Friday, July 3, 2020

Biofilms: The EPS matrix

Has ever the sight of slime on showerheads been revolting? Does the slipperiness encountered when walking into a shallow stream full of slurry-coated rocks cause aversion? In my case, I would answer 'yes' for both the accounts. Since young, I had always strongly disliked the formation of biofilm (a word that I learnt subsequently) on household items and even on the pebbles in my tiny fish tank. I was always scrubbing away the slimy surfaces as hard as I could and once my mother absent-mindedly questioned if I knew what was actually causing the build-up of mucous on pipes and sinks. All the while, it had never occurred to me to look up on biofilm before that day and I thank my mother for pointing a pathway for my academic future.
Biofilm are caused by adherence of bacterial cells to a surface through van der Waals forces (a weak attractive force) initially. Then, they go through irreversible attachment stage where cell adhesion structures are employed to anchor themselves onto the surface permanently. After the maturation step, this group of living cells is then dispersed to colonize new surfaces. Biofilms are involved in nearly all of microbial infections on humans. Microorganisms such as Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, Salmonella enterica, Haemophilus influenzae and even the notorious Mycobacterium tuberculosis are known biofilm producers and all these bacteria cause chronic infections in humans. Malaysia, being a tropical country, provides an optimal growth condition for these biofilm-forming bacteria to continuously thrive especially in the clinical settings .
This condition is often difficult to treat as the biofilm formation renders antibiotics from penetrating the extracellular polymeric substance (EPS) matrix as shown in Figure 1, which is the biofilm wall of defense. So, what is so special about this EPS matrix? How does this feature make biofilm stronger? EPS is actually polymers synthesized by the bacteria and it is mainly made up of proteins, polysaccharides, lipids and extracellular DNA. Harsh environmental conditions such as rise in temperature, altered pH levels, drought and even salinity can trigger bacteria to produce EPS. Once EPS is synthesized, it allows bacteria to adhere to the surface, interact with one another and also acts as a glue between individual cells. So, this results in a 3D formation of a gel-like substance around the bacterial cells (that’s the slime that we often see.!!).

Figure 1. A schematic representation of a biofilm where antibiotic molecules are not able to penetrate the biofilm layer. 

This EPS matrix acts as carbon reserve, traps nutrient from the environment, has high water-holding capacity and it also keeps bacteria from desiccation, shelters bacteria against extreme temperatures and most importantly EPS protects bacteria against antibiotics. There are several ways EPS inhibit antibiotics from penetrating the matrix; (1) EPS is negatively charged, so it has the ability to bind positively charged compounds and also repels negatively charged molecules from entering the matrix layer, (2) buildup of antibiotic-degrading enzymes in the EPS matrix to breakdown antibiotic molecules (3) presence of extracellular DNA which offers resistance to antibiotics and also (4) EPS causes nutrient gradient in the matrix which results in groups of bacteria at different stages of growth that may not respond to the antibiotic. Therefore, researchers are mainly focused on targeting EPS as one of the crucial ways of removing biofilms.

Costa, O. Y., Raaijmakers, J. M., & Kuramae, E. E. (2018). Microbial extracellular polymeric substances: ecological function and impact on soil aggregation. Frontiers in microbiology, 9, 1636.

Sharma, D., Misba, L., & Khan, A. U. (2019). Antibiotics versus biofilm: an emerging battleground in microbial communities. Antimicrobial Resistance & Infection Control, 8(1), 1-10.

Koo, H., Allan, R. N., Howlin, R. P., Stoodley, P., & Hall-Stoodley, L. (2017). Targeting microbial biofilms: current and prospective therapeutic strategies. Nature Reviews Microbiology, 15(12), 740.

Sunday, June 28, 2020

Three Minute Thesis Competition 2019

Joining 3 Minute Thesis (2019) competition at UM was indeed a fun experience. At first, I was quite nervous about skimming up my PhD research into just 3 minutes. Then, as I began to prepare for my participation in the competition, I braced myself for the challenge. It turned out to be an excellent experience in shaping myself to be a better science communicator as the main purpose of this competition was to explain my research findings to a non-specialist audience.

So, here you go, my prepared speech for the competition……


Have you ever been treated for a fever and the doctor does not prescribe you antibiotics? It happened to me long ago and when I questioned the doctor, he said “taking antibiotics when you don’t need them can cause antibiotic resistance”. That sparked my interest and a quick search through slow Internet Explorer of those days, I found that antibiotic resistance does not mean that our body is fighting the antibiotics, but it is the bacteria that is going against the antibiotics.

Millions of people are suffering from this problem everyday and World Health Organization has estimated that 10 million deaths can occur by year 2050 if this continues. Surprisingly, that’s even higher than what’s predicted for cancer. 

But wait, I am sure that some of you are wondering, how can this tiny, unseen organism can cause so much of problems to the humans, right? Well, the overuse and misuse of antibiotics in people and animals have caused the germs to become smarter through genetic changes, therefore harder to kill just as I have shown in Fig. 1(a).

Figure 1. A schematic diagram explaining my thesis findings for a non-specialist audience. 


    Did you know, that the discovery and the approval of a new antibiotic takes anywhere between 10 to 20 years? Do the terminally ill patients in the hospital have that much of time to wait before the germs take control of their life?

Therefore, I felt that it was really important that the use of antibiotics should be preserved for critical use only. So in my PhD, I focused on finding an agent that would restore antibiotics into its days of glory. Why? Try to imagine a world without antibiotics. Even a simple cut can be life-threatening.

So, I used graphene, a carbon-based nanomaterial that has its own bacteria killing properties. So I combined graphene and old antibiotic to gain best of both the worlds. Interestingly, I found that graphene helped to carry the antibiotics and deliver it right to the doorstep of the bacteria just like the magic carpet that I have shown in Fig. 1(b). How? Graphene causes damage to the bacteria and this in turn allows the previously unsuccessful antibiotic to gain entry into the bacteria and kill it.

Why is this so important? By using graphene, I am giving life to the old antibiotics that are not being prescribed by the doctors anymore and the chances of bacteria fighting the newer antibiotics can be drastically reduced. If you are thinking “is graphene safe?”, be rest assured that I found graphene to be not toxic in human cells. I repeat, not toxic, (at low concentrations, of course) Therefore, graphene is greatly beneficial in helping mankind to fight bacterial infections and it also saves the antibiotics. 

Biofilms: The EPS matrix

Has ever the sight of slime on showerheads been revolting? Does the slipperiness encountered when walking into a shallow stream full of sl...