Gut flora

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 - 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, 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, 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. 

Event Date: 
Wednesday, May 29, 2013 - 18:15 - 18:30
Institution: 
Macquarie University
Title: 

Dissemination of antibiotic resistance determinants via sewage discharge from Davis Station, Antarctica

Abstract: 

Discharge of untreated or macerated sewage presents a significant risk to Antarctic marine ecosystems by introducing non-native microorganisms that potentially impact microbial communities and threaten health of Antarctic wildlife. Despite these risks, disposal of essentially untreated sewage continues in the Antarctic and sub-Antarctic. As part of an environmental impact assessment of the Davis Station, we investigated carriage of antibiotic resistance determinants in Escherichia coli isolates from marine water and sediments, marine invertebrates (Laturnula and Abatus), birds and mammals within 10 km of the Davis sewage outfall. Class 1 integrons typical of human pathogens and commensals were detected in 12% of E. coli isolates. E. coli carrying these integrons were primarily isolated from the near shore marine water column and the filter feeding mollusc Laturnula. Class 1 integrons were not detected in E. coli isolated from seal (Miroungaleonina, Leptonychotes weddellii) or penguin (Pygoscelis adeliae) feces. However, isolation of E. coli from these vertebrates’ faeces was also low. Consequently, sewage disposal is introducing non-native microorganisms and associated resistance genes into the Antarctic environment. The impact of this “gene pollution” on the diversity and evolution of native Antarctic microbial communities is unknown. 

 

Event Date: 
Wednesday, April 24, 2013 - 18:00 - 18:15
Institution: 
University of Sydney
Title: 

Domesticating E. coli

Abstract: 

Adaptation of environmental bacteria to laboratory conditions can lead to modification of important traits, what we term domestication. Little is known about the rapidity and reproducibility of domestication changes, the uniformity of these changes within a species or how diverse these are in a single culture. We analysed phenotypic changes in nutrient-rich liquid media or on agar of four E. coli strains newly isolated through minimal steps from different sources. The laboratory-cultured populations showed changes in metabolism, morphotype, fitness and in phenotypes associated with the sigma factor RpoS. Domestication events and phenotypic diversity started to emerge within 2-3 days in replicate sub-cultures of the same ancestor. In some strains, increased amino acid usage and higher fitness under nutrient limitation resembled those in mutants with the GASP (Growth Advantage in Stationary Phase) phenotype. The domestication changes are not uniform across a species or even within a single domesticated population. However, some parallelism in adaptation within repeat cultures was observed. Differences in the laboratory environment also determine domestication effects, which differ between liquid and solid media or with extended stationary phase. Important lessons for the handling and storage of organisms can be based on these studies.

JAMS celebrated July at the Australian Museum with a diverse series of talks and food and drinks, kindly supported by ASM.

Rita Rapa (UTS) started us off describing the integron/gene cassette system in the Vibrio genus. These gene cassettes add to the adaptive potential of Vibrio and are likely to be an important driver in the evolution of Vibrio in their respective niches. Through whole cell proteomic analysis, deletions in the gene cassette array exhibit altered surface associated structures. Her future work will focus on how these deletions impact Vibrio physiology.
Event Date: 
Wednesday, July 27, 2011 - 19:15 - 20:00
Institution: 
University of Queensland
Title: 

The healthy human gut microbiota and how chemotherapy and antibiotics affect its composition.

Abstract: 

Recent science associates the gut microbiota composition with the development of complex diseases such as for example cardio-vascular diseases, diabetes and inflammatory bowel diseases. Now, the human gastro-intestinal microbiota must be understood as a microbial organ whose metabolism provides essential functions to the host rather than just supplementary nutrient acquisition.
The first aim of this talk is to discuss what makes a “healthy” gut microbiota together with results from analysing vegetarian and elderly gut microbiota.
The second aim will be to discuss results from analysing the gut microbiota of people undergoing chemotherapy and antibiotics.
Whether (and how) diet and age affect the gut microbiota composition is not only really interesting; knowing the diversity of healthy gut microbiotas may help us to decide which composition to restore a perturbed microbiota to, for example after chemotherapy and antibiotic treatment.

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