Tim is a research associate at the Climate Change Cluster with expertise in bioinformatics and computational biology. His research interest focusses on marine ecology, specifically on understanding the genetic and molecular bases of complex relationships between marine microbial organisms such as microalgae, bacteria and viruses.
After finishing his PhD at the Arctic University of Norway, Tromsø, Norway, in the field of bacterial comparative genomics and bioinformatics in 2013 Tim started a postdoc at CSIRO’s Oceans and Atmosphere Flagship in Tasmania where he joined the Environmental Genomics Team of Dr. Levente Bodrossy.
In 2016 Tim joined the Climate Change Cluster (C3) as a Research Associate where he works across the different research projects as the lead bioinformatician to strengthen bioinformatics capabilities at the C3.
Tim has applied his expertise in omics data analysis, e.g. comparative genomics, transcriptomics and metagenomics, in large scale projects such as the Ocean Sampling Day and the Australian Marine Microbes project.
Given the growing importance of computers and data analysis in biological sciences Tim is also providing bioinformatics support and training to researchers and students across the C3. He is applying an inclusive and open teaching philosophy that takes into account the challenges that many life scientists face when they are confronted with bioinformatics and dta analysis for the first time.
Can supervise: YES
- microbial genomics including microalgae, bacteria and viruses
- metagenomics / metatranscriptomics
- pathway reconstruction and systems biology
Kretzschmar, AL, Verma, A, Murray, S, Kahlke, T, Fourment, M & Darling, A 2019, 'Trial by phylogenetics - Evaluating the Multi-Species Coalescent for phylogenetic inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae)'.View/Download from: Publisher's site
ABSTRACT From publicly available next-gen sequencing datasets of non-model organisms, such as marine protists, arise opportunities to explore their evolutionary relationships. In this study we explored the effects that dataset and model selection have on the phylogenetic inference of the Gonyaulacales, single celled marine algae of the phylum Dinoflagellata with genomes that show extensive paralogy. We developed a method for identifying and extracting single copy genes from RNA-seq libraries and compared phylogenies inferred from these single copy genes with those inferred from commonly used genetic markers and phylogenetic methods. Comparison of two datasets and three different phylogenetic models showed that exclusive use of ribosomal DNA sequences, maximum likelihood and gene concatenation showed very different results to that obtained with the multi-species coalescent. The multi-species coalescent has recently been recognized as being robust to the inclusion of paralogs, including hidden paralogs present in single copy gene sets (pseudoorthologs). Comparisons of model fit strongly favored the multi-species coalescent for these data, over a concatenated alignment (single tree) model. Our findings suggest that the multi-species coalescent (inferred either via Maximum Likelihood or Bayesian Inference) should be considered for future phylogenetic studies of organisms where accurate selection of orthologs is difficult.
Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunensse, T, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs.View/Download from: Publisher's site
© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. High-latitude coral communities are distinct from their tropical counterparts, and how they respond to recent heat wave events that have decimated tropical reefs remains unknown. In Australia, the 2016 El Niño resulted in the largest global mass coral bleaching event to date, reaching as far south as Sydney Harbour (~ 34°S). Coral bleaching was observed for the first time (affecting ca., 60% of all corals) as sea surface temperatures in Sydney Harbour remained > 2 °C above the long-term mean summer maxima, enabling us to examine whether high-latitude corals bleached in a manner described for tropical corals. Responses of the geographically cosmopolitan Plesiastrea versipora and southerly restricted Coscinaraea mcneilli were contrasted across two harbour sites, both in situ and among samples-maintained ex situ in aquaria continually supplied with Sydney Harbour seawater. While both coral taxa hosted the same species of microalgal endosymbiont (Breviolum spp; formerly clade B), only P. versipora bleached both in situ and ex situ via pronounced losses of endosymbiont cells. Both species displayed very different metabolic responses (growth, photosynthesis, respiration and calcification) and bleaching susceptibilities under elevated temperatures. Bacterial microbiome profiling, however, revealed a convergence of bacterial community composition across coral species throughout the bleaching. Corals species found in temperate regions, including the generalist P. versipora, will therefore likely be highly susceptible to future change as heat waves grow in frequency and severity unless their thermal thresholds increase. Our observations provide further evidence that high-latitude systems are susceptible to community reorganisation under climate change.
Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunesse, TC, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Correction to: Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave (Coral Reefs, (2019), 10.1007/s00338-019-01797-6)', Coral Reefs.View/Download from: Publisher's site
© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. Co-author name was misspelt and should read as Todd C. LaJeunesse.
Kahlke, T & Ralph, PJ 2019, 'BASTA – Taxonomic classification of sequences and sequence bins using last common ancestor estimations', Methods in Ecology and Evolution, vol. 10, no. 1, pp. 100-103.View/Download from: Publisher's site
1. Identification of the taxonomic origin of a DNA sequence is crucial for many sequencing projects, e.g. metagenomics studies, identification of contaminations in whole genome sequencing projects and filtering of organisms of interest in marker‐gene based community analyses.
2. Last common ancestor algorithms are powerful approaches to estimate the taxonomy of a given sequence and have been widely used for classification of next‐generation sequencing (NGS) reads, also known as 2nd generation sequencing reads.
3. Here, we present BASTA (https://github.com/timkahlke/BASTA), a basic sequence taxonomy annotator, which extends last common ancestor estimations from sequencing reads to any kind of nucleotide or amino acid sequence utilizing NCBI taxonomies of user‐defined best hits.
4. BASTA can be configured to use the output of many common sequence comparison tools, e.g. BLAST and Diamond, in conjunction with either provided or user‐defined target sequence databases.
King, WL, Siboni, N, Williams, NLR, Kahlke, T, Nguyen, KV, Jenkins, C, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2019, 'Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 mu var Disease', FRONTIERS IN MICROBIOLOGY, vol. 10.View/Download from: UTS OPUS or Publisher's site
Gardner, SG, Camp, EF, Smith, DJ, Kahlke, T, Osman, EO, Gendron, G, Hume, BCC, Pogoreutz, C, Voolstra, CR & Suggett, DJ 2019, 'Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave.', Ecology and Evolution, vol. 9, no. 3, pp. 938-956.View/Download from: UTS OPUS or Publisher's site
Repeat marine heat wave-induced mass coral bleaching has decimated reefs in Seychelles for 35 years, but how coral-associated microbial diversity (microalgal endosymbionts of the family Symbiodiniaceae and bacterial communities) potentially underpins broad-scale bleaching dynamics remains unknown. We assessed microbiome composition during the 2016 heat wave peak at two contrasting reef sites (clear vs. turbid) in Seychelles, for key coral species considered bleaching sensitive (Acropora muricata, Acropora gemmifera) or tolerant (Porites lutea, Coelastrea aspera). For all species and sites, we sampled bleached versus unbleached colonies to examine how microbiomes align with heat stress susceptibility. Over 30% of all corals bleached in 2016, half of which were from Acropora sp. and Pocillopora sp. mass bleaching that largely transitioned to mortality by 2017. Symbiodiniaceae ITS2-sequencing revealed that the two Acropora sp. and P. lutea generally associated with C3z/C3 and C15 types, respectively, whereas C. aspera exhibited a plastic association with multiple D types and two C3z types. 16S rRNA gene sequencing revealed that bacterial communities were coral host-specific, largely through differences in the most abundant families, Hahellaceae (comprising Endozoicomonas), Rhodospirillaceae, and Rhodobacteraceae. Both Acropora sp. exhibited lower bacterial diversity, species richness, and community evenness compared to more bleaching-resistant P. lutea and C. aspera. Different bleaching susceptibility among coral species was thus consistent with distinct microbiome community profiles. These profiles were conserved across bleached and unbleached colonies of all coral species. As this pattern could also reflect a parallel response of the microbiome to environmental changes, the detailed functional associations will need to be determined in future studies. Further understanding such microbiome-environmental interactions is likely critical to target more effective manag...
Ajani, PA, Kahlke, T, Siboni, N, Carney, R, Murray, S & Seymour, J 2018, 'The microbiome of the cosmopolitan diatom Leptocylindrus reveals significant spatial and temporal variability', Frontiers in Microbiology, vol. 9.View/Download from: UTS OPUS or Publisher's site
Brown, MV, van de Kamp, J, Ostrowski, M, Seymour, JR, Ingleton, T, Messer, LF, Jeffries, T, Siboni, N, Laverock, B, Bibiloni-Isaksson, J, Nelson, TM, Coman, F, Davies, CH, Frampton, D, Rayner, M, Goossen, K, Robert, S, Holmes, B, Abell, GCJ, Craw, P, Kahlke, T, Sow, SLS, McAllister, K, Windsor, J, Skuza, M, Crossing, R, Patten, N, Malthouse, P, van Ruth, PD, Paulsen, I, Fuhrman, JA, Richardson, A, Koval, J, Bissett, A, Fitzgerald, A, Moltmann, T & Bodrossy, L 2018, 'Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative.', Scientific data, vol. 5, pp. 180130-180130.View/Download from: UTS OPUS or Publisher's site
Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.
Kahlke, T, Jumppanen, P, Westram, R, Abell, GCG & Bodrossy, L 2018, 'ProbeSpec: batch specificity testing and visualization of oligonucleotide probe sets implemented in ARB'.View/Download from: Publisher's site
High-throughput molecular methods such as quantitative polymerase chain reaction (qPCR) and environmental microarrays are cost-effective methods for semi-quantitative assessment of bacterial community structure and the identification of specific target organisms. Both techniques rely on short nucleotide sequences, so-called oligonucleotide probes, which require high specificity to the organisms in question to avoid cross-hybridization with non-target taxa. However, designing oligonucleotide probes for novel taxa or marker genes that show sufficient phylogenetic sensitivity and specificity is often time- and labor-intensive, as each probe has to be in-silico tested for its specificity and sensitivity. Here we present ProbeSpec, to our knowledge the first batch sensitivity and specificity estimation and visualization tool for oligonucleotide probes integrated into the widely used ARB software. Using ProbeSpec's interactive 'mismatch threshold' and 'clade marked threshold' we were able to reduce the development time of highly specific probes for a recently published environmental oligonucleotide microarray from several months to one week.
Lawson, CA, Raina, J-B, Kahlke, T, Seymour, JR & Suggett, DJ 2018, 'Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium.', Environmental microbiology reports, vol. 10, no. 1, pp. 7-11.View/Download from: UTS OPUS or Publisher's site
Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α-proteobacterium Labrenzia and the γ-proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.
Goodwin, KD, Thompson, LR, Duarte, B, Kahlke, T, Thompson, AR, Marques, JC & Caçador, I 2017, 'DNA sequencing as a tool to monitor marine ecological status', Frontiers in Marine Science, vol. 4, no. MAY.View/Download from: UTS OPUS or Publisher's site
© 2017 Goodwin, Thompson, Duarte, Kahlke, Thompson, Marques and Caçador. Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. Most traditional methods to assess biological quality rely on specialized expertise to provide visual identification of a limited set of specific taxonomic groups, a time-consuming process that can provide a narrow view of ecological status. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. Molecular-based assessments of biodiversity and ecosystem function offer advantages over traditional methods and are increasingly being generated for a suite of taxa using a "microbes to mammals" or "barcodes to biomes" approach. Progress in these efforts coupled with continued improvements in high-throughput sequencing and bioinformatics pave the way for sequence data to be employed in formal integrated ecosystem evaluation, including food web assessments, as called for in the European Union Marine Strategy Framework Directive. DNA sequencing of bioindicators, both traditional (e.g., benthic macroinvertebrates, ichthyoplankton) and emerging (e.g., microbial assemblages, fish via eDNA), promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.
McLaughlin, RL, Schijven, D, van Rheenen, W, van Eijk, KR, O'Brien, M, Kahn, RS, Ophoff, RA, Goris, A, Bradley, DG, Al-Chalabi, A, van den Berg, LH, Luykx, JJ, Hardiman, O, Veldink, JH, Project MinE GWAS Consortium & Schizophrenia Working Group of the Psychiatric Genomics Consortium 2017, 'Genetic correlation between amyotrophic lateral sclerosis and schizophrenia.', Nature communications, vol. 8, pp. 14774-14774.View/Download from: UTS OPUS or Publisher's site
We have previously shown higher-than-expected rates of schizophrenia in relatives of patients with amyotrophic lateral sclerosis (ALS), suggesting an aetiological relationship between the diseases. Here, we investigate the genetic relationship between ALS and schizophrenia using genome-wide association study data from over 100,000 unique individuals. Using linkage disequilibrium score regression, we estimate the genetic correlation between ALS and schizophrenia to be 14.3% (7.05-21.6; P=1 × 10-4) with schizophrenia polygenic risk scores explaining up to 0.12% of the variance in ALS (P=8.4 × 10-7). A modest increase in comorbidity of ALS and schizophrenia is expected given these findings (odds ratio 1.08-1.26) but this would require very large studies to observe epidemiologically. We identify five potential novel ALS-associated loci using conditional false discovery rate analysis. It is likely that shared neurobiological mechanisms between these two disorders will engender novel hypotheses in future preclinical and clinical studies.
Jiang, Z, Kumar, M, Padula, MP, Pernice, M, Kahlke, T, Kim, M & Ralph, PJ 2017, 'Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis.', Frontiers in Plant Science, vol. 8, pp. 1-14.View/Download from: UTS OPUS or Publisher's site
The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2% PVPP and protease inhibitors. Further, the extracted proteins were solubilized in 0.5% of zwitterionic detergent (C7BzO) instead of 4% CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoenolpyruvate carboxylase (PEPC-a key enzyme for carbon metabolism). ...
ten Hoopen, P, Amid, C, Buttigieg, PL, Pafilis, E, Bravakos, P, Cerdeno-Tarraga, AM, Gibson, R, Kahlke, T, Legaki, A, Murthy, KN, Papastefanou, G, Pereira, E, Rossello, M, Toribio, AL & Cochrane, G 2016, 'Value, but high costs in post-deposition data curation', DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.View/Download from: UTS OPUS or Publisher's site
Williamson, A, Hjerde, E & Kahlke, T 2016, 'Analysis of the distribution and evolution of the ATP-dependent DNA ligases of bacteria delineates a distinct phylogenetic group 'Lig E'', MOLECULAR MICROBIOLOGY, vol. 99, no. 2, pp. 274-290.View/Download from: UTS OPUS or Publisher's site
Thode, SK, Kahlke, T, Robertsen, EM, Hansen, H & Haugen, P 2015, 'The immediate global responses of Aliivibrio salmonicida to iron limitations', BMC MICROBIOLOGY, vol. 15.View/Download from: UTS OPUS or Publisher's site
Cavanagh, JP, Hjerde, E, Holden, MTG, Kahlke, T, Klingenberg, C, Flaegstad, T, Parkhill, J, Bentley, SD & Sollid, JUE 2014, 'Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 69, no. 11, pp. 2920-2927.View/Download from: UTS OPUS or Publisher's site
Kahlke, T & Thorvaldsen, S 2012, 'Molecular Characterization of Cold Adaptation of Membrane Proteins in the Vibrionaceae Core-Genome', PLOS ONE, vol. 7, no. 12.View/Download from: UTS OPUS or Publisher's site
Kahlke, T, Goesmann, A, Hjerde, E, Willassen, NP & Haugen, P 2012, 'Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation', BMC GENOMICS, vol. 13.View/Download from: UTS OPUS or Publisher's site
Dondrup, M, Albaum, SP, Griebel, T, Henckel, K, Juenemann, S, Kahlke, T, Kleindt, CK, Kuester, H, Linke, B, Mertens, D, Mittard-Runte, V, Neuweger, H, Runte, KJ, Tauch, A, Tille, F, Puehler, A & Goesmann, A 2009, 'EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data', BMC BIOINFORMATICS, vol. 10.View/Download from: Publisher's site
Robertsen, EM, Kahlke, T, Raknes, IA, Pedersen, E, Semb, EK, Ernstsen, M, Bongo, LA & Willassen, NP, 'META-pipe - Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data'.
The marine environment is one of the most important sources for microbial
biodiversity on the planet. These microbes are drivers for many biogeochemical
processes, and their enormous genetic potential is still not fully explored or
exploited. Marine metagenomics (DNA shotgun sequencing), not only offers
opportunities for studying structure and function of microbial communities, but
also identification of novel biocatalysts and bioactive compounds. However,
data analysis, management, storage, processing and interpretation are
significant challenges in marine metagenomics due to the high diversity in
samples and the size of the marine flagship projects. We provide a new
pipeline, META-pipe, for marine metagenomics analysis. It offers pre-
processing, assembly, taxonomic classification and functional analysis. To
reduce the effort to develop and deploy it, we have integrated existing
biological analysis frameworks, and compute and storage infrastructure
resources. Our current META-pipe web service provides integration with identity
provider services, distributed storage, computation on a Supercomputer, Galaxy
workflows, and interactive data visualizations. We have evaluated the
scalability and performance of the analysis pipeline. Our results demonstrate
how to develop and deploy a pipeline on distributed compute and storage
resources, and discusses important challenges related to this process.