Women in STEM

Investigating Bacterial Metabolism as a Model for Cancer Cells

By Women in STEM

In the 2022 SIRE program at the Genetic Technology Access Centre, we explored bacterial metabolism as a model for cancer cells. The bacteria we used was E. coli and was chosen because it can grow very quickly in a range of environments, in comparison to cancer cells which need very specific growing environments and advanced technology. Furthermore, E. coli has similar metabolic pathways to cancer cells. Glucose was our control because it is a major nutrient source for both cancer and E. coli cells, and adenosine was used because it encourages cancer cell multiplication, blood vessel growth and potentially alters metabolism. Our aim for the program was to learn about cancer cells and their metabolism, and to use new scientific techniques such as mass spectrometry to identify potential metabolomes and drug targets. This research is significant to society as cancer kills more than 50,000 people a year in Australia, hence identifying a metabolite that can kill the malignant growths would be extremely valuable.

Women in STEM

Setting up bacterial cultures


On our first day of the program, we set up the bacterial cultures for the rest of the experiments throughout the week. We created culture broths so that the bacteria had optimal growing conditions, using sodium chloride, yeast powder, distilled water, tryptone, adenosine and glucose. Additionally, we also had the opportunity to learn how to use new scientific tools such as a micropipette, electronic Bunsen burner and an autoclavable.

Setting up bacterial cultures


To obtain a greater understanding of the bacteria we were working with during the program, we looked at E. coli cells under a light microscope. This allowed us to see the shape of the bacteria and the different colonies, in comparison to other bacteria samples such as S. epidermidis.

Kegg bioinformatics and metabolomics

Before we could commence the next stage of our experiment, it was important for our group to learn about metabolomics, which is the study of small molecules (metabolites) that are involved in metabolism. To do so, we had the help of some scientists from the Bio21 institute who taught us about these processes in the human body. Furthermore, we used Kegg bioinformatics which is a database resource to look at the pathways and molecules in greater detail.

Protein Modelling

Bacteria harvest and metabolic arrest

The next day, we collected our bacteria samples and put them into the centrifuge to create a bacterial pellet. Then, we removed the liquid, added a saline solution and vortexed the bacteria for a few seconds. This was repeated around 5 times. We removed the last of the liquid and added them into separate tubes. These were then put into liquid nitrogen, followed by warm water for a total of 9 times to break the cell wall.

Bacteria Harvest

Fluorescence microscopy

On the 3rd day, we were given the opportunity to learn how to use a fluorescence microscope, which uses special stains to highlight organelles in a cell. In our case, we viewed the retina of Zebrafish, or danio rerio, and identified the different blood vessels in this species. This was a highly valuable experience, because we all had never had the opportunity to use such a cool piece of equipment.

Fluorescence Microscopy

Data processing and analytics

On the second last day of our program, we finally received the results of our experiment that were produced from the mass spectrometer. This piece of technology had identified over 600 molecules in our samples; hence it was our job to go through the data and identify relevant information. To do so, we loaded our data into software called Skyline which converted everything into graphs, demonstrating the number of molecules present in the sample at a certain time. While this process was a bit confusing, the Bio21 scientists helped us to understand the relation between our data and metabolism.

Data Processing Skyline

Identifying drug targets

The final step in our project was to find relevant molecules detected by the mass spectrometer that could potentially be inhibited in a metabolic pathway, to furthermore kill the cancer cells. We did this by choosing molecules we interpreted to be significant, searching them up on the Human Metabolome Database and researching their properties in the human body. If we thought that a particular metabolite had significance in relation to cancer, we would then locate its place in metabolic pathways to find potential drug targets.


Bio21 tour

The Bio21 lab tour was a highlight of the week, as we got to see many machines that are used in scientific research, meet a few of the scientists and learn about what happens in a real research lab. We also viewed the equipment that was used to process our bacteria and were given an overview of how this technology works. This gave all of us a great insight into future career pathways into science research as well.

Bio21 Tour

The bio21 lab tour was really interesting, seeing all these machines and people that help research diseases, it was really inspiring to me as I have personal experience with medication not working for disease. – Charlotte


I enjoyed gaining an insight into the scientific industry. I’ve always wanted to pursue a science-based career so learning about all the different pathways into the field was extensively motivating. – Cassidy


I really enjoyed when we looked at the blood vessels in the zebrafish retina and how we can stop the blood vessels to the cancerous tumour. Throughout this week's experiences I learned lots of new terms like metaboanalyst. – Ella


This experience was an amazing opportunity to learn about the type of work that research scientists undertake on a daily basis, and the processes involved to undertake a research project. My favourite part of the program was learning how to use many different types of scientific equipment that I would otherwise not have been exposed to at my own school. – Poppy


I thoroughly enjoyed using the fluorescence microscope, and using the computer to control the focus, and watch the changes the different types of fluorescent modes made on the zebrafish retina. Additionally, I thoroughly enjoyed learning how to all the new computer programs and expanding my knowledge on all areas of scientific research. - Renee