In my field, many things that cause the average man-on-the-street to get a bit squeamish or squicked are rather commonplace. My own studies include two types of bacteria that are carried rectally in humans (and other animals), so I spend an absurd amount of time thinking about, well, shit, and the lifeforms that inhabit it and collectively make up our normal gut flora. The vast majority of these species don’t harm us at all, and many are even beneficial: priming our immune system; assisting in digestion; and filling niches that could be colonized by their nastier bacterial brethren.

It’s typically when there’s some disturbance in these flora that bad things happen. For example, you may ingest food contaminated with a foreign bacterial strain that may transiently colonize your intestines, resulting in cramping and diarrhea. Typically these infections are self-limited and your normal flora ‘resets itself’ after a short time, but some pathogenic bacteria have a propensity for making themselves at home in your gut. How to get rid of these nasty invaders then? Antibiotics are one option, but they also kill your regular bacteria, potentially making the problem worse (especially if the nasty invader happens to be resistant to many antibiotics). […]