It used to be that news of microbes was invariably alarming: They were the cause of strep throat or tuberculosis or those terrifying antibiotic-resistant infections. But lately, microbes have been undergoing an image shift. We hear a lot about the "good" bacteria found in yogurt and probiotic supplements. It's microbes, we're told, that help wines' terroir and give beers their unique flavor. And the right mix of organisms in the digestive tract might help prevent obesity.
People have begun thinking about their microbiomes — their internal menageries of bacteria and their kin — as something to be proud of, as an exclusive signature more personal than a fingerprint. A new company even promises to manufacture cheese from the bacterial components of your armpits, although this seems like something a party host might not want to announce to the guests when serving the hors d'oeuvres.
We are, it seems, rethinking the idea that microbes are villains and beginning to understand that killing them indiscriminately can cause bigger problems than the ones we are trying to solve. We're moving away from calling them "germs," which has always been a kind of garbage term to mean microorganisms we don't like (in the same way we call plants we don't want in the garden "weeds").
It even seems possible that one day we will overcome our compulsion to sanitize ourselves to death, as increasing evidence points to potentially harmful side effects of anti-bacterial products and antibiotics, including that they can disrupt hormones in humans and fish and lead to outbreaks of disease-causing microbes that are antibiotic resistant.
On balance, this acknowledgment of the sunnier side of microbial life is a good thing. At the same time, though, a note of caution is warranted. The truth is that notions of good and bad have little relevance when talking about microscopic organisms. They don't want to be your friend, and they don't want to be your enemy. They are in it for themselves, and our immune systems have adapted in reaction to an unending deluge of potential invaders that are always testing the boundaries. Microbes live on our skin and in our hair, guts and mouths (whether we like it or not), and the nasal hair, eye membranes and other barriers we've evolved to keep them out are regularly breached.
We can try to choose which microbes we live with, but the correct choice isn't always obvious. Some members of the minuscule crowd around us are unambiguously hostile, such as the flesh-eating Streptococcus pyogenes. These bacteria can kill in days, making the benefits of antibiotics unquestionable, assuming you can use them in time.
With other bacterial infections, though, the benefits of antibiotics aren't as clear. Because they kill indiscriminately, they disturb the normal microbial community, creating opportunities for truly weedy microbial species to take root. Like weeds everywhere, these microbial weeds can be almost impossible to eliminate once they are established. At the same time, we can't manage our bacteria as though they were crops, because they evolve in response to our every move.
Take Clostridium difficile, which causes severe gastrointestinal distress after antibiotic treatment has wiped out most other bacteria in the colon. Clostridium infections can be cured initially by discontinuing antibiotics. But with repeated antibiotic use, each new Clostridium infection is more difficult to overcome than the last. The best approach to date seems to be to fight microbes with microbes: reseed the colon with bacteria from a healthy person, which then compete with and defeat the Clostridium. Whether that will work forever is unclear.
In other cases, the co-evolution between us and our microbes can create some peculiar bedfellows. For example, Italian military recruits who showed signs of having been infected with toxoplasma, a one-celled parasite, or Helicobacter pylori, a bacteria that can cause stomach ulcers, were far less likely to have hay fever or asthma than their unexposed peers. Children from Gabon with signs of schistosomiasis, another parasite, were 32 times less likely to have dust mite allergies.
No one is suggesting that this makes such infections desirable, of course, but for better or worse our bodies are used to the onslaught of microbes, and having evolved with them since the beginning, removing or adding them can have unintended consequences. The bottom line is that they are in it for them, not us — something we would do well to remember.