What’s A MicroBiome and Why Should You Care? 5 Questions with Dr. Rob Knight

January 28, 2023

Every once in a while a buzzword starts to pop up everywhere. We’re seeing that lately with the microbiome. So we asked Dr. Rob Knight a biologist and microbiome expert at the University of Colorado, Boulder what it is and what—if anything—parents can do to boost their kids health by paying attention to their microbes. It turns out that though humans have been living with their microbes forever, studying them is quite new. Which means there is no real how to information to give parents—just yet. “We are finding out how this stuff works rather than new things you should do,” says Knight. “That is what makes this so much fun; we are finally discovering the reasons for things that have been puzzling for a long time. Like mosquitoes, one component of who gets bitten and who does not is microbes on skin.”

Pretty amazing stuff. Read on to clue in.

1. What is the microbiome and why is it suddenly all over the news?

It’s all of the genes in the microbes that live in or on the human body. Bacteria, fungi, and viruses make up the microbiota, and their genes make up the microbiome. There are more in the gut than cells in your entire body—bacterial cells outdo human cells. We have known that microbes were very diverse since the 1600s, with the invention of microscopes. We are hearing more about it now as DNA sequencing technology advances and makes it easier to find out specifically what microbes are in there. They are just now being linked to all kinds of aspects of health and of disease. People are getting a much better understanding what microbes can have an impact on health, but people are still unclear what is in the gut, the mouth, and the skin. Everyone is very different, which is surprising. A family or people who live in the same household tend to be more similar. The scientific community is still very much in the process of discovering how these similarities come about, including about where the microbes come from. We know some places our microbes come from are other people, environmental, surfaces we touch, stuff we breathe, in our food sometimes, livestock and pets, sometimes soil. What we don’t know is quantitatively how important they are, or which microbes are best at colonizing us. More research is needed.

2. Let’s address how this pertains to children. What childhood diseases are linked to imbalance in microbiome? Is there some way for parents to help boost the microbiome to keep kids healthy?

This is being researched at the moment; there is not a lot of information out there. Until we have good clinical data, it’s difficult to make a clear recommendation. We have seen that C-sections increase the risk of allergies. There are some reports that bottle fed rather than breast fed babies have increased risk of several immune problems including allergies. Some scientific articles suggest an increased risk of obesity with C-section, antibiotics, and bottle feeding, which seem to increase the same risks. The issue is confounding variables like socioeconomic status, what region you live in, an urban or rural environment, and few cluster-randomized trials that control for these variables have been done so far. A lot of the most compelling studies relating the microbiome to allergies have been done in mice, where more control is possible than in humans. We see having dogs early in life, and even before birth, may lower the risk of allergies but that doesn’t mean you can be sure. Dog owners may be predisposed to something, so getting a dog won’t necessarily help. So there is no concrete recommendation to make yet to parents based on the current state of research.

3. You mentioned antibiotics; do you think their use should be limited? How do you determine if your kid has to take them and what to do then? Is eating antibiotic-free meat and dairy important?

Those are clear to recommend for other reasons—not so much because of antibiotics coming through meat and dairy in trace amounts. You should be worried that those livestock antibiotics are breeding antibiotic-resistant bacteria, which is a big public health problem. You should avoid antibiotics in general unless your doctor thinks it’s very likely that you have a bacterial infection that antibiotics can treat, and that the benefits outweigh the risks – and there are risks. They are overprescribed in the U.S. when they aren’t needed. We are just beginning to understand their effects on the microbiome. Initial reports show the effects are different on different people, but antibiotics have been shown to be linked to obesity later in life. You need to be really sure your doctor knows your disease is bacterial versus viral and what the consequence would be in waiting to see if the infection would resolve without antibiotics. At the same time, it’s important to remember that antibiotics can be a life saving treatment, so don’t refuse them if they’re needed medically. If you must take them, take the whole course, because if you don’t you will be contributing to the antibiotic resistance problem.

4. Are we over-disinfecting at home? If we invite germs in in an effort to expose our kids to beneficial microbes, how to we balance the risk?

That is very likely. There are a lot of epidemiological studies that suggest that extremely clean homes and lack of exposure to microbes and to healthy animals and soil can affect the microbiome and cause immune system problems. At the same time, it’s important to remember that there are bad microbes, and there are environmental toxins, that you need to avoid. The only way to balance the risks for certain is knowing what the risks are in your particular region, but use your common sense. Don’t give your kids exposure to soil by having them play in a toxic waste dump. You need unpolluted places, just as you need healthy animals. With playgrounds, it probably depends on the specific playground but there’s no data that would be relevant to informing a parent’s decision. You’d need to do substantial amounts of research to quantify the risks and know about your individual playground.

5. What are good foods to feed the gut? Should we all be on probiotics?

There are a few probiotics with excellent clinical trial data—some have been shown to be effective for IBS, for example. However the vast majority on sale does not have any scientific evidence supporting them. A lot of foods that benefit your microbiome are the things parents should feed their children anyway. Fiber is good in general, as are brightly colored vegetables like carrots, tomatoes, eggplants, and fruits like raspberries (surprisingly high in fiber) and blueberries (high in anthocyanins and other antioxidants). You should probably avoid fries, but probably you knew that before you knew anything about the microbiome.

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