Microbial population biology

Event Date: 
Wednesday, February 25, 2015 - 17:30 - 18:00
Institution: 
University of Melbourne
Title: 

Genomic epidemiology of antibiotic resistant bacteria

Abstract: 

Microbial populations contribute to human disease in a variety of ways, both as agents of infection and as healthy components of the microbiome. Genomic approaches can offer deep insights into this hidden microbial world, including revealing the composition of microbial communities, tracking the movement of individual organisms, and illuminating evolutionary changes. Here I will present recent work applying genomic epidemiology to investigate the emergence and spread of antibiotic resistance in a range of important pathogens, including typhoid, dysentery and the emerging hospital superbug Klebsiella.

Event Date: 
Wednesday, February 26, 2014 - 15:15 - 15:45
Institution: 
Singapore Centre on Environmental Life Sciences Engineering
Title: 

Dissecting Structure-Function Relationships In Complex Microbial Communities Using Perturbation Transcriptomics

Abstract: 

Application of ‘omics technologies, including high-throughput nucleic acid sequencing and advanced mass spectrometry, show huge potential to increase our understanding of bioprocesses occurring in both natural and engineering microbial ecosystems. Field studies of such systems are inherently complicated, while laboratory reactor models involve extensive community modifications following inoculation and may not accurately reflect the biology of the source community. Here we develop a complementary approach to dissecting structure-function relationships of complex microbial communities, by applying experimental perturbations to freshly sourced, intact communities in a controlled fashion. In an investigation examining nitrogen transformation in wastewater treatment, we use metatranscriptomics in a time series design (n=20 samples) to study changes associated with onset of oxygenation. This stimulus switches the community between de-nitrification and nitrification phases of the nitrogen cycle, thus modeling a key aspect of wastewater process control. This model permits identification of functional genes, in both known and previously unknown taxa, and represents a readily adaptable model studying structure-function relationships in microbial communities. If time permits, I will discuss how this perturbation metatranscriptomics approach has implications for improving our ability to perform metagenome assembly.

Event Date: 
Wednesday, October 30, 2013 - 19:00 - 20:00
Institution: 
USyd
Title: 

How microbial community structure is shaped

Abstract: 

 
Microbes profoundly influence biological systems. Owing to their small individual size, but extremely large populations, their influence is typically an emergent property of the microbial community.  As such understanding how microbial community structure is shaped is a generic question relevant to almost all biological systems.
A major focus of my research is the interplay between diet, gut microbiota and health. Our health is the product of interplay between many different factors with arguably three of the most important being adequate nutrition, homeostatic regulation and exclusion of foreign cells. Gut functions influence all these, but occur in the immediate proximity of a huge community of microorganisms – our gut microbiome. The gut microbiome profoundly effects our health via its contribution to and influence on gut functions.
Arguably the most significant aspect of our gut microbiome is that differences in composition matter. The contribution of our microbiome to nutrition, metabolism, gut and immune functions varies from person-to-person. Thus the clinical manifestation of many diseases will be influenced by the individual’s microbiome. Secondly, environmental or lifestyle differences such as diet and hygiene may modulate microbiome composition and thus its influence on health. This gives rise to two basic opportunities for improving healthcare. These are, using the microbiome as a metric to improve diagnosis and targeting the microbiome for therapeutic intervention. We are specifically exploring forces that shape microbial community structure in mouse and human models of with a view to developing diagnostic and intervention strategies across a range of health issues. 

REPORT
Mike Manefield

Amazing turn out for JAMS last night at the Australian Museum. Three excellent presentations from Nathan Lo (Blattabacterium genome evolution - USyd), Tom Jeffries (Sydney Harbour Microbiome - UTS) and Yit Heng Chooi (Fungal metabolite genetics and biochemistry - ANU). The audience was also on the money with probing questions reassuring the speakers that their labours are well appreciated by an elite body of microbiology professionals.

The idea of a two day microbial community analysis workshop was also re-introduced and planning for this has commenced. A call is also out for volunteers for the Australian Museum Sciecne Festival (10th August, 13th-15th August and 20th-22nd August).

Please email Mike Manefield if you're interested. As of the 1st of August, we still need around 10 more volunteers.

Event Date: 
Wednesday, July 31, 2013 - 18:15 - 18:30
Institution: 
University of Technology Sydney
Title: 

The Sydney Harbour microbiome: bacterioplankton diversity and dynamics

Abstract: 

Sydney Harbour and its surrounding coast is an iconic habitat that supports a diverse ecosystem however the composition and dynamics of bacterioplankton in the system remain a major knowledge gap. The harbour and coast also provide a model system for investigating the spatiotemporal distribution of microorganisms across multiple physicochemical gradients and their response to anthropogenic input. Using next-generation DNA sequencing, we provide a comprehensive profile of microbial communities from a range of habitats inside the harbour and show strong biogeographic patterns in taxonomic composition.  Using network analysis to visualize correlations between community structure and environmental variables we have identified the key drivers of community partitioning. Combined these results lead to a more detailed understanding of the diversity and roles of bacterioplankton in Sydney Harbour and its surrounds, and provide insight into marine microbial ecology generally. 

Event Date: 
Wednesday, April 24, 2013 - 19:15 - 20:00
Institution: 
University of Technology Sydney
Title: 

Observing the developing infant gut microbiome with time-series metagenomics.

Abstract: 

The human body plays host to a complex microbial ecosystem, the
development of which begins around the time of birth. Routine monitoring
of the development of microbial ecosystems in newborns (or other
environments) using metagenomic methods is currently extremely
challenging and expensive. I will describe some recent technological
advances that could enable routine sequencing and computational analysis
of hundreds of metagenomes, and demonstrate their application on samples
taken from a developing infant gut microbiome. In this study forty-five
samples were subjected to transposon-catalyzed Illumina library prep and
metagenomic sequencing on a HiSeq 2000 instrument. The resulting data
was subjected to analysis of microbial community structure using a new
approach called phylogenetic Edge Principal Component Analysis (Edge
PCA) that can identify which lineages in a phylogeny explain the
greatest degree of variation among the samples. We also investigate the
population genomics of Bacteroides thetaiotaomicron, one of the dominant
members of the gut microbial community.

Event Date: 
Wednesday, March 27, 2013 - 18:15 - 18:30
Institution: 
Hawkesbury Institute for the Environment, University of Western Sydney
Title: 

Effect of Huanglongbing on the structure and functional diversity of microbial communities associated with citrus.

Abstract: 

Plant-microbe interactions lie at the heart of plant performance and ecology. It has been postulated that disruption of multi-trophic interactions in a stable ecosystem under the influence of invading phytopathogens will cause community reorganization and changes in the local feedback interactions. However, there is a paucity of knowledge on the extent to which such community shifts may occur, on the dynamics of changes and on the putative effects regarding the functioning of ecosystems. We have used Citrus-‘Candidatus Liberibacter asiaticus’ [Las, causal agent of devastating Huanglongbing (HLB) disease] as a host pathogen model to characterize the structure, function and interactions of plant-associated microbial communities. We applied a suit of metagenomic techniques to provide detailed census of citrus associated microbiomes. Our results confirmed that Las is the sole causal agent of HLB in Florida and revealed that HLB significantly re-structures the composition of native microbial community present either in leaf, roots and rhizosphere of citrus. Functional microarray (Geochip) and shotgun metagenomic sequencing showed that HLB has severe effects on various functional guilds of bacteria involved in key ecological processes including nitrogen cycling and carbon fixation. Overall, the metagenomic studies provided evidence that change in plant physiology mediated by Las infection could elicit shifts in the composition and functional potential of plant associated microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability of citrus producing agro-ecosystems.

Report by Jeff Powell

On 12 April, the 'cowboys' at the Hawkesbury Institute for the Environment played host to the 'aliens' from the Sydney region for JAMS Goes West. The mood was both enthusiastic and informative and approximately 30 people participated. The morning consisted of five short talks by representatives of five Sydney-based institutions.

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