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Probiotics and the Human Microbiome: Beyond the Gut

Probiotics and the Human Microbiome: Beyond the Gut

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Dr. Don Brown, ND, discusses cutting edge research on the use of probiotics

Biography: Naturopathic physician Dr. Donald Brown is one of the leading authorities in the U.S. on evidence-based herbal medicine and the safety and efficacy of nutritional supplements and probiotics. He currently serves as the Director of Natural Product Research Consultants in Seattle, WA, sits on the Advisory Board of the American Botanical Council, and was a member of the Board of Directors of the International Probiotics Association for two years.

Below is an interview with Dr. Brown on the rapidly developing field of probiotics, and evidence for their use in supporting the health of the gut, immune system, skin, brain, and genitourinary system.

NutritionInFocus: Today we are exploring the impact of probiotics on the microbiome. It seems like research in this area has really exploded. Why is that?

Dr. Brown: It’s ironic, talking about it as a naturopath, because we’ve always talked about the impact of the intestinal tract on health. But more recently, probiotic research has led us to realize that there are trillions of microbes in and on our body. We’re not just looking at the microbes in the gut, but the microbes in other parts of the body as well, like the skin and genitourinary tract. And we have a tendency in probiotic discourse to focus on bacteria, but there are viral and fungal components of the microbiome that are natural inhabitants of the body as well. All of these microbes play an important part in our health and our wellness, and when the balance tips in the wrong direction, our health does too.

NutritionInFocus: So when it comes to the human microbiome, remind us of the mechanism of action of probiotics. How and why do probiotics even work?

Dr. Brown: In thinking about the gut, I like to use the analogy of a busy parking lot. You have organisms that are health-promoting, and then you have organisms that are potential pathogens, and they’re all looking for parking spots. Bacteria have to adhere to intestinal cells to be able to either promote health or promote disease. So, one of the first things probiotic bacteria do is to compete for spots with these potential pathogens.

Then, once they set up house, the probiotic bacteria start creating a micro-environment that is inhospitable to potential pathogens by altering the pH slightly and by producing substances that are antimicrobial. They really create a situation where they say to pathogens, “Hey, this is our home, and you’re not welcome here.” They also help produce mucin and keep the tight junctions between cells in the intestinal tract healthy and intact. That’s important for intestinal barrier function, and it’s very important for preventing leaky gut.

NutritionInFocus: Can you give us a few examples of how probiotic bacteria support a healthy colon and our immune system?

Dr. Brown: In the colon, probiotics boost the production of short-chain fatty acids, which help with not only digestive health but the health of the body systemically. Short-chain fatty acids help to regulate inflammation in the body,[1] and butyrate, one of these acids, also has protective effects against cancer.[2] Concerning the immune system, one of the really interesting things that’s been discovered in the last ten or so years is that when these beneficial bacteria attach to the intestinal wall they communicate with certain cells in the immune system known as dendritic cells.[3] Dendritic cells are funny-looking starfish-shaped things that send feelers into the cells that line the intestinal tract. And the probiotic bacteria are actually communicating through dendritic cells to influence the production of immune mediators. Inflammatory responses are modulated through these processes as well.

NutritionInFocus: How broad are these effects? Give us a sense of how you see this in terms of human health.

“Although the microbiota can be negatively impacted by stress, it also can positively impact stress and mood, which is a whole new mechanism of action we now are beginning to understand.”

Dr. Brown: We’ve already touched on the impact on gut health and immune health. And now we’re beginning to realize that the intestinal tract is communicating with the brain, through what’s called the gut-brain axis. Stress, for instance, can negatively impact the healthy bacteria in the gastrointestinal tract. The gut microbiota, in turn, modulates the stress response through the vagus nerve,[4] which goes all the way from the gut to the brain. So, although the microbiota can be negatively impacted by stress, it also can positively impact stress and mood, which is a whole new mechanism of action we now are beginning to understand. And then, there is the female genitourinary tract which also has its own population of probiotic bacteria that positively affect genitourinary tract health, possibly even helping to prevent sexually transmitted infections such as HIV.[5]

NutritionInFocus: What conditions have the most compelling research in terms of improved outcomes with probiotic use? I realize this may be a pretty long list, but take us through that list from a scientific perspective.

“What they’re finding is that the use of probiotics starting in pregnancy is reducing the incidence of atopic dermatitis by about 50%.”

Dr. Brown: I like to start with the things that are accepted by the medical community at large. And one of those is the fact that probiotics have a positive effect on prevention of antibiotic-associated diarrhea.[6],[7],[8] That’s a good starting point because we have really solid data that probiotics are good at preventing that.

Another area that has reached a critical mass of evidence is the prevention of atopic dermatitis [eczema] in children who are potentially at risk. The studies started in the early 2000s, looking at the mom’s risk of atopic diseases and allergic diseases, and starting to give the mother probiotics during the second half of her last trimester.[9] And then once the baby is born, if mom is nursing, continuing to give the probiotics to the mom until she stops. In some studies, they have provided probiotics to the at-risk infant as well.[10],[11] What they’re finding is that the use of probiotics starting in pregnancy is reducing the incidence of atopic dermatitis by about 50%. That’s amazing to me.

NutritionInFocus: You’ve mentioned the role of probiotics in gut health, immune health, stress responses, and the skin. What are some of the other organ systems that can be impacted by probiotics?

Dr. Brown: Another area with considerable research in the realm of probiotics is female genitourinary tract health. Conditions like bacterial vaginosis would probably be at the top of the list,[12] as well as prevention of recurrent urinary tract infections.[13] We’re finding that probiotics taken orally can actually populate the vagina and produce significant effects,[14],[15] which is amazing. We used to think you’d have to administer probiotics through the vagina, for example with a pessary, to get an effect, and that’s no longer true.

Also, studies now suggest that routine use of probiotics can reduce the incidence of upper respiratory tract infections, at least in adults.[16] There is a lot more research emerging on other conditions as well.

NutritionInFocus: You’ve talked about antibiotics and how they disrupt the microbiome. Give us some specific examples of how probiotics may be useful with these and other medications.

“Probiotics can help break up biofilm and make standard UTI treatments perform better. And then continuing to use the probiotics, after the antibiotic course has ended, actually reduces recurrence rates of UTI.”

Dr. Brown: One of the great things about probiotics is they can be used as an adjunct to standard treatments. Take Helicobacter pylori infection, for instance. The standard triple-drug treatment for H. pylori [the bacterium associated with gastric ulcers] is very tough on people and recurrence rates are really high. As a result of the drugs, the healthy bacteria in the gastrointestinal tract are reduced by as much as 80%. But if we administer probiotics during the treatment period, it cuts the loss of “good” bacteria considerably, and if patients continue to use probiotics afterwards, they tend to bounce back more quickly.[17],[18]

Another example is urinary tract infections (UTIs). The infectious E. coli bacteria are really good at setting up what are called biofilms. It’s like they are taking a Teflon sheet and putting it over themselves. Antibiotics can reach the bacteria that are outside the protective shield, but the bacteria that are under it are not touched by antibiotics. Probiotics can help break up biofilm and make standard UTI treatments perform better.

Other examples include proton pump inhibitors, which are drugs often used for gastroesophageal reflux disease or GERD; they can have a very negative effect on the microbiome.[22] And some of the more aggressive anti-inflammatory medicines that people take may have an effect as well. We’re still in the early stages of learning which specific drugs impact the microbiome and what the effects are.

NutritionInFocus: Thank you so much for sharing your knowledge with us today Dr. Brown! We really look forward to seeing more developments in the future with probiotics, as you probably do as well!

Dr. Brown: Very much so! Always happy to help educate on a topic which I enjoy as much as this one!


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The information provided is for educational purposes only. Consult your physician or healthcare provider if you have specific questions before instituting any changes in your daily lifestyle including changes in diet, exercise, and supplement use.

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