Thursday, January 29, 2015

Engineering Skin Bateria

I think that the future of wearable technology is engineered bacteria.

So I started working with skin bacteria for a project. I am trying to see how well skin bacteria can be engineered and used to colonize the skin and perform the process that they were engineered to do. The processes I want them to do at the moment are very basic, express fluorescent proteins or use luciferase to glow. This project then a little more difficult than I expected. 

What I did not know is that many of the bacteria on our skin are antibiotic resistant. A little scary? Actually not that scary as it seems a natural step in our symbiotic evolution. So why is this important then? When engineering bacteria scientist often use selection markers and most of the time these are antibiotics. This is because genetic engineering is not quite as efficient as you would hope it to be and also because finding the bacteria that have been engineered can be a difficult process if one is searching through a thousand different bacterial colonies. Antibiotics are great because they kill off all the bacteria that have not been engineered and you are usually left with the ones that have been engineered! But that's not always the case as I'm seeing now. 

First, I started off isolating bacteria from my skin by taking swabs and streaking the swabs on plates and then growing them at different temperatures. Next, I chose some bacteria and grew them up and put them in a solution that would make them more tenable to uptake foreign DNA (The DNA I wanted to put inside them). What I found was that the antibiotics that I was using for selection were not working. So then I started again. 

First I had to test each bacteria isolated from my skin and see if the antibiotics that I was using for engineering selection actually kill the bacterium.

Even after I found a bacterium that was not resistant to the antibiotic I was using (Ampicillin) I found out it was still resistant to other antibiotics (Kanamycin). You can see in the image above that bacteria #2 and #3 both survive on ampicillin fine. I ended up finding out the #1 also doesn't mind ampicillin much when doing liquid cultures so I have been working with #4.

Currently, I am using bacteria #4 and trying to put plasmid DNA inside of them. Once I can tell that this works and the bacteria grow and function on media I will test the bacteria to see if they can grow at all on my skin. The test after that will involve seeing if the bacteria actually colonize my skin so that even after washing the affected area there will still be some bacteria left. 

I think this will be the most difficult problem. 

As many scientists suggest engineered bacteria that are creating proteins or products that are not meant for survival are at a disadvantage when fighting for a spot on your skin amongst all the other bacteria. However, there are many ways to overcome this including giving the bacteria some sort of selective advantage by altering its metabolism to be more robust than naturally occurring bacteria. 

I am about to sequence the DNA of bacteria #4. By the looks of it I would say it is either a Streptococcus or a Enterococcus (This is an attempt to impress myself with my weak bacterial knowledge). As my work has made me quite the amateur microbiologist lately being able to identify by colony morphology and color pretty well.

I will keep updating as this experiment progresses.

Originally this idea was bounced around by myself and Jun Axup, though I am sure it is probably not original and has been tried by others. My goal is just to test some proof of concept ideas.