June 2017

Event Date: 
Tuesday, August 8, 2017 (All day) - Friday, August 18, 2017 (All day)

Dear JAMS community,

JAMS will once again be representing grassroots microbiology at the Australian Museum Science Festival!


We are seeking volunteers from within the JAMS community and from the larger microbiology community to help run our microbiology booth at the Australian Museum Science Festival,  which runs in August and aims to engage school children with different areas of science. If you or someone you know might be willing to give half a day to the cause of microbiology outreach and staffing our JAMS booth, please let me know.

Email t.jeffries@westernsydney.edu.au and specify your preferred week and any days during that week that you are unavailable.

The dates are:

  • 8-11th August (Primary Schools)
  • 15th-18th August (High Schools).

It’s a crazy and frantic experience, but also fun and rewarding and it looks great on your CV!

I would greatly appreciate it if you could circulate this message to your lab groups and wider network and please let me know ASAP if you can make it!


Tom Jeffries on behalf of JAMS

Event Date: 
Tuesday, June 27, 2017 - 18:00 - 18:15
Mejio University (Nagoya, Japan)

Proteotyping of methanogenic archaea by the ribosomal protein mass spectrum


Microbial identification methods that analyze whole cells or cell lysates by MALDI-TOF MS fingerprinting have been developed to determine microbial species in the clinical research field. However, these whole cell fingerprinting methods, which can determine bacteria at the species level, have difficulty in classifying bacteria at the strain level. Therefore, we developed a bioinformatics-based approach called the S10-GERMS method (S10-spc-alpha operon gene encoding ribosomal protein mass spectrum), to identify bacteria at the strain level by using ribosomal subunit proteins (R-proteins) as biomarkers. In this study, we analyzed whether anaerobic methanogenic archaea {two strains of Methanococcus maripaludis (S2 & C6) and three strains of Methanosarcina barkeri (Wiesmoor, 227 & MS) etc.} could be classified at strain level by the S10-GERMS method.
A molecular weight database for R-proteins of genome sequenced strains was constructed by DNA sequences and calculation of molecular weight. Analyzed methanogens were cultured and resuspended in ethanol (70%). Cells were mixed with 1/5 vol % of matrix solution {Sinapinic acid (15 mg/mL) in 50% acetonitrile with 1% trifluoroacetate}. Then, mass spectra of cells were observed with positive linear mode.
In the case of two strains of M. maripaludis that are closely affiliated with 16S rRNA gene sequences (99% similarity), four-sevenths of R-proteins chosen as biomarkers differed in their mass spectra (both theoretical and observed), indicating that strain S2 and C6 are classified as different strains according to this method. M. barkeri could also be identified using R-protein. These results implied that S10-GERMS method provides an identification platform for environmental samples.

Event Date: 
Tuesday, June 27, 2017 - 19:00 - 19:30
Ohio State University

Bacterial Biofilms: Built for Persistence in Nature and Chronic Infection.


Bacterial biofilms are microscopic assemblages of bacterial cells usually attached to a surface and held together by a self-produced extracellular polymeric slime (EPS) matrix. Biofilms are ubiquitous in nature and are highly problematic in industry and medicine where they cause corrosion, fouling, contamination and chronic medical and dental infections. The EPS matrix is chemically complex and is composed of polysaccharides, lipids, proteins and DNA and protects the bacteria within from antibiotics chemical challenges and host immunity. Mass transfer through the EPS is dominated by diffusion which, allows the development of gradients in nutrients, waste products and cell signals. The highly localized and heterogeneous chemical microenvironment caused by the metabolic activity of the biofilm can be corrosive and cytotoxic and facilitates the development of a dormant persister population.  Additionally, the bulk mechanical properties of biofilms also appear to play a role in survival by allowing the biofilm to respond to imposed mechanical loads over very short (ms) and very long (days to weeks) time scales. Creep and relaxation tests show that generally biofilms behave as viscoelastic liquids allowing them to flow over surfaces with velocities of meters per second. In this seminar Dr. Stoodley will give an overview of biofilm development using case studies to illustrate the consequences of biofilm formation in infection and the difficulties in prevention and treatment. 

Event Date: 
Tuesday, June 27, 2017 - 18:15 - 18:30
University of New South Wales

Metagenomic and geochemical changes following rainfall at a legacy radionuclide waste disposal site


The rapid proliferation of the nuclear industry after World War II resulted in the generation of substantial volumes of radioactive waste. This material was often buried in shallow trenches, a standard practice at the time, of which the Little Forest Legacy Site near Sydney (Australia) is an example. It has been reported that during heavy rain, the trenches exhibit an overflowing effect, analogous to a bathtub. The aim of this work was to test the hypothesis that intense rainfall events, are likely to introduce oxygen, and will therefore have an effect on the biology and chemistry inside the trenches during a fill-drain cycle.
Shotgun metagenomics was performed on water samples collected from a sample trench in triplicate across four time points during a 47-day period after a heavy rainfall event. Chemical parameters were monitored as well.
Functional analysis of the metagenome shows clear differences between the initial sampling points characterised by higher gene frequencies related to aerobic heterotrophic metabolism such higher cytochrome-c oxidase and several sugar transporters. The maximum for these indicators is reached at day 4, matching a surge in the proportion of Proteobacteria (63.6% total prokaryotes). Conversely, anaerobic metabolism genes such those specific of methanogenesis or dissimilatory sulfate reduction, and anaerobic taxa such class Methanomicrobia, show a progressive increase over time with a maximum at the final sampling day. These changes coincided with an increased proportion in soluble Fe, Am, and Pu, supporting our hypothesis that rainfall events can induces transient aerobic conditions potentially altering radiochemical mobility.

Course Description
The twoday Longread Data Analysis Workshop aims to introduce attendees to genome assembly using longread data. As part of this workshop participants will perform a handson comparison between short and longread microbial genome assemblies. This workshop will consist of a mixture of lectures, handson practical sessions, and open discussions.
Target Audience