I started writing a lengthy response to a reader comment on one of Heather's posts, but decided it could use a post of it's own. The question:
As to being pathogenic, is it possible that many bacteria are pathogenic if given sufficient opportunity? [snip] It seems largely to me that the line between pathogenic and non-pathogenic is pretty blurry.
Let's get some definitions out of the way first - a pathogen is an organism that causes disease. That seems simple enough, but when you examine the real world more carefully, things turn complicated pretty fast. What do I call the cold I was infected with last year? It can't infect me anymore (my immune system would recognize it immediately and smack it down), but it might infect you just fine. Or what about E. coli? There are billions of them in your gut right now, and you can get along with them quite well. But give that same bug a little stretch of DNA, and they can become deadly.
Commenter Mike also mentioned a previous post of mine, where I talked about Clostridium difficile, a bacterial species that is normally present in the human gut at very low concentrations without causing problems. But a heavy dose of antibiotics can clear away other commensal bugs, allowing Clostridium populations to explode and cause severe inflammation (take a look at part 3 of this lecture). So what do you think - is Clostridium a pathogen?
It turns out there's a spectrum of pathogenicity that any organism can fall on:
1) Some bugs could never survive in our body's environment therefore are never pathogenic.
2) Some bugs (like Candida albicans, a fungus) could survive, but don't have ways of evading the immune system so they're efficiently mopped up. These aren't generally pathogens in normal individuals, but if you have a compromised immune system (from AIDS or immunosuppression for instance), they can cause infections.
3) Other bugs (like E. coli), have non-pathogenic forms but can also acquire DNA that codes for proteins called virulence factors that allow the bug to be pathogenic (usually virulence factors are proteins that allow a bug to invade cells, or pump cells with things that disrupt the immune system).
4) Some bugs are just wired for infection, and can only make their living as a pathogen (Vibrio cholerae is a timely example)
If you're willing to think a bit outside the box, I would throw Clostridium in category 2. The microbes that live in our gut are functionally part of our immune system. They fill the niches that many pathogens need to survive. In this case, the antibiotics act a bit like immunosuppressants, and allow a bug that's normally harmless to gain a foothold and start causing disease.
Don't get me wrong - if you're prescribed antibiotics, you should take them faithfully. Clostridium infection is a pretty rare side effect and usually only happens with the massive antibiotic doses that are necessary when some other bacterial infection is running wild. Besides, pretty soon we'll be able to cure you with a poop-infusion.