I obtained my PhD in microbiology from the University of New South Wales in 2010. My research focused on the ecology of host associated bacterial communities from the marine environment, and I now employ the same techniques to study microbial communities associated with the human body (the human microbiota). I use observational techniques to examine differences in various states of health and disease, to infer possible relationships between our reisdent bacteria and health.
- Member of ASM (Australian Society for Microbiology)
Can supervise: YES
I am interested in understanding the ecology of microbial communities, and how those communities interact with living hosts. In the case of microbial communities that live on humans (the human microbiome), these microbes are thought to play important roles in our immune development, and to protect us from pathogenic microbes. Many diseases have been linked to shifts in our microbial communities, and these shifts are implicated in disease development. My ultimate aim is to understand how our native microbial communities interact with us to keep us healthy, and how these communities can be manipulated in the case of disease to achieve better health outcomes.
Subject co-ordinator for Research Methods (60207) and Drug Discovery (91815)
Epidemiology and Public Health microbiology
Chahwan, B, Kwan, S, Isik, A, van Hemert, S, Burke, C & Roberts, L 2019, 'Gut feelings: A randomised, triple-blind, placebo-controlled trial of probiotics for depressive symptoms', Journal of Affective Disorders, vol. 253, pp. 317-326.View/Download from: Publisher's site
© 2019 Background: Depression is the leading cause of disability worldwide; with evidence suggesting that decreased gut barrier function and inflammation are correlated with depressive symptoms. We conducted a clinical trial to determine the effect of consumption of probiotic supplements (Winclove's Ecologic® Barrier) on depressive symptoms in a sample of participants with mild to severe depression. Method: 71 participants were randomly allocated to either probiotic or placebo, which was, consumed daily over eight weeks. Pre- and post-intervention measures of symptoms and vulnerability markers of depression as well as gut microbiota composition were compared. Clinical trial participants were also compared on psychological variables and gut microbiota composition to a non-depressed group (n = 20). Results: All clinical trial participants demonstrated improvement in symptoms, suggesting non-specific therapeutic effects associated with weekly monitoring visits. Participants in the probiotic group demonstrated a significantly greater reduction in cognitive reactivity compared with the placebo group, particularly in the mild/moderate subgroup. Probiotics did not significantly alter the microbiota of depressed individuals, however, a significant correlation was found between Ruminococcus gnavus and one depression metric. Limitations: There was a high attrition rate, which may be attributed to weekly monitoring visits. Additionally, modulation of the gut microbiota may need more specific testing to distinguish subtle changes. Conclusions: While microbiota composition was similar between all groups, probiotics did affect a psychological variable associated with susceptibility to depression. Further research is needed to investigate how probiotics can be utilised to modify mental wellbeing, and whether they can act as an adjunct to existing treatments.
Deutscher, AT, Burke, CM, Darling, AE, Riegler, M, Reynolds, OL & Chapman, TA 2018, 'Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.', Microbiome, vol. 6, no. 1.View/Download from: UTS OPUS or Publisher's site
BACKGROUND:Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets). RESULTS:Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae, and Leuconostocaceae) were detected in wild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full-length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains. CONCLUSIONS:Variation in the gut bac...
Burke, C, Burnard, D, Polkinghorne, A, Webb, J & Huston, WM 2018, 'Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll.', Microorganisms, vol. 6, no. 3.View/Download from: UTS OPUS or Publisher's site
The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically sampled. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The diversity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal.
Mediati, DG, Burke, CM, Ansari, S, Harry, EJ & Duggin, IG 2018, 'High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division.', BMC genomics, vol. 19, no. 1.View/Download from: UTS OPUS or Publisher's site
BACKGROUND:Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identified the cloned DNA with high-throughput DNA sequencing. We applied the method to an expression library made from fragmented genomic DNA of uropathogenic E. coli UTI89, which undergoes extensive reversible filamentation in urinary tract infections and might encode additional regulators of division. RESULTS:We identified 55 genomic regions that reproducibly caused filamentation when expressed from the plasmid vector, and then further localized the cause of filamentation in several of these to specific genes or sub-fragments. Many of the identified genomic fragments encode genes that are known to participate in cell division or its regulation, and others may play previously-unknown roles. Some of the prophage genes identified were previously implicated in cell division arrest. A number of the other fragments encoded potential short transcripts or peptides. CONCLUSIONS:The results provided evidence of potential new links between cell division and distinct cellular processes including central carbon metabolism and gene regulation. Candidate regulators of the UTI-associated filamentation response or others were identified amongst the results. In addition, some genomic fragments that caused filamentation may not have evolved to control cell division, but may have applications as artificial inhibitors. Our approach offers the opportunity to carry out in depth surveys of diverse DNA libraries to identify new genes or sequences encoding the capacity to inhibit division and cause filamentation.
Copeland, E, Leonard, K, Carney, R, Kong, J, Forer, M, Naidoo, Y, Oliver, BGG, Seymour, JR, Woodcock, S, Burke, CM & Stow, NW 2018, 'Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites', Frontiers in Cellular and Infection Microbiology, vol. 8, pp. 1-14.View/Download from: UTS OPUS or Publisher's site
Gardiner, M, Vicaretti, M, Sparks, J, Bansal, S, Bush, S, Liu, M, Darling, A, Harry, E & Burke, CM 2017, 'A longitudinal study of the diabetic skin and wound microbiome.', PeerJ, vol. 5, pp. e3543-e3543.View/Download from: UTS OPUS or Publisher's site
BACKGROUND: Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections. The skin microbiome is thought to play important roles in skin defence and immune functioning. Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing. This study examines the skin and wound microbiome in type II diabetes. METHODS: Eight type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, sampling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of eight control subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks. Samples were processed for DNA and subject to 16S rRNA gene PCR and sequencing of the V4 region. RESULTS: The diabetic skin microbiome was significantly less diverse than control skin. Community composition was also significantly different between diabetic and control skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds tended to be dominated by the most abundant skin Staphylococcus, while other abundant wound taxa differed by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa. DISCUSSION: The major difference observed in this study of the skin microbiome associated with diabetes was a significant reduction in diversity. The long-term effects of reduced diversity are not yet well understood, but are often associated with disease conditions.
Darling, AE, Liu, M, Worden, P, Monahan, L, Demaere, M, Burke, C, Djordjevic, S & Charles, I 2017, 'Evaluation of ddRADseq for reduced representation metagenome sequencing', PeerJ, vol. 5.View/Download from: UTS OPUS or Publisher's site
'Who is doing what' is the ultimate open question in microbiome study. Shotgun metagenomics is often applied to gain knowledge of functional roles for bacteria in microbial communities, where the data can be used to predict protein encoding genes and enzymatic pathways present in the community, sometimes leading to testable hypotheses for microbial
function. We describe a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence
specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can
be tuned by size selection.
We assessed the performance of the metagenomic ddRADseq approach by applying the method to human stool samples and generating sequence data. We evaluate the extent to which ddRADseq data provides an unbiased reduced representation for microbiome profiling.
Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
Donnelly, S, Huston, WM, Johnson, M, Tiberti, N, Saunders, B, O'Brien, B, Burke, C, Labbate, M & Combes, V 2017, 'Targeting the master regulator mTOR: a new approach to prevent the neurological of consequences of parasitic infections?', Parasites & Vectors, vol. 10, no. 1, pp. 1-6.View/Download from: UTS OPUS or Publisher's site
A systematic analysis of 240 causes of death in 2013 revealed that parasitic diseases were responsible for more than one million deaths. The vast majority of these fatalities resulted from protozoan infections presenting with neurological sequelae. In the absence of a vaccine, development of effective therapies is essential to improving global public health. In 2015, an intriguing strategy to prevent cerebral malaria was proposed by Gordon et al. 2015 mBio, 6:e00625. Their study suggested that inhibition of the mammalian target of rapamycin prevented experimental cerebral malaria by blocking the damage to the blood brain barrier and stopping the accumulation of parasitized red blood cells and T cells in the brain. Here, we hypothesize that the same therapeutic strategy could be adopted for other protozoan infections with a brain tropism, to prevent cerebral parasitosis by limiting pathogen replication and preventing immune mediated destruction of brain tissue.
Chernomoretz, A, Stolovitzky, G, Labaj, PP, Graf, AB, Darling, A, Burke, C, Noushmehr, H, Moraes, MO, Dias-Neto, E, Guo, Y, Xie, Z, Lee, P, Shi, L, Ruiz-Perez, CA, Mercedes Zambrano, M, Siam, R, Ouf, A, Richard, H, Lafontaine, I, Wieler, LH, Semmler, T, Ahmed, N, Prithi-viraj, B, Nedunuri, N, Mehr, S, Banihashemi, K, Lista, F, Anselmo, A, Suzuki, H, Kuroda, M, Yamashita, R, Sato, Y, Kaminuma, E, Alpuche Aranda, CM, Martinez, J, Dada, C, Dybwad, M, Oliveira, M, Schuster, S, Siwo, GH, Jang, S, Seo, SC, Hwang, SH, Ossowski, S, Bezdan, D, Chaker, S, Chatziefthimiou, AD, Udekwu, K, Liungdahl, P, Sezerman, U, Meydan, C, Elhaik, E, Gonnet, G, Schriml, LM, Mongodin, E, Huttenhower, C, Gilbert, J, Mason, CE, Eisen, J, Hirschberg, D & Hernandez, M 2016, 'The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report', MICROBIOME, vol. 4.View/Download from: UTS OPUS or Publisher's site
Joss, TV, Burke, CM, Hudson, BJ, Darling, AE, Forer, M, Alber, DG, Charles, IG & Stow, NW 2016, 'Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients.', Frontiers in Microbiology, vol. 6, pp. 1-11.View/Download from: UTS OPUS or Publisher's site
Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs, and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus.
Lu, J, Turnbull, L, Burke, CM, Liu, MY, Carter, DA, Schlothauer, RC, Whitchurch, CB & Harry, L 2014, 'Manuka-type honeys can eradicate biofilms produced by Staphylococcus aureus strains with different biofilm-forming abilities', PeerJ, vol. 2.View/Download from: UTS OPUS or Publisher's site
Chronic wounds are a major global health problem. Their management is difficult and costly, and the development of antibiotic resistance by both planktonic and biofilm-associated bacteria necessitates the use of alternative wound treatments. Honey is now being revisited as an alternative treatment due to its broad-spectrum antibacterial activity and the inability of bacteria to develop resistance to it. Many previous antibacterial studies have used honeys that are not well characterized, even in terms of quantifying the levels of the major antibacterial components present, making it difficult to build an evidence base for the efficacy of honey as an antibiofilm agent in chronic wound treatment. Here we show that a range of well-characterized New Zealand manuka-type honeys, in which two principle antibacterial components, methylglyoxal and hydrogen peroxide, were quantified, can eradicate biofilms of a range of Staphylococcus aureus strains that differ widely in their biofilm-forming abilities. Using crystal violet and viability assays, along with confocal laser scanning imaging, we demonstrate that in all S. aureus strains, including methicillin-resistant strains, the manuka-type honeys showed significantly higher anti-biofilm activity than clover honey and an isotonic sugar solution. We observed higher anti-biofilm activity as the proportion of manuka-derived honey, and thus methylglyoxal, in a honey blend increased. However, methylglyoxal on its own, or with sugar, was not able to effectively eradicate S. aureus biofilms. We also demonstrate that honey was able to penetrate through the biofilm matrix and kill the embedded cells in some cases. As has been reported for antibiotics, sub-inhibitory concentrations of honey improved biofilm formation by some S. aureus strains, however, biofilm cell suspensions recovered after honey treatment did not develop resistance towards manuka-type honeys. New Zealand manuka-type honeys, at the concentrations they can be applie...
Egan, S, Harder, T, Burke, CM, Steinberg, P, Kjelleberg, SL & Thomas, T 2013, 'The Seaweed Holobiont: Understanding Seaweed-bacteria Interactions', FEMS Microbiology Reviews, vol. 37, no. 3, pp. 462-476.View/Download from: UTS OPUS or Publisher's site
Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on
Burke, CM, Liu, MY, Britton, WJ, Triccas, JA, Thomas, T, Smith, A, Allen, S, Salomon, R & Harry, L 2013, 'Harnessing Single Cell Sorting To Identify Cell Division Genes And Regulators In Bacteria', Plos One, vol. 8, no. 4, pp. 1-13.View/Download from: UTS OPUS or Publisher's site
Cell division is an essential cellular process that requires an array of known and unknown proteins for its spatial and temporal regulation. Here we develop a novel, high-throughput screening method for the identification of bacterial cell division genes and regulators. The method combines the over-expression of a shotgun genomic expression library to perturb the cell division process with high-throughput flow cytometry sorting to screen many thousands of clones. Using this approach, we recovered clones with a filamentous morphology for the model bacterium, Escherichia coli. Genetic analysis revealed that our screen identified both known cell division genes, and genes that have not previously been identified to be involved in cell division. 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.
Burke, CM, Steinberg, P, Rusch, DB, Kjelleberg, SL & 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, no. 34, pp. 14288-14293.View/Download from: UTS OPUS or Publisher's site
The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be ï½speciesï½ (by means of rRNA taxonomy), but rather the more functional level of genes.
Yung, P, Burke, CM, Kjelleberg, SL, Thomas, T & Lewis, M 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, no. 4, pp. 1512-1515.View/Download from: UTS OPUS or Publisher's site
The functional metagenomic screening of the microbial communities associated with a temperate marine sponge and a green alga identified three novel hydrolytic enzymes with antibacterial activities. The results suggest that uncultured alpha- and gammaprot
Burke, CM, Thomas, T, Lewis, M, Steinberg, P & Kjelleberg, S 2011, 'Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis', ISME Journal, vol. 5, no. 4, pp. 590-600.View/Download from: UTS OPUS or Publisher's site
Green Ulvacean marine macroalgae are distributed worldwide in coastal tidal and subtidal ecosystems. As for many living surfaces in the marine environment, little is known concerning the epiphytic bacterial biofilm communities that inhabit algal surfaces. This study reports on the largest published libraries of near full-length 16S rRNA genes from a marine algal surface (5293 sequences from six samples) allowing for an in-depth assessment of the diversity and phylogenetic profile of the bacterial community on a green Ulvacean alga. Large 16S rRNA gene libraries of surrounding seawater were also used to determine the uniqueness of this bacterial community. The surface of Ulva australis is dominated by sequences of Alphaproteobacteria and the Bacteroidetes, especially within the Rhodobacteriaceae, Sphingomonadaceae, Flavobacteriaceae and Sapropiraceae families. Seawater libraries were also dominated by Alphaproteobacteria and Bacteroidetes sequences, but were shown to be clearly distinct from U. australis libraries through the clustering of sequences into operational taxonomic units and BrayCurtis similarity analysis. Almost no similarity was observed between these two environments at the species level, and only minor similarity was observed at levels of sequence clustering representing clades of bacteria within family and genus taxonomic groups. Variability between libraries of U. australis was relatively high, and a consistent sub-population of bacterial species was not detected. The competitive lottery model, originally derived to explain diversity in coral reef fishes, may explain the pattern of colonization of this algal surface.
Ballestriero, F, Thomas, T, Burke, C, Egan, S & 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. 76, no. 17, pp. 5710-5717.View/Download from: UTS OPUS or Publisher's site
Tujula, NA, Crocetti, GR, Burke, C, Thomas, T, Holmstrom, C & Kjelleberg, S 2010, 'Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga', ISME JOURNAL, vol. 4, no. 2, pp. 301-311.View/Download from: Publisher's site
Yung, PY, Burke, C, Lewis, M, Egan, S, Kjelleberg, S & Thomas, T 2009, 'Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion', NUCLEIC ACIDS RESEARCH, vol. 37, no. 21.View/Download from: UTS OPUS or Publisher's site
Burke, C, Kjelleberg, S & Thomas, T 2009, 'Selective Extraction of Bacterial DNA from the Surfaces of Macroalgae', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 75, no. 1, pp. 252-256.View/Download from: UTS OPUS or Publisher's site
Thomas, T, Evans, FF, Schleheck, D, Mai-Prochnow, A, Burke, C, Penesyan, A, Dalisay, DS, Stelzer-Braid, S, Saunders, N, Johnson, J, Ferriera, S, Kjelleberg, S & Egan, S 2008, 'Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment', PLOS ONE, vol. 3, no. 9.View/Download from: UTS OPUS or Publisher's site
Burke, C, Thomas, T, Egan, S & 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, no. 3, pp. 814-818.View/Download from: Publisher's site