Microbiome



The Centre for Systems Genomics is holding a 1-day symposium on metagenomics and microbiome research, Tuesday November 17 at Bio21. 

Interested in presenting? Register now! and complete the abstract section.

This free event will feature talks on a range of microbiome-related topics including new computational and lab methods, covering a range of application areas including the human microbiome in health and disease, environmental metagenomics, ecology, agriculture and ancient DNA.

Event Date: 
Wednesday, May 27, 2015 - 18:15 - 18:30
Institution: 
University of Western Sydney & Macquarie University
Title: 

Structure, diel functional cycling and viral ecological filtering in the microbiome of a pristine coral atoll in the Indian Ocean

Abstract: 

Given the role of microbes as both indicators and drivers of ecosystem health, establishing baselines in pristine environments is crucial to predicting the response of marine habitats to environmental change.  Here we describe a survey of microbial community composition and metatranscriptomic gene expression across the Indian Ocean, encompassing the first samples from the pristine Salomon Atoll in the Chagos Archipeligo.  We observed strong patterns in beta-diversty  which reflected  Longhurst biogeographical  provinces established  using primary productivity and thermohaline properties of ocean currents.  Samples from within Salomon Atoll showed a highly unique community which was remarkably different even from adjacent samples despite constant water exchange.  This pattern was driven by the dominance of the photosynthetic cyanobacterium Synechococcus within the lagoon, the diel activity of which was responsible for driving shifts in the transcriptional profile of samples.  Inside the lagoon, increases in the expression of genes related to photosynthesis and nutrient cycling associated with the bottom-up control of bacterial populations, however the expression of viral proteins increased five-fold within the lagoon during the day, indicating a concomitant top-down control of bacterial dynamics byphage.  Indeed, genome recruitment against Synechococcus reference genomes suggested  viruses  provide  an  ecological filter for determining the diversity patterns in this system. This study also represented a proof of concept for  using a ‘citizen oceanography’ approach utilzing tools that may easily be adapted to deployment on any ocean going yacht, greatly expanding the scale and outreach of marine microbiology studies. 
 

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, September 24, 2014 - 19:00 - 19:15
Institution: 
CSIRO
Title: 

Animating the Gut Microbiome

Abstract: 

Animation can be a powerful way to inspire and educate people with science. Creating biomedical animations which depict advanced scientific concepts in a clear way requires 2 main considerations, 1) rigorous investigation of the underlying science, and 2) careful development of the story to express the ideas in a meaningful way.

In this talk Christopher Hammang will present his first biomedical animation “The Hungry Microbiome”. He will explore the challenges involved in animating the human gut microbiome and the unique insight gained from creating an animation about resistant starch. The talk will also explore the workflow and technology which can be used to create these biomedical animations, as well as a brief review of the science underlying resistant starch research.

 

Event Date: 
Wednesday, March 26, 2014 - 18:15 - 18:30
Institution: 
Radboud University Nijmegen, Netherlands
Title: 

The gut microbiome of phytopathogenic root fly larvae: insights into the detoxification of plant secondary metabolites by insect-associated microbes

Abstract: 

Plants of the genus Brassica produce various toxic compounds such as isothiocyanates in response to herbivore damage. Despite their toxicity, some insects can cope well with these compounds. One example is the larva of the cabbage root fly (Delia radicum) which is a serious agricultural pest. The mechanism by which these root feeding insects detoxify isothiocyanates is not explored. Our hypothesis is that microorganisms residing in the gut contain enzymes that break down the isothiocyanates and are thus crucial for survival of the root fly larvae. We substantiated this hypothesis by metagenome studies of the microbial gut community. Combined with functional screens of isolated gut microbes these analyses indicated that indeed the gut microbiota plays a vital role in the breakdown of isothiocyanates. Some genes encoding proteins that are involved in this process have already been identified. Ongoing genome and transcriptome studies of isolated gut microbes will enable us to find new candidate genes encoding proteins used for isothiocyanate breakdown that will subsequently be functionally characterized. This will lead to an in-depth understanding of the role of microbes in the plant secondary metabolite – insect interaction.

Event Date: 
Wednesday, February 26, 2014 - 15:45 - 16:15
Institution: 
University of Perugia, Italy
Title: 

The intricate cross-talk of the microbiome in Resistance and Tolerance to pathogens

Abstract: 

The diverse microbial population characterizing the human host represents the result of different complex scenarios impacting the human microbiome assembly. The variety of the microbial species involved plays an important role on the human health by affecting the tissue differentiation, the modulation of the immune system as well as the general response against infectious pathogens, which has been recently revised and divided into two different strategies named Resistance and Tolerance. Resistance being the strategy where the host protects himself by reducing the pathogen load whereby the Tolerance being the opposite strategy, which consists in tolerating the pathogen to avoid tissue damage due to the occurrence of subsequent inflammatory pathologies. The host microbiome seems to play a crucial role in determining which strategy the host will exploit to avoid infection. We recently found that highly adaptive lactobacilli, switching from sugar to Tryptophan (Trp) as an energy source  are expanded and produce an aryl hydrocarbon receptor (AhR) ligand—indole-3-aldehyde—that contributes to AhR-dependent IL-22 transcription, which then trigger the release of antimicrobial peptides by the gut epithelium. Importantly, innate lymphocytes IL-22 producers were already described as a typical innate Resistance strategy to protect the host from intragastrical Candida albicans infections in mice. Thus, the resulting IL-22-dependent balanced mucosal response allows for survival of mixed microbial communities yet provides colonization resistance to the fungus Candida albicans. Therefore, the microbiota-AhR axis might represent an important strategy pursued by co-evolutive commensalism for fine-tuning host mucosal reactivity contingent on Trp catabolism.

Another great JAMS evening at the Australian Museum. Nicolas Barraud from UNSW kicked off with a biotechnology story about the use of nitric oxide in biofilm control. John-Sebastien Eden from Eddie Holmes group at USyd gave us the low down on norovirus evolution using the Sydney 2012 strain (the chunder from downunder) as a case study. Somehow our two 15 min presentations consumed an hour so starting back late after the break JAMS co-founder Prof Andrew Holmes gave an excellent presentation on what shapes microbial communities in the the gut. Despite the late start Andy had the audience glued to their seats with a showcase of technology used to unravel human-gut microbiome interactions.

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. 

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