Bacteria Expert: When To Play With Dirt, When To Say No To Antibiotics

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Dads can’t win. If you let your kids roll around in the mud, then you’re negligent. If you keep them squeaky clean, then you’re not exposing them to enough healthy bacteria. Children’s developing gut microbiomes—comprised of the microscopic organisms, including bacteria, that inhabit their digestive tracts and influence physiological processes throughout their bodies—are a constant source of confusion. Are petting zoos reservoirs for zoonotic diseases, or rich microbiome resources that act as panaceas for seasonal allergies? Are antibiotics, which kill bacteria, lifesaving drugs or evil incarnate? If germs are so good, then why are we vaccinating kids?

“I think no matter what you do you’re going to be criticized by almost everyone about everything,” says Rob Knight, a professor at the University of California, San Diego and the co-founder of the American Gut Project and author of the new book Dirt Is Good: The Advantage of Germs for Your Child’s Developing Immune System. But that doesn’t mean the microbiome is a black box. Fatherly spoke with Knight about how gut bacteria can affect depressionn when to turn to probiotics, and precisely how much dirt is “good”.

Is dirt actually good for my kid?

Yes. There’s a lot of evidence that keeping your kids too clean is a problem, in a lot of ways, for health. Obviously, you wouldn’t want to expose them to a hospital or a sewage dump, but if you’re talking about getting muddy or exposure to germs from healthy soil, healthy, animals, or healthy people — that’s totally fine.

Last generation it was no dirt, this generation it’s all about the microbiome — concerned parents are getting whiplash. How do we know the scientists got it right this time?

We have a pretty solid evidence base at this point. We know a lot more about which particular germs are awful, and a lot of germs that were previously ignored turn out to not just be harmless but beneficial. No matter what you do you’re going to be criticized by almost everyone about everything, at least in my own experience. I don’t think this is a new phenomenon.

Should future parents trying to conceive be thinking about their microbiomes? 

That’s a really good question. There’s some evidence that the microbiome affects fertility, although in terms of male fertility there’s relatively little data. In terms of female fertility, the vaginal microbiome has been linked to infertility in a few studies.

Is the mother’s microbiome linked to premature birth or birth defects?

Premature birth, in particular. If microbes get into the amniotic fluid, that has been linked to premature birth. Researchers are now investigating whether you can use the microbiome as a relatively non-invasive indicator of who is at risk of premature birth and who isn’t. There’s also some data to suggest that birth defects like spina bifida may be related to the microbiome and nutritional status of the mother. But in general, when you’re thinking about birth defects, other risks such as chemical hazards are a lot more important.

When should I refuse antibiotics — and when does my kid actually need them?

If your physician is adamant that you need the antibiotics for a medical reason, you should probably take them. Where you want to be more skeptical and ask more questions is if antibiotics are being suggested as a precautionary measure, or being presented as though there’s no risk of harm to your child’s microbiome. Antibiotic eyedrops [given to babies shortly after birth] are specifically aimed at reducing blindness from gonorrhea — so if you don’t have gonorrhea or test negative for it, you probably don’t need the eye drops.

The questions you want to ask are things like: “Are there alternatives?” or “Would it be okay to wait until a later stage and take the antibiotics?” or “What are the consequences of not taking the antibiotics now?”. Just letting your physician know that your preference would be to minimize the use of antibiotics can be really helpful.

Let’s talk about probiotics. How can I tell the good ones from the unscientific scams?

The only probiotics you should consider are the ones backed by some sort of scientific evidence. The way people treat probiotics is largely as though they’re indistinguishable when, in fact, each probiotic is a particular kind of organism that makes very specific chemicals when it gets into your body and affects different processes. And just because a probiotic has been shown to be good for, say, diarrhea, doesn’t mean it generalizes or makes you healthier than the baseline. You take aspirin for a headache, for instance. That doesn’t mean that you should take aspirin all the time because it might make you feel better—it won’t. The same is true for probiotics, in general.

There are now resource guides available that essentially give you a summary of what probiotics are supported by evidence and what probiotics are not. We point to that literature in our book.

You mention in your book that the bacteria in our guts can impact depression. How?

There are a lot of links between the microbiome and your brain, and there’s a lot of evidence building up that links the microbiome to depression. A Chinese study found that you can take the microbiome from healthy people versus people with major depression, transplant those microbiomes into mice, and change the behavior of the mice based on whichever microbiome they got. One Canadian study involving a mouse model of depression showed that a particular probiotic can rescue the mouse from depression only if the vagus nerve is intact, which suggests the microbes in the gut are somehow mediating depression by signaling the brain, via the vagus nerve.

Does the microbiome impact my kid’s risk of allergies?

What’s most exciting is that, recently, a group in Australia showed that they could reverse peanut allergies using a probiotic to stimulate the immune system—reversing an allergy type that has never been reversed before.

As for seasonal allergies, many studies have shown that components in house dust, including bacteria, and bacteria associated with cows in a farm setting, can protect against the development of allergies. Also, having a dog seems to have a substantial influence, making children much less likely to have allergies.

If germs are so good for my kid, why am I vaccinating to prevent infection?

A lot of people are worried about the effect that vaccines have on the microbiome. But antibiotics (which people are much less worried about) have a huge dramatic effect, whereas vaccines tend to be very selective, targeting just the pathogen they’re developed to target and not really having an effect on anything else. It’s important to keep in mind that the early version of the hygiene hypothesis was that exposure to childhood diseases was good. But subsequent literature found no evidence of that whatsoever and supports the idea that most of these diseases are just bad. So these germ parties [in which parents intentionally expose their kids to diseases to build up immunity] are wrong. It’s much better to interact with a healthy cow than a sick five-year-old.

How clean (and bacteria-free) should I keep my house?

Obviously, you don’t want to live in a den of filth and clutter. At the same time, if you’re obsessively scrubbing down every surface with antibiotics, you’re probably keeping your house too clean. The exact balance is going to depend on a lot of factors and is still being studied. It’s more about balance. Not that you should live in a pig sty, but trying to scrub every germ from your environment may be doing more harm than good.

Finally, do you have any advice for exposing my kid to bacteria without getting him sick?

Playing in the dirt, or going to the petting zoo on a quiet day, or interacting with healthy livestock — these are much less likely to transmit disease than interacting with other children. Basically, having your children interact with healthy adults that you know is a great way to get that microbial exposure with fewer risks.

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