April 2013

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

Domesticating E. coli


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.

Event Date: 
Wednesday, April 24, 2013 - 18:15 - 18:30
University of Western Sydney

Comparative Analysis Of Saxitoxin-Producing And Non-Toxic Ecotypes Of Anabaena circinalis


During bloom events, freshwater cyanobacteria often produce a variety of harmful toxins with devastating health, environmental and economic consequences. The paralytic shellfish toxins are a large group of neurotoxic alkaloids including saxitoxin (STX), which is the most potent identified to date. In Australia, STX production is strain dependent within the cyanobacterium Anabaena circinalis. The following study utilised two strains of cyanobacteria, A. circinalis AWQC131C (131C) and A. circinalis AWQC310F (310F), as model organisms; 131C is a saxitoxin-producer whilst 310F serves as a non-toxic control. We aimed to characterise 131C and 310F at the genomic and proteomic levels using genome sequencing and isobaric tags for relative and absolute quantitation (iTRAQ), respectively, in order to identify key differences in not only their secondary but, primary metabolic pathways.
Draft genome sequencing of 131C and 310F revealed a genome length of 4.4 Mbp and a GC content of 37%, and the number of encoded genes was predicted to be 4447 and 4443 for 131C and 310F, respectively. A scan of each genome revealed a total of 740 unique coding regions within 131C, and 651 within 310F. Interestingly, the proteomic profile of 131C was significantly different from 310F. Using iTRAQ, we found that under standard laboratory conditions, 131C was highly abundant in photosynthetic and metabolic proteins compared to the non-toxic control.  This suggests a high C:N ratio and intracellular 2-oxoglutarate concentration and may be a novel site for posttranslational regulation of STX. Overall, 131C is potentially a high energy ecotype likely to inhabit the water surface. Conversely, 310F was more abundant in molecular chaperones and proteins that neutralise reactive oxygen species, indicating activation of cellular stress response. Therefore, 310F seems to be experiencing cellular stress under laboratory conditions and in the environment, may inhabit low-light areas below the water surface.
In conclusion, this study has provided an insight into fundamental differences between the toxic 131C and non-toxic 310F strains of A. circinalis. These findings will provide a platform for future experiments and hopefully pave the way to identify the cellular function of STX.

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

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


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.