There's something nasty in the water, but Maggie Koerth-Baker has you covered.

In September last year, authorities announced that they'd found Naegleria fowleri in the public water supply of Louisiana's St. Bernard Parish. N. fowleri is an amoeba — a single-celled organism that oozes its way around the world, enveloping any potential food sources in "arms" of ectoplasmic goo. This particular amoeba lives in warm water, eating bacteria, and generally being non-threatening to humans. But, if it gets pushed far enough up your nose, N. fowleri can end up discovering a whole new food source — human brain cells.

It's this combination of sci-fi horror and it-could-be-anywhere proximity that makes N. fowleri the stuff of nightmares. But the scientists who study microbial ecology say that you have to put an announcement like this into context. Every day, wherever we go, we're surrounded by microorganisms — bacteria, viruses, fungi, and amoebas. They live in our houses, in our water, and in our bodies. Some are helpful, actively doing good things for us. Some are benign, essentially ignoring us. Some are dangerous. But the really interesting ones — including N. fowleri — are those that straddle the lines between classifications. The benign that can turn pathogenic. The helpful that can turn benign. And whole populations of microorganisms whose relationship with us can change dramatically, depending on the conditions they live in. To get a better grasp on this, I spoke with several experts about their favorite microbes-next-door — the tiny creatures who share our lives but who we seldom notice.


"Anthrax is everywhere," said UC Davis evolutionary biologist Jonathan Eisen. "If you go out into the soil just about anywhere, you'll find some of it." And this fact is particularly relevant to the discovery of brain-eating amoebas in tap water. That's because the announcements surrounding N. fowleri left out two key details that you need to know before you panic about the presence of scary-sounding microbes.

First is abundance. There's a big difference between finding anthrax in the soil (or N. fowleri in the water) at high concentrations and simply finding it. There is anthrax in the dirt. Probably in your backyard. But that doesn't mean that the average gardener is going to breathe it in and get sick. That's because the abundance of anthrax in any particular patch of ground is generally low, Eisen said. Lower than it seems to take for the bacterium to actually infect people.

The second issue has to do with the specificity of the test. When you find anthrax in the soil, are you finding the deadly-to-humans sort of anthrax, or are you finding close relatives that may or may not be able to infect people? For instance, anthrax (Bacillus anthracis) is related to Bacillus thuringiensis, the bacteria from which we derive insect-killing bt toxin. In fact, they're so closely related, Eisen said, that evolutionary biologists argue about whether they should be classified as the same thing. The only difference is that they make different toxins — one that infects mammals and one that infects insects. Other kinds of Bacillus don't produce any toxins at all. "Do you remember after 9/11 how there was announcement every six months or so about finding anthrax in air samples from a subway or an airport?" Eisen said. "Turns out, it was never actually anthrax." The tests were made to detect anthrax and all its close relations. The result: A scary bacterium appeared to be more common than it actually is. Before you get freaked out about any microbe, you first need to know whether the tests used to find it will also find lots of benign things that happen to be related to it.

Mycobacterium avium

Tests that look for dangerous microorganisms can end up producing false positives, but they can also produce false negatives. That's because the tests can only find the things they're specifically looking for. We know that there's E.coli living everywhere from handbags to holy water largely because E.coli is easy to grow in a laboratory culture dish. Meanwhile, there might be other microbes in the same sample that we miss entirely.

Mycobacterium avium is one of those. Thirty years ago, it was basically unknown. It doesn't grow well in culture, and really only attracted attention when it turned out to be one of the many opportunistic infections that attack AIDS patients. A decade ago, scientists started looking for this bacteria (and its relatives) through DNA-based studies, and found it was a lot more prevalent, and harmed a lot more people, than anyone had previously guessed, said Norman Pace, a biochemist at the University of Colorado Boulder who studies microbial ecosystems in our water supply.

Today, we know that several species collectively called the Mycobacterium Avium Complex (or MAC) can make up 20% or more of all the microorganisms in your shower head — which also aerosolizes that bacteria and blows it into your face. Breathed in, MAC can cause lung-constricting pulmonary disease and particularly infects people over 65. Studies of Medicare patients show infection rates as high as 200-300 people per 100,000 — near epidemic levels. But that only includes the cases we know about. It's not something that has to be reported to the Centers for Disease Control and Prevention, nor is it a disease that doctors are on the lookout for. Pace suspects that almost all of us have had a mild case of MAC at some point. It's just that, most of the time, the bacteria is killed by our immune systems before the infection ever reaches that "need to see a doctor" phase.

E. coli

If you really want to talk about a microbe that's everywhere, all the time, E. coli is your bug. There are 40-50 different species of E. coli in your gut, alone, and hundreds more species living all around us, said Jack Gilbert, an environmental microbiologist at the University of Chicago. Of these, only three are actually dangerous for people, he said. But it's who is at risk, and when, that makes E. coli really fascinating.

Jonathan Eisen told me about studies that matched patients with E. coli infections — pairing them up based on factors like gender, age, health status, race … all the little things that can create differences in how an infection plays out. But, inevitably, scientists find that these pairs don't always respond in the same way. You can have two people who, theoretically, should have the roughly same outcome. Instead, one of them barely even registers as sick and other dies. "E. coli is the best studied bacterium on the planet," Eisen said. "But nobody can really figure out what's going on."

E. coli isn't the only common microorganism that has wildly different impacts on different people for reasons we don't really understand. Epstein-Barr virus is part of the herpes family and as many of 95% of adults are infected. Most people pick it up when they're little and never even know it's there, said Dorothy Crawford, a virologist at the UK's Centre for Infectious Diseases. But the same virus causes the fatigue and fever of mono in some teenagers. In parts of Africa and China, it's even associated with tumors. Why is a mystery. In fact, the herpes viruses, in general, are all sort of weird this way, Crawford said. Large swaths of the population are infected. But, most of the time, the virus doesn't really do anything. It just hangs out in nerve cells, hiding from the immune system. Sometimes, for some people, though, it will suddenly create a noticeable problem — whether that's a cold sore, or chicken pox, or shingles — only to disappear again. Crawford said this behavior might have something to do with how this particular microbe evolved. Researchers think herpes has been with humans for ages, dating back to hunter-gatherer times, when there were a lot fewer of us living much further apart from one another. Instead of optimizing themselves to quickly spread from human to human, herpes viruses might have optimized to spread from generation to generation — flaring up just often enough to make sure it has a chance to pass on to your kids and grandkids.

Enterococcus faecalis

Billions of microbes live all around us and in us all the time. Mostly, we never notice them. But sometimes, and for some people, they can cause serious health risks. Why? One reason might be because we've changed their environment, Jack Crawford said.

Let's back up to E. coli for a second. There are E. coli in your intestines that are normally not a problem. In fact, they're good for us. But under certain conditions, those same bacteria can suddenly turn deadly. Say you get abdominal surgery that involves cutting into the intestine. When you do that, you take bacteria that normally live in an oxygen-free world and expose them to lots of air. "It's like being a fish out of water," Crawford said. Meanwhile, while its healing from surgery, your intestine becomes phosphorous depleted, removing the E. coli's major food source. Those environmental changes cause the E. coli to respond in ways that, for them, are just about finding food and getting healthy, but, for people, can quickly turn toxic. "We often blame surgeons and say the infection must have come from them. But what if infection was there all along. We just got unlucky by making harmless bacteria into a life-threatening bug," Crawford said.

The same thing can happen outside the body, as well. Left to its own devices, your bathroom floor will become colonized with a diverse mixture of microbes, many of which come in from outside, most of which are completely harmless. But when you show up and sterilize the floor with antibacterial cleaners you leave behind an open field where invasive species quickly take over. Those species — including Enterococcus faecalis — come from us, and specifically, from our poop. Unlike the microbes that lived on the bathroom floor before sterilization, E. faecalis isn't harmless. It can cause urinary tract infections and (horrifyingly enough) is strongly associated with teeth that need root canals. It's also really resistant to antimicrobial cleaners, so more sterilization won't get rid of it. Instead, the best way to reduce your exposure to E. faecalis is to increase your exposure to all those harmless bacteria you killed off, to begin with.

If this sounds familiar, that's because it's roughly the same concept as the fecal transplants you've heard so much about — it's easier to replace bad bacteria with good bacteria than to try and kill off the bad bacteria. Same concept applies to your bathroom floor, Crawford said. And your kitchen counters. The trouble is, we don't yet know the best way to make sure that those those spaces both get clean and remain populated with harmless bacteria. In the future we might have probiotic wipes and cleaners that promote a healthy microbial ecosystem. But, before anybody would want to buy something like that, scientists first have to get a better understanding of what the right balance of microbes really is. "We can't rush this," Crawford said. "If we start spreading bacteria around willy-nilly without understanding why, we might end up killing someone." In the meantime, he said, it's best to keep your house clean, but not sterile.