Microbiology

Event Date: 
Wednesday, September 24, 2014 - 18:00 - 18:15
Institution: 
University of Sydney
Title: 

Microbiota characterisation in the Tasmanian devil

Abstract: 

The Tasmanian devil (Sarcophilus harrisii), the world’s largest remaining carnivorous marsupial, faces extinction due to the spread of a contagious cancer called Devil Facial Tumour Disease (DFTD). The lack of a description of the bacterial community composition in the species represents a major gap in our knowledge of Tasmanian devil biology. In this study we characterised 12 microbiomes from four body sites, including mouth, gut, skin and pouch, in five Tasmanian devils via PCR amplification of 16S rRNA gene V1-V3 regions followed by 454 sequencing.  A total of 249,224 reads with an average sequence length of 489 bp were obtained after length and quality filtering. The reads further clustered into 14533 operational taxonomic units (OTUs; sequence identity cutoff of >97%) that were classified to 24 phyla spanning 275 families. Higher levels of bacterial species richness were observed in the pouch and skin than in the mouth and gut. The pouch and skin showed similar microflora compositions, which may vary between animals, possibly due to different environments. Distinct from the previously reported koala gut microbiota [1], which is dominated by Bacteroidetes and Firmicutes, the devil gut microbiota was found to be dominated by Fusobacteria, Firmicutes and Proteobacteria, comprising up to 73.7-94.3% of the community. This study has greatly improved our understanding of the microbial communities in the Tasmanian devil, which will significantly contribute to the effort to conserve the species.

Event Date: 
Wednesday, August 27, 2014 - 19:00 - 20:00
Institution: 
Macquarie University
Title: 

"Xenbiotics and Xenogenetics: Human Influence over Microbial Evolution"

Abstract: 

The extent of human effects on planetary and biological processes means that we are now the world’s greatest evolutionary force. Perhaps the best example of human driven selection is the rapid evolution of antibiotic resistance in a wide range of bacterial pathogens. Continued antibiotic use has resulted in the assembly of complex DNA molecules composed of diverse resistance determinants and mobile elements, each with independent phylogenetic origins. These novel plasmids, transposons, integrons and genomic islands are xenogenetic, in that they have arisen in human-dominated ecosystems as a direct result of human activity. Xenogenetic elements are being released via human waste streams along with significant quantities of selective agents and other xenobiotic compounds, creating environmental reactors that foster even more complex interactions between genes, mobile elements and diverse bacterial species. Saturation of the environment with selective agents is also likely to increase the basal rates of mutation, recombination and lateral gene transfer in all bacterial species. Consequently, the antibiotic revolution may now be having unintended, second order consequences that will affect the entire microbial biosphere.

Event Date: 
Wednesday, August 27, 2014 - 18:15 - 18:30
Institution: 
UNSW
Title: 

Analysis of gene co-expression networks reveals mechanisms underlying synergistic antifungal treatment in S. cerevisiae

Abstract: 

 
Background: Fungal pathogens are difficult to treat. There are few effective antifungal drugs available, and resistance is emerging. Iron chelators are promising synergents due to the importance of iron availability during host infection, but the mechanistic role of antifungal-chelator combinations is poorly understood. The project analyses cellular pathways that are differentially expressed during the synergistic response to elucidate the mechanisms and targets of drug-chelator treatment.
Method: To measure the effect of synergistic treatment on the S. cerevisiae transcriptome, cells were treated with i) amphotericin B only; ii) a combination of amphotericin B + lactoferrin, an iron chelator; and iii & iv) corresponding matching controls. RNA-seq data were generated using Illumina HiSeq 2000 with biological triplicates multiplexed and randomized across two sequencing lanes. Differential expression analyses were performed using EdgeR, and the results were co-visualized with biological networks using Cytoscape.
Results: Amphotericin B alone resulted in the down-regulation of nine genes involved in ergosterol biosynthesis and the up-regulation of AFT1, a transcription factor involved in iron transport. Amphotericin B + lactoferrin co-treatment halted AFT1 up-regulation and down-regulated genes involved in iron transport. These genes were co-expressed with YAP5, a second transcription factor that co-ordinates the expression of genes that control the nuclear localization of AFT1 and also governs the expression of oxidative stress response genes.

Event Date: 
Wednesday, August 27, 2014 - 18:00 - 18:15
Institution: 
USyd
Title: 

Bowel movement: resistance plasmid transfer in the gut

Abstract: 

The treatment of endogenous infections caused by commensal Escherichia coli are often complicated by antibiotic resistance. Strains of resistant E. coli in the gastrointestinal tract serve as a reservoir of resistance determinants, and dissemination of resistance genes is often facilitated by conjugative plasmids. It is important to understand these plasmids in order to track the movement of resistance determinants between populations.
 
Three faecal E. coli isolates from a healthy adult were examined. Two of these (838-98B and -3B) were resistant to ampicillin (Ap), streptomycin (Sm) and sulphamethoxazole (Su). The other (838-50A) was susceptible. 838-50A and -3B were indistinguishable by biochemical and molecular analysis (API20E, phylogenetic group PCR, RAPD). 838-98B was a distinct strain. B/O plasmid replicons were detected in both resistant isolates using PCR-based plasmid replicon typing. A B/O replicon was not detected in the susceptible strain. This suggested that a plasmid bearing a B/O replicon might be responsible for ApSmSu resistance. Conjugation experiments with a laboratory adapted E. coli strain (UB5201) confirmed that the movement of a B/O plasmid from both 838-98B and -3B conferred ApSmSu resistance. Plasmid sequencing revealed that an identical B/O plasmid, p838B-R (94.8kb), was present in 838-98B and -3B, and carried ApSmSu resistance determinants. p838B-R was also observed to mobilise small plasmids, allowing the direction of in situ transfer to be determined.
 
The observed transfer of antibiotic resistance plasmid p838B-R between two unrelated strains in the gastrointestinal tract highlights the important role commensal bacteria play in the spread of resistance determinants. While not well documented, the association of B/O-type plasmids with antibiotic resistance is evident not only through p838B-R but also other available plasmid sequences. Further studies will allow us to determine the extent to which these plasmids influence antibiotic resistance in commensal E. coli

Event Date: 
Wednesday, July 30, 2014 - 18:00 - 18:15
Institution: 
UTS
Title: 

Exploring coral-bacteria interactions: where are they, how do they get there and what do they do?

Abstract: 

Microorganisms live in tight ecological associations with corals, but microbial community composition, functions and behaviours within coral reef ecosystems are not yet fully understood. To examine the community structure, metabolic capacity and the potential role of chemotaxis in the ecology of coral reef bacterial communities, we performed a suite of laboratory, in-situ and thermal stress experiments on Heron Island, the Great Barrier Reef (GBR). To characterise patterns in microbial composition and metabolic capacity across different niches on a coral reef, metagenomes were sequenced from seawater samples associated with the surfaces of corals, the sandy substrate and in open water, outside of the reef. Within these environments we also examined the potential ecological role of chemotaxis among coral associated bacteria, by using laboratory and in situ chemotaxis assays to test for levels of chemotaxis towards several chemoattractants known to be released by corals and their symbiotic dinoflagelletes including amino acids, carbohydrates, ammonium chloride, and dimethylsulfonopropionate (DMSP). Finally, to determine how environmental variability, specifically thermal stress, influences bacterial community composition, behaviour and metabolic capacity, manipulation experiments were conducted using Pocillopora damicornis in flow-through aquatic systems on Heron Island.
 We found that the composition and metabolic potential of coral reef bacteria is highly heterogeneous across a coral reef ecosystem, with a shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. Among the major functional patterns observed were significant increases in genes associated with bacterial motility and chemotaxis in samples associated with the surfaces of coral colonies. These patterns were directly confirmed by chemotaxis experiments, which demonstrated that bacteria associated with the surfaces of the corals exhibited high levels of chemotaxis, particularly towards DMSP and several amino acids. Levels of chemotaxis by coral-associated bacteria were consistently higher than those demonstrated by non-coral associated bacteria. The phylogenetic composition of the chemotactic microbes, determined using 16S rRNA amplicon pyrosequencing, differed to the background community in the surrounding seawater, and incorporated several known coral-associated bacteria, Rhodobacteraceae, Flavobacteriaceae, Pseudomonadaceae and included potentially pathogenic Vibrios. Notably many of these bacteria, specifically Rhodobacterales, Flavobacterales and Vibrionales also became the dominant coral associated organisms under conditions of thermal stress experiments, indicating that these copiotrophic and chemotactic bacteria become key colonisers of thermally stressed corals.
Taken together our data demonstrate that coral reef bacterial communities are highly dynamic and that key groups of copiotrophic bacteria have the capacity to use sensitive chemotaxis to exploit nutrient gradients and potentially locate their coral hosts. Under conditions of heat stress, these behaviours may allow pathogenic organisms to locate and infect compromised hosts. 

Event Date: 
Wednesday, July 30, 2014 - 19:00 - 19:45
Institution: 
UTS
Title: 

The production of public goods in bacterial biofilms

Abstract: 

“Public goods” in bacterial communities are extracellular products that are released by a sub-set of individuals that provide benefits to the local population.  Extracellular DNA (eDNA) is a public good that has been found to be required for the formation of sessile biofilms by many species of bacteria including Pseudomonas aeruginosa.  We have recently shown that eDNA also facilitates the active expansion of P. aeruginosa biofilms by engineering the formation of a network of interconnected furrows and directing traffic flow throughout the furrow network to efficiently supply cells to the leading edge of the expanding biofilm. The mechanism by which eDNA is produced by P. aeruginosa and many other bacterial species is poorly understood. We have discovered a novel mechanism that accounts for the production of eDNA as well as other “public goods” in P. aeruginosa biofilms. 

Event Date: 
Wednesday, June 25, 2014 - 19:00 - 20:00
Institution: 
UTS
Title: 

Honey: Return of an Ancient Remedy

Abstract: 

Chronic wounds are a tremendous burden to human health worldwide, currently affecting 2% of the population in developed countries, with significant social and economic costs. Treatment of these wounds is becoming increasingly difficult due to infections caused by multidrug resistant bacteria. Honey is increasingly being used as a topical treatment for these wounds. New Zealand manuka honey has potent broad-spectrum antimicrobial activity and resistance to honey has not been attainable in the laboratory. Approved medical-grade manuka honey and honey dressings are readily available for use in wound treatment but their use is limited, largely due to lack of information about how they work. This talk will provide an overview of where we are at with research examining the value of honey as an antibacterial agent in wound treatment. It will include how different bacteria respond to honey, synergistic interaction studies using manuka honey and antibiotics currently used to treat infected wounds, and biofilm prevention and eradication studies.

Event Date: 
Wednesday, June 25, 2014 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

Biomes of Australian Soil Environments (BASE)

Abstract: 

The Biomes of Australian Soil Environments (BASE) is a soil microbial diversity database faciliatated by Bioplatforms Australia and currently involving 14 Australian agencies. The BASE project is collecting biodiversity data from Australian soils in the form of amplicon sequences and amplication free metagenomic sequences. Sequence data is accompanied by rich contextual data describing soil physical and chemical attributes, land use, overlying vegetation and climate. All information collected is made publicly available via the BASE database. Thus far BASE has collected approximately 900 samples, with data from over 400 of these being currently available. I will briefly introduce the BASE project and its newly deployed database by describing the sampling and sequencing protocols and demonstrating the databases search capabilities.

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