Question: You said that your "Gene Gym" helps you to see whether being antibiotic resistant actually makes bacteria unhealthy. Firstly, what inspired you/gave you the idea of calling it that? Could you please explain the gym concept of it all? Secondly, I do know that there are bacteria which don't do any harm, but could you please name a few and their functions?

Jim Caryl answered on 22 Jun 2011:

Hi, great question!

You can read some of what I’ve written about how the Gene Gym works here:

/genesj11-zone/2011/06/what-do-you-mean-by-fitness-gym

The concept arose for a blog that I write on the Nature Network (http://blogs.nature.com/drjim/). I had to think of a name that people could relate to, as the aim of my blog was to describe antibiotic resistance in bacteria.

There is a hypothesis in evolutionary biology, first made popular by Professor Richard Dawkins in his book called ‘The Selfish Gene’ (well worth a read one day), that describes the gene as the ‘unit of selection’. What he’s suggesting is that rather than you, or me, making use of our DNA in order to survive (which, of course, we do), his suggestion is that it is in fact your DNA – your gene – that are using US to continue to survive. In effect, it is the genes that were here first, long before the cells that contained those genes were ‘human’ cells.

All the effects of the environment that make some cells do better, and others worse are really also a measure of which genes are doing better, and which are doing worse. The environment of the cell basically acts like a gymnasium and by the cell interacting with the environment, the genes inside are given a work out. Only the fittest survive; and by ‘fittest’, I mean the most suited to a particular environment – not necessary meaning those for strength or speed.

I force my bacterial cells to compete with each other, when the only difference between them may be the presence of a single gene. I can then see whether cells containing that one extra gene do better or worse, and therefore see how healthy that gene is.

So, an example of cooperation between our body and the bacteria that live on us would include:

On your skin you have Staphylococcus epidermidis (a cousin of S. aureus) – this can sometimes be bad, as can other ‘good’ bacteria, but S. epidermidis also works with our bodies to prevent invading ‘bad’ bacteria. Our skin produces molecules called ‘antimicrobial peptides’ (AMPs), like our own natural antibacterial covering. S. epidermidis also produce similar molecules (they’re immune to their own). Whilst our AMPs and the S. epidermidis AMPs work well on their own, together they work even better, and they can kill bad bacteria such as Enterococcus and Streptococcus if it gets on the skin. This is an example of ‘synergy’, where two things work better together than alone.

This same bacteria can also produce a chemical that prevents your body going into over-drive when you get a cut in your skin. Inflammation is a response by the body to bring more blood and special immune cells to the site of a cut, to clear foreign bodies and begin healing, however, it can go too far and cause more damage to surrounding tissue. S. epidermidis doesn’t want to get caught up in an inflammation response, so produces a chemical to calm things down. This benefits both the bacteria, and us.

In your gut you have a zoo of different bacteria, many of which we can’t culture in the lab – we only know they’re there because we can still look at their DNA. You can read something about what some of these bacteria do for us here: http://www.hhmi.org/bulletin/winter2005/bacteria/good.html