Modern Medicine May Not Be Doing Your Microbiome Any Favors

This is a wonderful interview with Dr. Martin Blaser, expert on the human microbiome. If you want to have a basic understanding of how bacteria support our immune system, listen to or read this interview between Dr. Blaser and Terri Gross on

There are lots of theories about why food allergies, asthma, celiac disease and intestinal disorders like Crohn’s disease have been on the rise. Dr. Martin Blaser speculates that it may be connected to the overuse of antibiotics, which has resulted in killing off strains of bacteria that typically live in the gut.

Blaser is an expert on the human microbiome, which is the collection of bacteria, viruses, fungi and other microbes that live in and on the body. In fact, up to 90 percent of all the cells in the human body aren’t human at all — they’re micro-organisms.

Blaser is the director of NYU’s Human Microbiome Program and a former chairman of medicine there. His new book is called Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues.

He tells Fresh Air’s Terry Gross that with the overuse of antibiotics, as well as some other now-common practices like cesarean sections, we’ve entered a danger zone — a no man’s land between the world of our ancient microbiome and an uncharted modern world.

Interview Highlights

On why he thinks the number of diseases has risen

Since World War II, we’ve seen big rises in a number of diseases: asthma, allergies, food allergies, wheat allergy, juvenile diabetes, obesity…. These are all diseases that have gone up dramatically in the last 50 or 70 years. One of the questions is: Why are they going up? Are they going up for 10 different reasons, or perhaps there is one reason that is fueling all of them.

My theory is that the one reason is the changing microbiome; that we evolved a certain stable situation with our microbiome and with the modern advances of modern life, including modern medical practices, we have been disrupting the microbiome. And there’s evidence for that, especially early in life, and it’s changing how our children develop.

On the potential link between antibiotics and obesity

We have experiments in mice where, since we’re very interested in obesity, if we put mice on a high-fat diet, they gain weight; they get fat. If we put them on antibiotics early in life, they also get fat. If we put [them] on both together, they get very fat. … It’s clear that the effects of the antibiotics potentiate the effects of the high-fat diet. We’re not letting [the] high-fat diet off the hook, we’re saying that there’s another factor there. …

There’s a choreography; there’s a normal developmental cycle of the microbiome from birth over the first few years of life, especially the first three years, [that] appear[s] to be the most important. And that’s how nature has, how we have, evolved together so that we can maximize health and create a new generation, which is nature’s great purpose. And because of modern practices, we have disrupted that. And then the question is: Does that have consequence[s]? Our studies in mice show that it does have consequences. We’ve done epidemiologic studies in people that show that some of these modern practices are increasing the risk of obesity as well.

On how the birth process informs a baby’s microbiome

As far as we know, when the baby is inside the womb it is apparently sterile. … The big moment of truth is when the membranes rupture, the water breaks, and the baby starts coming out. And that’s where they first get exposed to the bacteria of the world, and the first bacteria they’re exposed to is their mother’s bacteria in the birth canal. So as labor proceeds, the babies are in contact with the microbes lining their mother’s vagina and, as they’re going out, they’re covered by these bacteria. They swallow the bacteria; it’s on their skin. …

That’s their initial exposure to the world of bacteria. That’s how mammals have been doing it for the last 150 million years, whether they’re dolphins or elephants or humans. … And we know a little about what those bacteria are. The most common bacteria are lactobacillus and there’s evidence that over the course of pregnancy the microbiome in the vagina changes, just as many other parts of the body are changing. The microbiome is changing in its composition in terms of maximizing lactobacilli, and these are bacteria that eat lactose, which is the main component of milk. So the baby’s mouth is filled with lactobacilli. The first thing that happens is they go up against their mom’s breast and they inoculate the nipple with lactobacilli and now milk and lactobacilli go into the new baby and that’s the foundation for their microbiome and that’s how they start their life. …

You could project that if they didn’t acquire these organisms or they didn’t acquire them normally or at the normal time, then the foundations might be a little shaky.

On a study comparing the microbiomes of babies born via C-section and those born vaginally

Shortly after birth, they compared the microbiomes in the babies that came out. The babies that were born vaginally, their microbiome, not surprisingly, looked like the mom’s vagina everywhere in the body — in their GI tract, on their skin, in their mouth. But the babies born by C-section, their microbiome looked like skin and it didn’t even necessarily look like the mom’s skin, maybe it was somebody else in the operating room. So it’s clear that the microbiome is different immediately depending on the kind of birth.

There have been more and more epidemiologic studies asking the question, really for the first time: Are there long-term health consequences of being born by C-section?

On how the microbiome can determine a person’s immunity and allergies

I’m concerned that the microbiome is part of our whole developmental process and if we disrupt it early, there are potentially consequences. …

What I can tell you is that our immune system is quite complex. There are many kinds of immune cells. There are cells that strongly recognize foreign substances, there are ones that try to damp [the immune system] and down-regulate it. There’s what we call innate immunity, which is the immunity we’re all born with, and then there’s adaptive immunity — the immunity that develops when we experience different kinds of exposures. So it’s very complex.

It’s developing early in life. That’s what sets, in essence, [the] immunological tone that will determine how allergic a person is, or how stoical a person is in an immunologic sense.

On probiotics

There are many different probiotics. If you go to the grocery store, the health food store, the drugstore, there are shelves and shelves full of probiotics [with] different names, different compositions. I think I can say three things: The first is that they’re almost completely unregulated; second is that they seem to be generally safe; and third is that they’re mostly untested. …

Right now, it’s the Wild West. I’m actually a big believer in probiotics; I think that’s going to be part of the future of medicine, that we’re going to understand the science of the microbiome well enough so that we can look at a sample from a child and say this child is lacking such-and-such an organism and now we’re going to take it off the shelf and we’re going to give it back to that child. … Just as today the kids are lining up for the vaccines, in the future, maybe the kids are going to be drinking certain organisms so that we can replace the ones that they’ve lost.

Energy of the Year of the Wood Horse: A Time for Positive Change

I know that Chinese New Year was in February, but while we are still in spring (associated with the liver and wood energy), I wanted to post this description of the energy of the Year of the Wood Horse that we are now in.  It is a great year to get things done and to make positive change!  See this exerpt below from Ling Gui International Healing Qigong School.

We now step into the Year of the Wood Horse. This Horse year carries the potential to channel the upward movement of Wood Qi  through the Heart Qi of Fire and into every new beginning we reach for. The Horse is the animal that represents endurance and the term “Qianli Ma” (a horse that covers 500 li per day – 1 li is 500 meters) is often used to designate an able person and represents the energy of this year. With that said, this is the best year for making unremitting effort to create healthy habits in all aspects of life. In order to do this we must look first at our foundation: health and Qi level.

Your Gut: Why You Should Be Very Afraid

We think it’s so easy — just take that probiotic to make up for whatever damage might have happened from the prescription antibiotic your doctor gave you, and you’ll be fine, right? And that antibiotic — you hear about antibiotic resistance, but you take it correctly, and you really needed it for that sinus infection, so it’s not that big of a deal either, right? You’re wrong in ways that you can’t possibly imagine and that should make you very, very nervous.

The World Health Organization has started to use the phrase “The Post-Antibiotic Era” to describe our current period of time. In September 2013, the Centers for Disease Control issued its first solid numbers regarding antibiotic resistance. It estimates at least 2 million Americans fall ill to antibiotic-resistant infections and between 23,000 to 100,000 people die from them every year. There are 23 known bacteria that are COMPLETELY resistant to anything we throw at them and that number is, of course, climbing.

This resistance has occurred for a couple of reasons: one is, the CDC says that 50 percent of the prescriptions written for antibiotics are unnecessary or inappropriate (for example, when a broad-spectrum antibiotic is given when a culture isn’t taken to determine a more targeted drug), and two, because 80 percent of available antibiotics are actually given to animals in confined feed lots (which might make you decide to buy grass-fed, or at least, antibiotic-free meat). Roundup® glyphosphate, found in conventionally raised farming, has been shown to have an inhibitory effect on food microorganisms  and suppress beneficial bacteria in the gut.

You probably have no idea how ineffective antibiotics are for the things they’re prescribed for most often. They’re not effective for bronchitis, sinus infections or ear infections. They are incorrectly prescribed in 80 percent of strep infections. And, of course, they are often given for the common cold or the flu, despite the fact that those are both viral, because either the patient demands a prescription, or because the doctor wants to prophylactically prevent a secondary bacterial infection. Think about all the times in your life you’ve taken an antibiotic — it’s most often for respiratory conditions and yet are the least effective. The person who says, one or two months after his sinus infection, that he’s gotten another one, probably has the same infection that wasn’t properly handled or was resistant to medication. When people feel better taking an antibiotic, it’s often just because of a reduction in the pathogenic bacteria, not because it’s actually killing them off, and it’s been shown time and time again that taking an antibiotic only reduces your illness time by a day or two. “But that’s a lot!” you cry. However, if you knew, though, that taking that antibiotic might PERMANENTLY damage your gut flora, or cause other bacteria to become resistant, you might pause, or possibly decline taking that medicine. And it’s now been found that bacteria “talk” to each other, and convey resistance to medications. Yes, that means bacteria are passing on antibiotic resistance to other bacteria.

The biggest problem is, our gut flora can’t take this abuse. Let’s start with some basics that will explain why this is potentially such a problem. You inherit your gut flora from your mother in a vaginal birth and continue to populate your gut with different strains from the air, food, soil, etc., until the age of two, when it’s “set.” Going back to your mother, how healthy was her gut flora? How many antibiotics did she take in her lifetime? How about your grandmother? We’ve had antibiotics for 80 years now and while there’s no doubt that they’ve saved a lot of lives, there’s no doubt they are less and less effective, and the collective damage to gut flora is irreparable. Add in the high Caesarean section rate, and you can begin to get an idea that our gut flora is currently the weakest in human history. Studies are showing that babies born of C-sections have higher rates of Celiac disease, autoimmune disorders like Type 1 diabetes and obesity.

Our gut flora outnumbers our body cells by 10-to-1. Yes, we’re only 10 percent human. The Human Microbiome Project is attempting to distinguish all the different actions and functions of the gut flora, but to give you some idea on this:

■ It is estimated that 70-90 percent of your immune system resides in your gut. Autoimmune diseases have been directly linked to imbalances in gut flora, and Celiac disease has been directly linked to dysbiosis. We had, a patient in her 60s who got debilitating Celiac disease after a single round of antibiotics and another who improved his ulcerative colitis 80 percent by not washing the vegetables from his garden.

■ Gut bacteria are responsible for B vitamins, vitamin K and the production of amino acids and fatty acids.

■ It is now being thought that gut microbes, along with some of the inflammatory foods we’re eating, like junk food and bad fats, make endotoxins, which are one of the root causes of inflammation. Rats with no gut microbes can eat any amount of “bad” foods and not gain weight or have inflammation, but when given gut flora, immediately develop high levels of endotoxins, and the resulting inflammation. And those endotoxins? Huge contributors to leaky gut syndrome.

■ Your gut has the same number of neurons as your spinal cord, and about 95% of your body’s serotonin is produced in the gut, as well as many other neurotransmitters. It almost seems odd, then, to have prescriptions for SSRI medications and never actually deal with what might be happening in the gut.

■ Your gut flora individuality is like a fingerprint, in that it’s different for everyone. That being said, diversity is the key to health, in regards to microbes, and if you don’t have diversity, or you don’t have the right type of bacteria, it leaves you open to a host of diseases, including obesity. It’s this diversity of your gut, not just the number of bacteria, which seems to be key to staying healthy. First world children have less diversity than third world children, with corresponding levels of asthma and allergies, and even though rural third-world countries have greater exposure to infectious diseases and lower life expectancies, they also have much lower rates of overall degenerative and chronic diseases.   The use of antibiotics is what’s frightening — they don’t just deplete gut bacteria, but can actually permanently wipe out whole strains. Scientists are now going into remote areas of the Amazon and collecting gut bacteria from tribes that have never been exposed to Westerners, antibiotics or modern foods, and are finding that a pristine microbiome not only has huge diversity, including species never before sequenced.

Of course, how we have tended to look at bacteria is a “good” versus “bad” scenario, but it is much more complicated than that. First, everyone has pathogenic bacteria in their gut, but they are often kept under control by adequate amounts of beneficial bacteria. Take an antibiotic, however, wiping down or out our good guys, and the bad guys can flourish, leading to deadly Clostridium difficile infections, for example. Or take Helicobacter pylori, which we’ve been trying to exterminate since 1983, when it was linked to peptic ulcers. But it’s also been shown that H.pylori regulates acid in the stomach — when people eliminate their H.pylori, they have less peptic ulcers, but higher rates of acid reflux, Barrett’s esophagus, and esophageal cancer, rates of which have soared since we’ve been eliminating H.pylori. It also calms the immune system (populations with higher H.pylori have lower rates of allergy and asthma), and regulates ghrelin and correspondingly, metabolism — obesity related to low H.pylori levels is currently being investigated.

What happens if you wipe out your home team so badly it can’t recover? The symptoms can range from chronic, debilitating diarrhea, to malnutrition, anemia, systemic infections, and death. When faced with a pathogenic infection as a result of taking antibiotics, most doctors employ the very method that got the patient in trouble in the first place — antibiotics — but what is becoming a quickly developing (and more effective) treatment are fecal transplants. A fecal transplant takes the gut bacteria from a healthy person and introduces it to the sick person, often with shockingly dramatic improvements. In a study done with patients who had a C. difficile infection and never properly recovered (most had over 150 days of incapacitating diarrhea), a fecal transplant reversed their symptoms in 24 hours, on average, with a total cure rate of over 90 percent. In fact, they halted the study because it became unethical to withhold such a successful treatment to the control group.

The problem is, you can’t actually replace what you’ve lost. We’re under the mistaken impression that you can simply take an antibiotic, and then follow with a probiotic and your gut will be completely back to normal, but that’s not what being seen in research. Even fecal transplants, with their dramatic impacts, simply buy time for the home team to recover. Probiotics, as well, help to keep the “bad guys” in check, but don’t replace lost strains. If my system got “flushed out” with some food-poisoning diarrhea, for example, I might use a probiotic pill to help my gut out while it repopulates, but when someone has to rely on probiotic pills for their digestion to be “normal,” that’s an indication that there’s some dysbiosis/dysfunction in their gut. Taking higher and higher amounts of probiotics isn’t great either — buying one with insane amounts of Colony Forming Units (CFU’s) can cause dysbiosis as well. And, of course, there’s no probiotic that is specific for your individual microorganism makeup.

Prebiotics, like the oligosaccharides found in vegetables and whole grains, as well as in breast milk (to encourage gut flora growth in a baby) are like food and housing for your home team — they encourage your native flora to grow. Focusing on good prebiotics, as well as severely reducing foods like sugar and bad fats (which cause that inflammatory reaction with the gut flora and can encourage dysbiosis) would be a better plan of action. “What if I take my home team and cultivate them in a Petri dish for sometime in the future?” I sometimes get asked. That doesn’t work either — when implanted back into the gut, your original “home team” bacteria don’t survive long enough to reinoculate.

This is where the impact starts to hit people — when we begin to realize that we’re destroying the biggest and most complicated “organ” we have from sheer lack of understanding. In labeling bacteria “good” and “bad”, we’ve sanitized our houses, our skin, our bodies, and our kids, and the result is a confused and weakened immune system, obesity, neurological dysfunction, chronic diseases, and more modern, deadly diseases.

It was after all this research that I began to see that I would literally have to be dying to take another antibiotic. It makes more sense to keep my immune system strong, and use herbs and nutrition to fight infections if necessary, while in the meantime to regularly eat the traditional foods that gave us a little probiotic help — fermented foods like sauerkraut, kimchi, kombucha, lacto-fermented vegetables, etc. It’s not just the specter of antibiotic resistance that should scare people silly, it’s also the depletion of their own gut flora and the resulting physiological damage for following generations that might make you, or your now-educated patients, choose differently the next time they’re in the doctor’s office.

By: Marlene Merritt, DOM, LAc, ACN