Torsten Thomas

Summary

Affiliation: University of New South Wales
Country: Australia

Publications

  1. ncbi request reprint 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
    Catherine Burke
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
    Environ Microbiol 9:814-8. 2007
  2. doi request reprint Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis
    Torsten Thomas
    Centre for Marine Bio Innovation, The University of New South Wales, Sydney, Australia
    ISME J 4:1557-67. 2010
  3. pmc Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra
    Neil Fernandes
    The Centre for Marine Bio Innovation CMB, University of New South Wales, Sydney, Australia
    PLoS ONE 6:e27387. 2011
  4. pmc Draft Genome Sequence of the Chronic, Nonclonal Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain 18A
    Jerry K K Woo
    School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, University of New South Wales, Sydney, Australia
    Genome Announc 1:e0000113. 2013
  5. pmc Reconstruction of ribosomal RNA genes from metagenomic data
    Lu Fan
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 7:e39948. 2012
  6. pmc Community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed Delisea pulchra
    Neil Fernandes
    The Centre for Marine Bio Innovation, University of New South Wales, Sydney, Australia
    PLoS ONE 7:e50854. 2012
  7. pmc Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion
    Pui Yi Yung
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2035 NSW, Australia
    Nucleic Acids Res 37:e144. 2009
  8. pmc Metagenomics - a guide from sampling to data analysis
    Torsten Thomas
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, The University of New South Wales, Sydney, NSW 2052, Australia
    Microb Inform Exp 2:3. 2012
  9. ncbi request reprint Cold adaptation of archaeal elongation factor 2 (EF-2) proteins
    Torsten Thomas
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, UNSW, 2052, Australia
    Curr Protein Pept Sci 3:223-30. 2002
  10. pmc Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment
    Torsten Thomas
    Centre of Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 3:e3252. 2008

Collaborators

Detail Information

Publications47

  1. ncbi request reprint 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
    Catherine Burke
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
    Environ Microbiol 9:814-8. 2007
    ..A biosynthetic pathway has been proposed based on analysis and annotation of the gene cluster...
  2. doi request reprint Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis
    Torsten Thomas
    Centre for Marine Bio Innovation, The University of New South Wales, Sydney, Australia
    ISME J 4:1557-67. 2010
    ..These data provide new insight into the evolution of symbiotic diversity, microbial metabolism and host-microbe interactions in sponges...
  3. pmc Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra
    Neil Fernandes
    The Centre for Marine Bio Innovation CMB, University of New South Wales, Sydney, Australia
    PLoS ONE 6:e27387. 2011
    ....
  4. pmc Draft Genome Sequence of the Chronic, Nonclonal Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain 18A
    Jerry K K Woo
    School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, University of New South Wales, Sydney, Australia
    Genome Announc 1:e0000113. 2013
    ..The genome of 18A was sequenced for comparison with environmental and clinical isolates to identify genes that might facilitate its persistence during infection...
  5. pmc Reconstruction of ribosomal RNA genes from metagenomic data
    Lu Fan
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 7:e39948. 2012
    ..Our approach is readily applicable to existing metagenomic datasets and is expected to lead to the discovery of new microbial phylotypes...
  6. pmc Community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed Delisea pulchra
    Neil Fernandes
    The Centre for Marine Bio Innovation, University of New South Wales, Sydney, Australia
    PLoS ONE 7:e50854. 2012
    ....
  7. pmc Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion
    Pui Yi Yung
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2035 NSW, Australia
    Nucleic Acids Res 37:e144. 2009
    ..Our approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA sequencing information...
  8. pmc Metagenomics - a guide from sampling to data analysis
    Torsten Thomas
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, The University of New South Wales, Sydney, NSW 2052, Australia
    Microb Inform Exp 2:3. 2012
    ..As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared...
  9. ncbi request reprint Cold adaptation of archaeal elongation factor 2 (EF-2) proteins
    Torsten Thomas
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, UNSW, 2052, Australia
    Curr Protein Pept Sci 3:223-30. 2002
    ..A key finding from these studies is that in addition to inherent properties of the EF-2 proteins, intracellular factors (e.g. ribosomes and intracellular solutes) play a central role in thermal adaptation...
  10. pmc Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment
    Torsten Thomas
    Centre of Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 3:e3252. 2008
    ..As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions...
  11. pmc An integrative study of a meromictic lake ecosystem in Antarctica
    Federico M Lauro
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    ISME J 5:879-95. 2011
    ..By exhaustively describing and modelling interactions in Ace Lake, we have developed an approach that may be applicable to learning how environmental perturbations affect the microbial dynamics in more complex aquatic systems...
  12. pmc Global biogeography of SAR11 marine bacteria
    Mark V Brown
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    Mol Syst Biol 8:595. 2012
    ..Our data demonstrate the importance of adaptive radiation in the organism's ability to proliferate throughout the world's oceans, and describe genomic traits characteristic of different phylotypes in specific marine biomes...
  13. pmc Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts
    Lu Fan
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
    Proc Natl Acad Sci U S A 109:E1878-87. 2012
    ..Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process...
  14. pmc Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis
    Catherine Burke
    School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, University of New South Wales, Sydney, New South Wales, Australia
    ISME J 5:590-600. 2011
    ..The competitive lottery model, originally derived to explain diversity in coral reef fishes, may explain the pattern of colonization of this algal surface...
  15. pmc Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress
    Lu Fan
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    ISME J 7:991-1002. 2013
    ..High symbiont specialization and low functional redundancy, thus make these holobionts extremely vulnerable to environmental perturbations, including climate change...
  16. doi request reprint The seaweed holobiont: understanding seaweed-bacteria interactions
    Suhelen Egan
    School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, The University of New South Wales, Sydney, NSW, Australia
    FEMS Microbiol Rev 37:462-76. 2013
    ....
  17. pmc The genomic basis of trophic strategy in marine bacteria
    Federico M Lauro
    Environmental Microbiology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
    Proc Natl Acad Sci U S A 106:15527-33. 2009
    ..Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining...
  18. pmc Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation
    Kerensa E McElroy
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, NSW 2052, Australia
    Proc Natl Acad Sci U S A 111:E1419-27. 2014
    ..Long-term bacterial evolution is known to proceed via few, nonsynonymous, positively selected mutations, and here we show that similar dynamics govern short-term, within-population bacterial diversification. ..
  19. pmc Metaproteogenomic analysis of a community of sponge symbionts
    Michael Liu
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, NSW, Australia
    ISME J 6:1515-25. 2012
    ..Our data clearly show that a combined metaproteogenomic approach can provide novel information on the activities, physiology and interactions of sponge-associated microbial communities...
  20. doi request reprint Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga
    Niina A Tujula
    Centre for Marine Bio Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    ISME J 4:301-11. 2010
    ....
  21. pmc Bacterial community assembly based on functional genes rather than species
    Catherine Burke
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
    Proc Natl Acad Sci U S A 108:14288-93. 2011
    ....
  22. pmc Novel antibacterial proteins from the microbial communities associated with the sponge Cymbastela concentrica and the green alga Ulva australis
    Pui Yi Yung
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    Appl Environ Microbiol 77:1512-5. 2011
    ..The results suggest that uncultured alpha- and gammaproteobacteria contain new classes of proteins that may be a source of antibacterial agents...
  23. ncbi request reprint Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis
    Mary T H D Nguyen
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, NSW 2052, Australia
    Mol Ecol 23:1635-45. 2014
    ..Our results show that ARP from sponge symbionts can function to interfere with phagocytosis, and we postulate that this might be one mechanism by which symbionts can escape digestion in a sponge host. ..
  24. ncbi request reprint Bacterial pathogens, virulence mechanism and host defence in marine macroalgae
    Suhelen Egan
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
    Environ Microbiol 16:925-38. 2014
    ..This review highlights important areas of research that require future attention to understand the link between environmental change, opportunistic pathogens and macroalgal health in the world's oceans. ..
  25. doi request reprint A polyphasic approach to the exploration of collagenolytic activity in the bacterial community associated with the marine sponge Cymbastela concentrica
    Pui Yi Yung
    Centre for Marine Bio Innovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    FEMS Microbiol Lett 321:24-9. 2011
    ..concentrica, and that some low-abundance bacteria have collagenase activities that have the potential to harm the sponge through tissue degradation...
  26. pmc 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
    Francesco Ballestriero
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney 2052, New South Wales, Australia
    Appl Environ Microbiol 76:5710-7. 2010
    ..The novel functional genomic screen presented here therefore detects new eukaryotic inhibitors with different chemical structures, kinetics, and predicted modes of actions...
  27. pmc Virophage control of antarctic algal host-virus dynamics
    Sheree Yau
    School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio Innovation, and Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales 2052, Australia
    Proc Natl Acad Sci U S A 108:6163-8. 2011
    ..These findings indicate that virophages regulate host-virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems...
  28. pmc Hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several gram-negative bacteria
    Anne Mai-Prochnow
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, Biological Sciences Building, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
    J Bacteriol 190:5493-501. 2008
    ..We propose that biofilm killing through hydrogen peroxide can be linked to AlpP homologue activity and plays an important role in dispersal and colonization across a range of gram-negative bacteria...
  29. ncbi request reprint Pathogenic archaea: do they exist?
    Ricardo Cavicchioli
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
    Bioessays 25:1119-28. 2003
    ..The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future...
  30. pmc Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges
    Jason N Woodhouse
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    ISME J 7:1842-51. 2013
    ..It is envisaged that this approach will be used across multiple environments, offering an insight into the biological processes that influence the production of secondary metabolites. ..
  31. pmc Assessing the effectiveness of functional genetic screens for the identification of bioactive metabolites
    Anahit Penesyan
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney 2052, New South Wales, Australia
    Mar Drugs 11:40-9. 2013
    ..Here we demonstrate that constructing libraries with strains known to produce bioactives can greatly enhance the screening efficiency, by increasing the "hit-rate" and unmasking multiple activities from the same bacterial source...
  32. pmc Identification of the antibacterial compound produced by the marine epiphytic bacterium Pseudovibrio sp. D323 and related sponge-associated bacteria
    Anahit Penesyan
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney 2052, New South Wales, Australia
    Mar Drugs 9:1391-402. 2011
    ..We propose that TDA in isolate D323 and related eukaryote-associated bacteria plays a role in defending the host organism against unwanted microbial colonisation and, possibly, bacterial pathogens...
  33. ncbi request reprint Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica
    Charmaine Ng
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    ISME J 4:1002-19. 2010
    ..As a result we are able to propose an explanation of the active biological processes promoted by cold-adapted GSB and the adaptive strategies they use to thrive under the severe physiochemical conditions prevailing in polar environments...
  34. ncbi request reprint Thermodynamic activation properties of elongation factor 2 (EF-2) proteins from psychrotolerant and thermophilic Archaea
    Khawar Sohail Siddiqui
    Microbiology and Immunology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    Extremophiles 6:143-50. 2002
    ....
  35. pmc Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
    Neil F W Saunders
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    Genome Res 13:1580-8. 2003
    ..This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles...
  36. doi request reprint Unlocking the diversity and biotechnological potential of marine surface associated microbial communities
    Suhelen Egan
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, University of New South Wales, Sydney, NSW 2052, Australia
    Curr Opin Microbiol 11:219-25. 2008
    ....
  37. pmc Primer fabrication using polymerase mediated oligonucleotide synthesis
    Murray J Cairns
    Schizophrenia Research Institute, Sydney, NSW 2006, Australia
    BMC Genomics 10:344. 2009
    ..PMOS can be used to generate primers directly in the end-users laboratory within the context of any DNA polymerase chemistry such as in PCR or sequencing reactions..
  38. pmc Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung
    Sharna Naughton
    Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
    PLoS ONE 6:e24526. 2011
    ..Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients...
  39. doi request reprint Simple high-throughput annotation pipeline (SHAP)
    Matthew Z DeMaere
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    Bioinformatics 27:2431-2. 2011
    ..The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources of many smaller research groups...
  40. pmc Harnessing single cell sorting to identify cell division genes and regulators in bacteria
    Catherine Burke
    The ithree Institute, University of Technology, Sydney, New South Wales, Australia
    PLoS ONE 8:e60964. 2013
    ..This novel screening strategy is applicable to a wide range of organisms, including pathogenic bacteria, where cell division genes and regulators are attractive drug targets for antibiotic development...
  41. pmc Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica
    Michael Yizhe Liu
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    ISME J 5:427-35. 2011
    ....
  42. doi request reprint The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation
    Michelle A Allen
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
    ISME J 3:1012-35. 2009
    ....
  43. ncbi request reprint Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated Archaea: the role of ammonia oxidizers
    Ricardo Cavicchioli
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
    Bioessays 29:11-4. 2007
    ..1 These findings not only highlight the undoubtedly critical yet unknown roles that archaea play in global nutrient cycles but illustrate the importance of genomic studies for informing us about the functional capacity of life on Earth...
  44. doi request reprint An experimental model for the spatial structuring and selection of bacterial communities
    Torsten Thomas
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    J Microbiol Methods 87:165-8. 2011
    ..8 under conditions of protozoan grazing. The competitive benefit provided by spatial structuring has implications for the evolution of natural bacterial communities in the environment...
  45. pmc Selective extraction of bacterial DNA from the surfaces of macroalgae
    Catherine Burke
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, The University of New South Wales, Sydney 2052, Australia
    Appl Environ Microbiol 75:252-6. 2009
    ..The DNA is suitable for a variety of subsequent applications, including the construction of large-insert clone libraries and metagenomic sequencing...
  46. pmc GemSIM: general, error-model based simulator of next-generation sequencing data
    Kerensa E McElroy
    Centre for Marine Bio Innovation and School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
    BMC Genomics 13:74. 2012
    ..Empirical fragment length and quality score distributions are also used. Reads may be drawn from one or more genomes or haplotype sets, facilitating simulation of deep sequencing, metagenomic, and resequencing projects...
  47. pmc A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes
    Susanne M D Goldberg
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 103:11240-5. 2006
    ....