Society of Microbiology (ASM). I have been a Member of the Organising Committee for the 10th International Marine Biotechnology Conference in Brisbane (2013) as well as the Australian New Zealand Marine Biotechnology Conference in Sydney (2019). I have made on-going contributions to public policy and engagement. From 2010-2014, I was on the National Scientific Advisory Committee of the ASM. In 2015, I was elected to the Ecosystem Science Council (ESC) for a 4-year term. These prestigious professional appointments allowed me to contribute to the overall directions of the scientific fields of microbiology and ecology, engage with end-users and communicate key findings to the public.

Research Activities

My research focuses on the interaction of bacteria with their environment and aims to understand the function of the enormous diversity of bacteria in natural systems. My students, co-workers and I explore the microbial world, for example by high-throughput DNA sequencing and the use of bioinformatics, to make predictions about functional and ecological properties of bacterial communities. Ultimately, we perform directed experiments to support our predictions and establish a clear link between function and diversity. Current project include:

1. Bacteria-sponge symbiosis

Marine sponges acquire nutrients by filtering and eating bacteria from the seawater, but they also at the same time harbour a remarkable diversity of bacterial symbionts that don’t get digested. We have discovered that the genomes of bacterial sponge symbionts carry a large number of proteins that are similar to eukaryotic proteins controlling phagocytosis and cytoskeletal formation (Fan et al. PNAS USA 2012, Nguyen et al. Molecular Ecology 2013, Reynolds & Thomas Molecular Ecology 2016). We hypothesise that symbionts use these protein to “manipulate” the sponge and will test this with a range of phylogenetic and molecular approaches. The outcome of this project will provide important information on the evolution of microbe-host interactions.

 

2. Functional diversity and redundancy of marine communities

Microbial diversity in the marine environment is enormous and often 1000s of different species are found in a single habitat (e.g. Thomas et al. Nature Communications 2016). We have recently postulated that much of the diversity encountered is due to chance (“lottery hypothesis”) and that bacterial communities are assembled from “guilds” of functional equivalent organisms (Burke et al. PNAS USA 2011). Through high-throughput sequencing we have provided evidence for this hypothesis (e.g. Roth-Schulze et al. Environmental Microbiology 2016 & Molecular Ecology 2018) and we are exploring, which functions define particular communities in specific habitats. This project will provide an important conceptual advancement in the field of microbial ecology as it aims to define the assembly of microbial communities by functional properties rather than by the species.

 

3. Genomics of evolving, bacterial populations and communities

Microbial genomes exhibit a high degree of plasticity (or variability) and any given microbial population (defined as a collection of closely-related individuals) is far more heterogenous in its genetic composition than previously assumed. Sequencing of entire populations now allows for a comprehensive observation of genome evolution on a molecular level. This approach is being employed to the model organism Pseudomonas aeruginosa to understand its adaptation and evolution to conditions of environmental and medical relevance (McElroy PNAS USA 2041). We also expanding this approach to entire microbial communities (i.e. collection of distantly-related individuals), with particular focus on how horizontal gene transfer influences microbial evolution. This work also often leads to the development of novel bioinformatics tool to process large volumes of next-generation sequencing data.

 

4. Antibiotics and resistance in the environment

Given the large diversity of microorganisms in the environment, it is likely that the harbour novel antibiotics as well as resistance against existing antibiotics. We explore this by classical microbiological approaches and also high-throughput screening and functional analysis of microbial communities. This research is particular important in the light of “superbugs” that are resistant to most existing antibiotics and that cause substantial problems in the health system.

 

Publications

Journal articles
add
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
2020
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
2020
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
2020
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
2020
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, http://dx.doi.org/10.1111/1758-2229.12835
2020
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
2020
Dewi DAPR; Götz B; Thomas 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
2020
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
2020
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
2020
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
Ozkan J; Coroneo M; Thomas T; Willcox M, 2019, 'Biogeography of the human ocular microbiota', Biogeography of the human ocular microbiota
2019
Coffey MJ; Low I; Stelzer-Braid S; Rawlinson W; Thomas T; Jaffe A; Ooi CY, 2019, 'THE INTESTINAL VIROME IN CHILDREN WITH CYSTIC FIBROSIS: A PILOT STUDY', in GASTROENTEROLOGY, W B SAUNDERS CO-ELSEVIER INC, San Diego, CA, Vol. 156, pp. S241 - S241, presented at Digestive Disease Week (DDW), San Diego, CA, 18 May 2019 - 21 May 2019, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000467106000635&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2019
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
2019
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
2019
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
2019
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
2019
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
2019
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
2019
McKay IR; Coffey MJ; Doumit M; Bramley L; Sharp M; Kasparian N; Chuang S; Stelzer-Braid S; Waters S; Thomas T; Jaffe A; Katz TE; Ooi CY, 2019, 'A GUT FEELING: CORRELATING DIETARY INTAKE WITH THE GASTROINTESTINAL AND RESPIRATORY MICROBIOTA IN CYSTIC FIBROSIS', in PEDIATRIC PULMONOLOGY, WILEY, Vol. 54, pp. S261 - S262, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000484544000375&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2019
Ozkan J; Willcox M; Wemheuer B; Wilcsek G; Coroneo M; Thomas T, 2018, 'The biogeography of the human ocular microbiota', in The biogeography of the human eye microbiota, European Molecular Biology Organisation/European Molecular Biology Laboratory Symposia - The Human Microbiome, Heidelberg, Germany, presented at European Molecular Biology Organisation/European Molecular Biology Laboratory Symposia - The Human Microbiome, Heidelberg, Germany, 16 September 2018 - 19 September 2018, http://dx.doi.org/10.1016/j.jtos.2018.11.005
2018
Ozkan J; Willcox M; Wemheuer B; Thomas T; Coroneo M, 2018, 'What is hiding in your eyes? The microbiome of ocular surface niches', in Investigative Ophthalmology & Visual Science, Association for Research in Vision and Ophthalmology, Honolulu, HI, presented at The Association for Research in Vision and Ophthalmology, Honolulu, HI, 29 April 2018 - 03 May 2018, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000442912502178&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
2018
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, vol. 59, pp. 4268 - 4276, http://dx.doi.org/10.1167/iovs.18-24651
2018
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, vol. 4, http://dx.doi.org/10.3389/fmars.2017.00441
2018
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, vol. 133, pp. 22 - 29, http://dx.doi.org/10.1016/j.jaap.2018.05.007
2018
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, vol. 27, pp. 1952 - 1965, http://dx.doi.org/10.1111/mec.14529
2018
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
2018
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
2018
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, vol. 54, pp. 137 - 147, http://dx.doi.org/10.1007/s00374-017-1246-5
2018
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
2018
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
2018
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, vol. 63, pp. 459 - 471, http://dx.doi.org/10.1002/lno.10739
2018
Nguyen MTHD; Thomas T, 2018, 'Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges', PeerJ, vol. 2018, http://dx.doi.org/10.7717/peerj.4965
2018
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
2018
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
2018
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
2018
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, vol. 255, pp. 52 - 61, http://dx.doi.org/10.1016/j.agee.2017.12.020
2018
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
2018
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, 2017, 'The sponge microbiome project', GigaScience, vol. 6, http://dx.doi.org/10.1093/gigascience/gix077
2017
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, vol. 7, http://dx.doi.org/10.1038/s41598-017-10231-2
2017
Ozkan J; Diez-Vives C; Nielsen S; Coroneo M; Thomas T; Willcox M, 2017, 'A Statistical Model to Filter Contaminant Bacteria in Ocular Microbiome Studies', in A Statistical Model to Filter Contaminant Bacteria in Ocular Microbiome Studies, International Society for Contact Lens Research, Portland, Oregon, USA, presented at International Society for Contact Lens Research, Portland, Oregon, USA, 13 August 2017 - 18 August 2017
2017
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, 2017, 'A communal catalogue reveals Earth's multiscale microbial diversity', Nature, vol. 551, pp. 457 - 463, http://dx.doi.org/10.1038/nature24621
2017
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, vol. 8, http://dx.doi.org/10.3389/fmicb.2017.00752
2017
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, vol. 26, pp. 1432 - 1451, http://dx.doi.org/10.1111/mec.14003
2017
Nielsen S; Walburn JW; Vergés A; Thomas T; Egan S, 2017, 'Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens', PeerJ, vol. 2017, http://dx.doi.org/10.7717/peerj.3317
2017
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', The application of zeta diversity as a continuous measure of compositional change in ecology, http://dx.doi.org/10.1101/216580
2017
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, vol. 6, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000407721500001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2017
Egan S; Kumar V; Zozaya-Valdes ; Gardiner ME; Hudson J; Deshpande N; Campbell A; Thomas T, 2017, 'BREAKING BAD: OPPORTUNISTIC BACTERIAL PATHOGENS OF SEAWEEDS', in PHYCOLOGIA, INT PHYCOLOGICAL SOC, Vol. 56, pp. 48 - 48, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000412892000098&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
2017
Song WZ; Thomas T, 2017, 'Binning-refiner: Improving genome bins through the combination of different binning programs', Bioinformatics, vol. 33, pp. 1873 - 1875, http://dx.doi.org/10.1093/bioinformatics/btx086
2017
Song W; Steensen K; Thomas T, 2017, 'HgtSIM: A simulator for horizontal gene transfer (HGT) in microbial communities', PeerJ, vol. 2017, http://dx.doi.org/10.7717/peerj.4015
2017
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, vol. 12, http://dx.doi.org/10.1371/journal.pone.0190178
2017
Esteves AIS; Cullen A; Thomas T, 2017, 'Competitive interactions between sponge-associated bacteria', FEMS MICROBIOLOGY ECOLOGY, vol. 93, http://dx.doi.org/10.1093/femsec/fix008
2017
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, vol. 11, pp. 1087 - 1101, http://dx.doi.org/10.1038/ismej.2016.187
2017
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, vol. 11, pp. 1651 - 1666, http://dx.doi.org/10.1038/ismej.2017.25
2017
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, vol. 19, pp. 3012 - 3024, http://dx.doi.org/10.1111/1462-2920.13758
2017
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, vol. 7, http://dx.doi.org/10.1038/s41598-017-10494-9
2017
Ozkan J; Diez-Vives C; Nielsen S; Thomas T; Coroneo M; Willcox M, 2017, 'The Temporal Stability and the Ocular Surface Microbiome', in INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, ASSOC RESEARCH VISION OPHTHALMOLOGY INC, Baltimore, Maryland, USA, presented at the Association for Research in Vision and Ophthalmology, Baltimore, Maryland, USA, 07 May 2017 - 11 May 2017, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000432176306051&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
2017
Esteves AIS; Amer N; Nguyen M; Thomas T, 2016, 'Sample processing impacts the viability and cultivability of the sponge microbiome', Frontiers in Microbiology, vol. 7, http://dx.doi.org/10.3389/fmicb.2016.00499
2016
Roth-Schulze AJ; Zozaya-Valdés E; Steinberg PD; Thomas T, 2016, 'Partitioning of functional and taxonomic diversity in surface-associated microbial communities', Environmental Microbiology, vol. 18, pp. 4391 - 4402, http://dx.doi.org/10.1111/1462-2920.13325
2016
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, vol. 6, http://dx.doi.org/10.1038/srep24857
2016
Ye J; Zhang R; Nielsen S; Joseph SD; Huang D; Thomas T, 2016, 'A combination of biochar-mineral complexes and compost improves soil bacterial processes, soil quality, and plant properties', Frontiers in Microbiology, vol. 7, http://dx.doi.org/10.3389/fmicb.2016.00372
2016
Aslam F; Yasmin A; Thomas T, 2016, 'Genome sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an effective bioremediator', Genome Announcements, vol. 4, http://dx.doi.org/10.1128/genomeA.01068-16
2016
Zozaya-Valdés E; Roth-Schulze AJ; Thomas T, 2016, 'Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community', Frontiers in Microbiology, vol. 7, http://dx.doi.org/10.3389/fmicb.2016.00161
2016
Lutz C; Thomas T; Steinberg P; Kjelleberg S; Egan S, 2016, 'Effect of interspecific competition on trait variation in Phaeobacter inhibens biofilms', Environmental Microbiology, vol. 18, pp. 1635 - 1645, http://dx.doi.org/10.1111/1462-2920.13253
2016
Lachnit T; Thomas T; Steinberg P, 2016, 'Expanding our understanding of the seaweed holobiont: RNA Viruses of the Red Alga Delisea pulchra', Frontiers in Microbiology, vol. 6, http://dx.doi.org/10.3389/fmicb.2015.01489
2016
Reynolds D; Thomas T, 2016, 'Evolution and function of eukaryotic-like proteins from sponge symbionts', Molecular ecology, vol. 25, pp. 5242 - 5253, http://dx.doi.org/10.1111/mec.13812
2016
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, vol. 18, pp. 3962 - 3975, http://dx.doi.org/10.1111/1462-2920.13403
2016
Webster NS; Thomas T, 2016, 'The sponge hologenome', mBio, vol. 7, http://dx.doi.org/10.1128/mBio.00135-16
2016
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, vol. 7, http://dx.doi.org/10.1038/ncomms11870
2016
Egan S; Thomas T, 2015, 'Editorial for: Microbial symbiosis of marine sessile hosts- diversity and function', Frontiers in Microbiology, vol. 6, http://dx.doi.org/10.3389/fmicb.2015.00585
2015
Ye J; Nielsen S; Joseph S; Thomas T, 2015, 'High-resolution and specific detection of bacteria on complex surfaces using nanoparticle probes and electron microscopy', PLoS ONE, vol. 10, http://dx.doi.org/10.1371/journal.pone.0126404
2015
JOSEPH S; POW D; DAWSON K; MITCHELL DRG; RAWAL A; HOOK J; TAHERYMOOSAVI S; ZWIETEN LV; RUST J; DONNE S; MUNROE P; PACE B; GRABER E; THOMAS T; NIELSEN S; Jun YE; LIN Y; PAN G; Lianqing LI; SOLAIMAN ZM, 2015, 'Feeding Biochar to Cows: An Innovative Solution for Improving Soil Fertility and Farm Productivity', Pedosphere, vol. 25, pp. 666 - 679, http://dx.doi.org/10.1016/S1002-0160(15)30047-3
2015
YAO C; JOSEPH S; Lianqing LI; PAN G; LIN Y; MUNROE P; PACE B; TAHERYMOOSAVI S; ZWIETEN LV; THOMAS T; NIELSEN S; Jun YE; DONNE S, 2015, 'Developing More Effective Enhanced Biochar Fertilisers for Improvement of Pepper Yield and Quality', Pedosphere, vol. 25, pp. 703 - 712, http://dx.doi.org/10.1016/S1002-0160(15)30051-5
2015
Gardiner M; Fernandes ND; Nowakowski D; Raftery M; Kjelleberg S; Zhong L; Thomas T; Egan S, 2015, 'VarR controls colonization and virulence in the marine macroalgal pathogen Nautella italica R11', Frontiers in Microbiology, vol. 6, http://dx.doi.org/10.3389/fmicb.2015.01130
2015
Gardiner M; Thomas T; Egan S, 2015, 'A glutathione peroxidase (GpoA) plays a role in the pathogenicity of Nautella italica strain R11 towards the red alga Delisea pulchra', FEMS Microbiology Ecology, vol. 91, http://dx.doi.org/10.1093/femsec/fiv021
2015
Gutierrez-Zamora ML; Lee M; Manefield M; Thomas T, 2015, 'Biotransformation of coal linked to nitrification', International Journal of Coal Geology, vol. 137, pp. 136 - 141, http://dx.doi.org/10.1016/j.coal.2014.12.001
2015
Thomas T; Gilbert J; Meyer F, 2015, 'A 123 of Metagenomics', in Encyclopedia of Metagenomics, Springer US, pp. 1 - 9, http://dx.doi.org/10.1007/978-1-4614-6418-1_728-4
2015
Luter HM; Widder S; Botté ES; Wahab MA; Whalan S; Moitinho-Silva L; Thomas T; Webster NS, 2015, 'Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens', PeerJ, vol. 2015, http://dx.doi.org/10.7717/peerj.1435
2015
Marzinelli EM; Campbell AH; Zozaya Valdes E; Vergés A; Nielsen S; Wernberg T; de Bettignies T; Bennett S; Caporaso JG; Thomas T; Steinberg PD, 2015, 'Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography', Environmental Microbiology, vol. 17, pp. 4078 - 4088, http://dx.doi.org/10.1111/1462-2920.12972
2015
Joseph S; Husson O; Graber ER; Van Zwieten L; Taherymoosavi S; Thomas T; Nielsen S; Ye J; Pan G; Chia C; Munroe P; Allen J; Lin Y; Fan X; Donne S, 2015, 'The electrochemical properties of biochars and how they affect soil redox properties and processes', Agronomy, vol. 5, pp. 322 - 340, http://dx.doi.org/10.3390/agronomy5030322
2015
Egan S; Fernandes ND; Kumar V; Gardiner M; Thomas T, 2014, 'Bacterial pathogens, virulence mechanism and host defence in marine macroalgae', Environmental Microbiology, vol. 16, pp. 925 - 938, http://dx.doi.org/10.1111/1462-2920.12288
2014
Gunawan C; Limbri H; Thomas T; Smith A; Scott J; Rosche B, 2014, 'Coal-Packed Methane Biofilter for Mitigation of Green House Gas Emissions from Coal Mine Ventilation Air', PLoS One, vol. 9, pp. e94641, http://dx.doi.org/10.1371/journal.pone.0094641
2014
Nielsen S; Minchin T; Kimber S; van Zwieten L; Gilbert J; Munroe P; Joseph S; Thomas T, 2014, 'Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilisers', Agriculture, Ecosystems and Environment, vol. 191, pp. 73 - 82, http://dx.doi.org/10.1016/j.agee.2014.04.006
2014
Thomas JM; Thomas T; Stuetz RM; Ashbolt NJ, 2014, 'Your garden hose: A potential health risk due to Legionella spp. growth facilitated by free-living amoebae', Environmental Science and Technology, vol. 48, pp. 10456 - 10464, http://dx.doi.org/10.1021/es502652n
2014
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
2014
McElroy K; Thomas T; Luciani F, 2014, 'Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions.', Microb Inform Exp, vol. 4, pp. 1, http://dx.doi.org/10.1186/2042-5783-4-1
2014
McElroy KE; Hui JGK; Woo JKK; Luk AWS; Webb JS; Kjelleberg S; Rice SA; Thomas T, 2014, 'Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation', Proceedings of the National Academy of Sciences of the United States of America, vol. 111, http://dx.doi.org/10.1073/pnas.1314340111
2014
Zozaya-Valdes E; Egan S; Thomas T, 2014, 'A comprehensive analysis of the microbial communities of healthy and diseased marine macroalgae and the detection of known and potential bacterial pathogens.', Frontiers in microbiology, vol. 6, pp. 146 - 146, http://dx.doi.org/10.3389/fmicb.2015.00146
2014
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://dx.doi.org/10.1002/9783527681501.ch07
2014
Bougouffa S; Yang JK; Le OO; Wang Y; Batang Z; Al-Suwailem A; Egan S; Harder T; Burke C; Steinberg P; others , 2013, 'Further Readings in Geomicrobiology', Geomicrobiology Journal, vol. 30, pp. 768 - 768, http://dx.doi.org/10.1080/01490451.2013.809976
2013
Woo JKK; McElroy K; Rice SA; Kirov SM; Thomas T; Kjelleberg S, 2013, 'Draft genome sequence of the chronic, nonclonal cystic fibrosis isolate Pseudomonas aeruginosa strain 18A', Genome announcements, vol. 1, http://dx.doi.org/10.1128/genomeA.00001-13
2013
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
Egan SG; Harder T; Burke CM; Steinberg PD; Kjelleberg S; Thomas T, 2013, 'The seaweed holobiont: understanding seaweed–bacteria interactions.', FEMS Microbiology Reviews, vol. 37, pp. 462 - 476, http://dx.doi.org/10.1111/1574-6976.12011
2013
Burke CM; Liu M; Britton WJ; Triccas J; Thomas T; Smith A; Allen S; Salomon R; Harry E, 2013, 'Harnessing Single Cell Sorting to Identify Cell Division Genes and Regulators in Bacteria', PLoS ONE, vol. 8, pp. e60964, http://dx.doi.org/10.1371/journal.pone.0060964
2013
Fan L; Liu ; Simister RL; Webster N; Thomas T, 2013, 'Marine microbial symbiosis heats up: The phylogenetic and functional response of a sponge holobiont to thermal stress', ISME Journal, vol. 7, pp. 991 - 1002, http://dx.doi.org/10.1038/ismej.2012.165
2013
Nguyen MTHD; Liu M; Thomas T, 2013, 'Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis', Molecular ecology, vol. 23, pp. 1635 - 1645, http://dx.doi.org/10.1111/mec.12384
2013
Weiss M; Kesbert AI; Labutti KM; Weiss ; Weiss ; Hauser L; Copealand AC; Woyke T; Lowry SR; Lucas S; Land M; Goodwin L; Kjelleberg SA; Cook AM; Buhmann MT; Thomas T; Schleheck DF, 2013, 'Permanent draft genome sequence of Comamonas testosteroni KF-1', Standards in Genomic Sciences, vol. 8, pp. 239 - 254, http://dx.doi.org/10.4056/sigs.3847890
2013
Joseph S; Graber ER; Chia C; Munroe PR; Donne SW; Thomas T; Marjo CE; Rutlidge HT; Pan G; Li L; Taylor P; Rawal A; Hook JM, 2013, 'Shifting paradigms: Development of high-efficiency biochar fertilizers based on nano-structures and soluble components', Carbon Management, vol. 4, pp. 323 - 343, http://dx.doi.org/10.4155/cmt.13.23
2013
Woodhouse JN; Fan L; Brown MV; Thomas T; Neilan BA, 2013, 'Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges', The ISME journal, vol. 7, pp. 1842 - 1851, http://dx.doi.org/10.1038/ismej.2013.65
2013
Kaakoush NO; Thomas T; Day AS; Leach ST; Lemberg D; Dowd S; Mitchell HM, 2012, 'MICROBIAL DYSBIOSIS IN PEDIATRIC PATIENTS WITH CROHN'S DISEASE', in HELICOBACTER, WILEY-BLACKWELL, Ljubljana, SLOVENIA, pp. 92 - 92, presented at 25th International Workshop on Helicobacter and Related Bacteria in Chronic Digestive Inflammation and Gastric Cancer, Ljubljana, SLOVENIA, 13 September 2012 - 15 September 2012, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000308581600103&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2012
Fan L; Mcelroy KE; Thomas T, 2012, 'Reconstruction of ribosomal RNA genes from metagenomic data', PLoS ONE, vol. 7, pp. e39948, http://dx.doi.org/10.1371/journal.pone.0039948
2012
Woodhouse JN; Fan L; Brown MV; Thomas T; Neilan BA, 2012, 'Deep sequencing of secondary meta-metabolomes: A preliminary screening tool for determining natural product diversity.', Planta Medica, vol. 78, pp. CL51, http://dx.doi.org/10.1055/s-0032-1320286
2012
Fan L; Reynolds D; Liu M; Stark M; Kjelleberg S; Webster N; Thomas T, 2012, 'Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts', Proceedings of the National Academy of Science. USA, vol. 109, pp. 1878 - 1887, http://dx.doi.org/10.1073/pnas.1203287109
2012
McElroy KE; Luciani F; Thomas T, 2012, 'GemSIM: General, Error-Model based SIMulator of next-generation sequencing data', BMC Genomics, vol. 13, pp. 1 - 9, http://dx.doi.org/10.1186/1471-2164-13-74
2012
Thole S; Kalhoefer D; Voget S; Berger M; Engelhardt T; Leisegang H; Wollherr A; Kjelleberg S; Danial R; Meinhardt S; Thomas T; Brinkhoff T, 2012, 'Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life', ISME Journal, vol. 6, pp. 2229 - 2244, http://dx.doi.org/10.1038/ismej.2012.62
2012
Fernandes N; Steinberg PD; Rusch D; Kjelleberg S; Thomas T, 2012, 'Community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed Delisea pulchra.', PLoS One, vol. 7, pp. e50854, http://dx.doi.org/10.1371/journal.pone.0050854
2012
Penesyan A; Ballestriero F; Daim M; Kjelleberg S; Thomas T; Egan SG, 2012, 'Assessing the effectiveness of functional genetic screens for the identification of bioactive metabolites', Marine Drugs, vol. 11, pp. 40 - 49, http://dx.doi.org/10.3390/md11010040
2012
Brown MV; Lauro FM; Demaere MZ; Muir L; Wilkins D; Thomas T; Riddle M; Fuhrman J; Andrews-Pfannkoch C; Hoffman JM; McQuaid J; Allen A; Rintoul S; Cavicchioli R, 2012, 'Global biogeography of SAR11 marine bacteria', Molecular Systems Biology, vol. 8, pp. 595, http://dx.doi.org/10.1038/msb.2012.28
2012
Thomas T; Gilbert J; Meyer F, 2012, 'Metagenomics - a guide from sampling to data analysis.', BMC Microbial Informatics and Experimentation, vol. 2, pp. 3, http://dx.doi.org/10.1186/2042-5783-2-3
2012
Fan L; Liu M; Zhong L; Kjelleberg S; Thomas T, 2012, 'Metaproteogenomic analysis of a community of sponge symbionts', ISME Journal, vol. 6, pp. 1515 - 1525, http://dx.doi.org/10.1038/ismej.2012.1
2012
Lauro FM; Demaere MZ; Yau S; Brown MV; Wilkins D; Ng SC; Raftery MJ; Gibson JA; Andrews-Pfannkoch C; Lewis M; Hoffman JM; Thomas T; Cavicchioli R, 2011, 'An integrative study of a meromictic lake ecosystem in Antarctica', ISME Journal, vol. 5, pp. 879 - 895, http://dx.doi.org/10.1038/ismej.2010.185
2011
Kumar V; Rao D; Thomas T; Kjelleberg S; Egan SG, 2011, 'Antidiatom and antibacterial activity of epiphytic bacteria isolated from Ulva lactuca in tropical waters', World Journal of Microbiology and Biotechnology, vol. 27, pp. 1543 - 1549, http://dx.doi.org/10.1007/s11274-010-0606-1
2011
Yung PY; Burke CM; Lewis M; Kjelleberg S; Thomas T, 2011, 'Novel antibacterial proteins from the microbial communities associated with the sponge Cymbastela concentrica and the green alga Ulva australis.', Applied and Environmental Microbiology, vol. 77, pp. 1512 - 1515, http://dx.doi.org/10.1128/AEM.02038-10
2011
Naughton S; Parker D; Seemann T; Thomas T; Turnbull L; Rose B; Bye P; Cordwell S; Whitchurch C; Manos J, 2011, 'Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung', PLoS ONE, vol. 6, pp. 1 - 8, http://dx.doi.org/10.1371/journal.pone.0024526
2011
Demaere MZ; Lauro FM; Thomas T; Yau S; Cavicchioli R, 2011, 'Simple high-throughput annotation pipeline (SHAP)', Bioinformatics, vol. 27, pp. 2431 - 2432, http://dx.doi.org/10.1093/bioinformatics/btr411
2011
Schleheck DF; Weiss M; Pitluck S; Bruce D; Land ML; Han S; Saunders E; Tapia R; Detter C; Brettin T; Han J; Woyke T; Goodwin L; Pennacchio L; Nolan M; Cook AM; Kjelleberg S; Thomas T, 2011, 'Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T).', Standards in Genomic Sciences, vol. 5, pp. 298 - 310, http://dx.doi.org/10.4056/sigs.2215005
2011
Penesyan A; Tebben J; Lee M; Thomas T; Kjelleberg S; Harder T; Egan S, 2011, 'Identification of the antibacterial compound produced by the marine epiphytic bacterium Pseudovibrio sp. D323 and related sponge-associated bacteria.', Marine Drugs, vol. 9, pp. 1391 - 1402, http://dx.doi.org/10.3390/md9081391
2011
Burke CM; Steinberg PD; Rusch D; Kjelleberg S; Thomas T, 2011, 'Bacterial community assembly based on functional genes rather than species', Proceedings of the National Academy of Sciences of the United States of America, vol. 108, pp. 14288 - 14293, http://dx.doi.org/10.1073/pnas.1101591108
2011
Fernandes N; Case RJ; Longford SR; Seyedsayamdost M; Steinberg PD; Kjelleberg S; Thomas T, 2011, 'Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra', PLoS ONE, vol. 6, pp. e27387, http://dx.doi.org/10.1371/journal.pone.0027387
2011
Thomas T; Kindinger I; Yu D; Blackall L; Forehead H; Johnson CR; Manefield MJ; Esvaran M, 2011, 'An experimental model for the spatial structuring and selection of bacterial communities', Journal of Microbiological Methods, vol. 87, pp. 165 - 168, http://dx.doi.org/10.1016/j.mimet.2011.08.010
2011
Thomas T; Kjelleberg S; Yung PY, 2011, 'Phylogenetic Screening of Metagenomic Libraries Using Homing Endonuclease Restriction and Marker Insertion', Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, pp. 245 - 249, http://dx.doi.org/10.1002/9781118010518.ch29
2011
Jacqueline T; Thomas T; Stuetz RM; Ashbolt NJ, 2011, 'The risk of Free-living amoebe interaction bacterial pathogens in drinking water', in Conference Proceedings, WaterMicro 2011, Proceeding 16th International Symposium on Health-Related Microbiology, Rotorua, NZ, presented at Proceeding 16th International Symposium on Health-Related Microbiology, Rotorua, NZ, 18 September 2011 - 23 September 2011
2011
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, http://dx.doi.org/10.1093/nar/gkp746
2011
Yau S; Lauro FM; Demaere MZ; Brown MV; Thomas T; Raftery MJ; Lewis M; Hoffman JM; Gibson J; Cavicchioli R; Andrews-Pfannkoch C, 2011, 'Virophage control of Antarctic algal host–virus dynamics', Proceedings of the National Academy of Sciences of the United States of America, vol. 108, pp. 6163 - 6168, http://dx.doi.org/10.1073/pnas.1018221108
2011
McElroy K; Luciani F; Hui J; Rice S; Thomas T, 2011, 'Bacteriophage evolution drives Pseudomonas aeruginosa PAO1 biofilm diversification', BMC Bioinformatics, vol. 12, pp. A2 - A2, http://dx.doi.org/10.1186/1471-2105-12-S11-A2
2011
Fan L; Kjelleberg S; Thomas T, 2011, 'Accurate Reconstruction of Microbial Community From Environmental Shotgun Sequences Avoiding Primer Bias', SHORT, pp. 58 - 58
2011
Liu MY; Kjelleberg S; Thomas T, 2011, 'Functional genomic analysis of an uncultured delta-proteobacterium in the sponge Cymbastela concentrica.', ISME Journal, vol. 5, pp. 427 - 435, http://dx.doi.org/10.1038/ismej.2010.139
2011
Burke CM; Thomas T; Lewis M; Steinberg PD; Kjelleberg S, 2011, 'Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis', ISME Journal, vol. 5, pp. 590 - 600, http://dx.doi.org/10.1038/ismej.2010.164
2011
Yung PY; Kjelleberg S; Thomas T, 2011, 'A polyphasic approach to the exploration of collagenolytic activity in the bacterial community associated with the marine sponge Cymbastela concentrica.', FEMS Microbiology Letters, vol. 321, pp. 24 - 29, http://dx.doi.org/10.1111/j.1574-6968.2011.02306.x
2011
Tujula NA; Crocetti GR; Burke CM; Thomas T; Holmstrom CG; Kjelleberg S, 2010, 'Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga', ISME Journal, vol. 4, pp. 301-311, http://dx.doi.org/10.1038/ismej.2009.107
2010
Ng SC; De Maere M; Williams TJ; Lauro FM; Raftery MJ; Gibson J; Andrews-Pfannkoch C; Lewis M; Hoffman J; Thomas T; Cavicchioli R, 2010, 'Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica.', ISME Journal, vol. 4, pp. 1002 - 1019, http://dx.doi.org/10.1038/ismej.2010.28
2010
Thomas J; Storey M; Thomas T; Stuetz RM; Ashbolt NJ, 2010, 'Diversity of free-living amoebal pathogen hosts in a dual distribution (drinking and recycled) water system', in Proceedings Water Quality Technology Conference, American Water Works Association (Curran Associates), Washington, pp. 193 - 196, presented at Water Quality Technology Conference and Exposition 2010, Savannah, Georgia U.S.A, 14 November 2010 - 18 November 2010
2010
Thomas T; Rusch D; Demaere MZ; Yung PY; Lewis M; Halpern A; Heidelberg KB; Egan SG; Steinberg PD; Kjelleberg S, 2010, 'Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis', ISME Journal, vol. 4, pp. 1557 - 1567, http://dx.doi.org/10.1038/ismej.2010.74
2010
Ballestriero F; Thomas T; Burke CM; Egan SG; Kjelleberg S, 2010, 'Identification of Compounds with Bioactivity against the Nematode Caenorhabditis elegans by a Screen Based on the Functional Genomics of the Marine Bacterium Pseudoalteromonas tunicata D2', Applied and Environmental Microbiology, vol. 17, pp. 5710 - 5717, http://dx.doi.org/10.1128/AEM.00695-10
2010
Thomas T, 2010, Proteins from Archaea, 1, Lambert Publishing Group, Saarbrücken, Germany
2010
Cairns MJ; Thomas T; Beltran C; Tillett D, 2009, 'Primer fabrication using polymerase mediated oligonucleotide synthesis', BMC Genomics, vol. 10, http://dx.doi.org/10.1186/1471-2164-10-344
2009
Lauro FM; McDougald D; Thomas T; Williams TJ; Egan SG; Rice SA; Demaere MZ; Ting LL; Ertan H; Johnson J; Ferriera S; Lapidus A; Anderson IM; Kyrpides N; Munkf A; Detter C; Hang C; Brown M; Robb F; Kjelleberg S; Cavicchioli R, 2009, 'The genomic basis of trophic strategy in marine bacteria', Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 15527 - 15533, http://dx.doi.org/10.1073/pnas.0903507106
2009
Allen MA; Lauro FM; Williams TJ; Burg DW; Siddiqui KS; De Francisci D; Chong K; Pilak O; Chew H; De Maere M; Ting LL; Katrib M; Ng SC; Sowers KR; Galperin M; Anderson I; Ivanova N; Dalin E; Martinez MP; Lapidus A; Hauser L; Land MH; Thomas T; Cavicchioli R, 2009, 'The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: The role of genome evolution in cold adaptation', ISME Journal, vol. 3, pp. 1012 - 1035, http://dx.doi.org/10.1038/ismej.2009.45
2009
Yung PY; Burke CM; Lewis M; Egan SG; Kjelleberg S; Thomas T, 2009, 'Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion', Nucleic Acids Research, vol. 37, pp. e144, http://dx.doi.org/10.1093/nar/gkp746
2009
Burke CM; Kjelleberg S; Thomas T, 2009, 'Selective extraction of bacterial DNA from the surfaces of macroalgae', Applied and Environmental Microbiology, vol. 75, pp. 252 - 256, http://dx.doi.org/10.1128/AEM.01630-08
2009
Siddiqui KS; Thomas T, (ed.), 2008, Protein Adaptation in Extremophiles, Original, Nova Biomedical Books, New York, https://www.novapublishers.com/catalog/product_info.php?cPath=23_29&products_id=6238&osCsid=523411be245aa875dc809b66c2ebf54b
2008
Mai-Prochnow AG; Lucas-Elio P; Egan SG; Thomas T; Webb JS; Sanchez-Amat A; Kjelleberg S, 2008, 'Hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several gram-negative bacteria', Journal of Bacteriology, vol. 190, pp. 5493 - 5501, http://dx.doi.org/10.1128/JB.00549-08
2008
Egan SG; Thomas T; Kjelleberg S, 2008, 'Unlocking the diversity and biotechnological potential of marine surface associated microbial communities', Current Opinion in Microbiology, vol. 11, pp. 219 - 225, http://dx.doi.org/10.1016/j.mib.2008.04.001
2008
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
2008
Thomas T; Evans FF; Schleheck D; Mai-Prochnow A; Burke C; Penesyan A; Dalisay DS; Stelzer-Braid S; Saunders N; Johnson J; others , 2008, 'Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment', Detail:, vol. 3, http://dx.doi.org/10.1371/journal.pone.0003252
2008
Burke CM; Thomas T; Egan SG; Kjelleberg S, 2007, 'The use of functional genomics for the identification of a gene cluster encoding for the biosynthesis of an antifungal tambjamine in the marine bacterium Pseudoalteromonas tunicata', Environmental Microbiology, vol. 9, pp. 814 - 818, http://dx.doi.org/10.1111/j.1462-2920.2006.01177.x
2007
Cavicchioli R; Demaere MZ; Thomas T, 2007, 'Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers', BioEssays, vol. 29, pp. 11 - 14, http://dx.doi.org/10.1002/bies.20519
2007
nil Siddiqui KS; De Francisci D; Thomas T, 2007, 'In: Methods in Protein Structure and Stability Analysis ISBN 1-60021-704-4 Editors: V. Uversky and E. Permyakov, pp. 147-158\copyright 2007 Nova Science Publishers, Inc.', Methods in Protein Structure and Stability Analysis: Conformational Stability, Size, Shape and Surface of Protein Molecules, pp. 147 - 147
2007
Thomas T; Egan SG; Burg DW; Ng SC; Ting LL; Cavicchioli R, 2007, 'Integration of genomics and proteomics into marine microbial ecology', Marine Ecology Progress Series, vol. 332, pp. 291 - 299, http://dx.doi.org/10.3354/meps332291
2007
Goldberg SMD; Johnson J; Busam D; Feldblyum T; Ferriera S; Friedman R; Halpern A; Khouri H; Kravitz SA; Lauro FM; Li K; Rogers YH; Strausberg R; Sutton G; Tallon L; Thomas T; Venter E; Frazier M; Venter JC, 2006, 'Erratum: A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes (Proceedings of the National Academy of Sciences of the United States of America (July 25, 2006) 30, 103 (11240-11245) DOI: 10.1073/pnas.0604351103)', Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 16057, http://dx.doi.org/10.1073/pnas.0607197103
2006
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, http://dx.doi.org/10.1016/S0580-9517(08)70020-5
2006
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, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000278001100046&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
2006
Goldberg S; Johnson J; Busam D; Feldblyum T; Ferriera S; Friedman R; Halpern A; Khouri H; Kravitz S; Lauro FM; Li KS; Rogers Y; Strausberg R; Sutton G; Tallon L; Thomas T; Venter E; Frazier M; Venter J, 2006, 'A Sanger/pyrosequencing hybrid approach tor the generation of high-quality draft assemblies of marine microbial genomes', Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 11240 - 11245, http://dx.doi.org/10.1073/pnas.0604351103
2006
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
2004
TILLETT D; THOMAS T, 2003, OPTIMISATION OF PRIMER LIBRARIES BY EXTENSION OF SHORT PRIMERS
2003
TILLETT D; THOMAS T, 2003, A METHOD OF SEQUESTERING AND/OR PURIFYING A POLYPEPTIDE
2003
Saunders NF; Thomas T; Curmi PM; Mattick JS; Kuczek E; Slade R; Davis J; Franzmann PD; Boone D; Rusterholtz K; Feldman R; Gates C; Bench S; Sowers KR; Kadner K; Aerts A; Dehal P; Detter C; Glavina T; Lucas S; Richardson P; Larimer F; Hauser L; Land M; Cavicchioli R, 2003, 'Mechanisms of Thermal Adaptation Revealed from the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii', Genome Research, vol. 13, pp. 1580 - 1588, http://dx.doi.org/10.1101/gr.1180903
2003
TILLETT D; THOMAS T, 2003, DNA AMPLIFICATION AND SEQUENCING IN COLLAPSIBLE EMULSIONS
2003
Cavicchioli R; Curmi PM; Saunders NF; Thomas T, 2003, 'Pathogenic archaea: do they exist?', BioEssays, vol. 25, pp. 1119 - 1128, http://dx.doi.org/10.1002/bies.10354
2003
Tillett D; Thomas T, 2000, A METHOD FOR INCREASING THE AFFINITY OF AN OLIGONUCLEOTIDE FOR A TARGET NUCLEIC ACID, Google Patents
2000
Torsten T; Cavicchioli R, 2000, 'Effect of temperature on the stability and activity of the elongation factor 2 proteins from low-temperature adapted and thermophilic methanogens', Journal of Bacteriology, vol. 182, pp. 1328 - 1332, http://dx.doi.org/10.1128/JB.182.5.1328-1332.2000
2000
Egan S; Torsten T; Holmstrom CG; Kjelleberg S, 2000, 'Phylogenetic relationship and antifouling activity of bacterial epiphytes from the marine alga Ulva lactuca', Environmental Microbiology, vol. 2, pp. 343 - 347, http://dx.doi.org/10.1046/j.1462-2920.2000.00107.x
2000
Thomas T, 2000, Low-temperature adaptation of elongation factor 2 proteins from Archaea, phdthesis, University of New South Wales
2000
Cavicchioli R; Torsten T; Curmi PM, 2000, 'Cold stress response in Archaea', Extremophiles, vol. 4, pp. 321 - 331, http://dx.doi.org/10.1007/s007920070001
2000
Berchet V; Torsten T; Cavicchioli R; Russell NJ; Gounot A, 2000, 'Structural analysis of the elongation factor G protein from the low-temperature-adapted bacterium Arthrobacter globiformis S155', Extremophiles, vol. 4, pp. 123 - 130, http://dx.doi.org/10.1007/s007920050146
2000
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
2000
Lim J; Torsten T; Cavicchioli R, 2000, 'Low temperature regulated DEAD-box RNA Helicase from the Antarctic Archaeon, Methanococcoides burtonii', Journal of Molecular Biology, vol. 297, pp. 553 - 567, http://dx.doi.org/10.1006/jmbi.2000.3585
2000
Torsten T; Cavicchioli R, 1998, 'Archaeal cold-adapted proteins: structural and evolutionary analysis of the elongation factor 2 proteins from psychrophilic, mesophilic and thermophilic proteins', FEBS Letters, vol. 439, pp. 281 - 286, http://dx.doi.org/10.1016/S0014-5793(98)01375-1
1998