Modern Medicine May Not Be Doing Your Microbiome Any Favors

Transcript

TERRY GROSS, HOST:

This is FRESH AIR. I'm Terry Gross. There's a lot of theories about why food allergies, asthma, celiac disease and intestinal disorders like Crohn's disease have been on the rise. My guest, 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 microbe biome, which is the collection of bacteria, viruses, fungi and other microbes that live in and on the body. In fact, about 70 to 90 percent of all the cells in the human body aren't human at all; they're microorganisms.

Blaser is the director of the Human Microbiome Program and former chair of medicine at NYU. And he's the former president of the Infectious Diseases Society of America. His new book is called "Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues."

He says that with the overuse of antibiotics, as well as some other now-common practices like Caesarian sections - he'll explain the connection a little later - we've entered a danger zone, a no man's land between the world of our ancient microbiome and an uncharted modern world.

Dr. Martin Blaser, welcome to FRESH AIR. So when there are imbalances in the microbiome, things can go wrong, and you say that scientists now are beginning to think that some of what's often described as the modern plagues of medicine today, that some of those might be caused by imbalances of these microbes. So what are the, quote, "modern plagues" that you're talking about?

MARTIN BLASER: Yeah, and that's a good place to start. Since World War II we've seen big rises in a number of diseases: asthma, allergies, food allergies, wheat allergy, juvenile diabetes, obesity, autism. These are all diseases that have gone up dramatically in the last 50 or 70 years. And one of the questions is: Why are they going up?

Are they going up for 10 different reasons? Or perhaps there's one reason that's fueling all of them.

GROSS: And your theory is that one reason might be the microbiome?

BLASER: 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. That's my big theory. That's what I expound in the book.

GROSS: Well, I will say that people who are involved in environmental issues think that it's, you know, toxins in the environment that are causing a lot of these, you know, quote, modern plagues; and people who deal with food and nutrition issues think that it's, like, you know, bad nutrition and, you know, fatty foods and fast food, empty calories that's causing a lot of today's modern plagues.

And your specialty is the human microbiome, and you think it's that. So you know, I just wanted to point that out to everybody; everybody thinks it's from their field, yeah.

BLASER: I don't discount those, and in fact nothing says that causation has to be exclusive.

GROSS: Right.

BLASER: Causation could be additive. And in fact we have experiments in mice where, since we were 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. And if we put them on both together, they get very fat. And we've done this in male mice. We've done this in female mice. It's clear that the effects of the antibiotics potentiate the effects of the high-fat diet.

So it's not - we're not letting high-fat diet off the hook. We're saying there's another factor there.

GROSS: Well, that's really interesting, and why would antibiotics contribute to obesity?

BLASER: Yeah, well, I'm very glad you asked that question. We've been interested in this for more than 10 years, and it began with the - all of a sudden the light bulb went off. We know that farmers have been feeding antibiotics to their farm animals, to their livestock for almost 70 years. And the reason they do that is that it promotes their growth. They grow bigger faster. They use their food more efficiently to convert food calories into body mass.

And one day I thought, well, if farmers are using antibiotics to promote the growth in their livestock, is it possible that the antibiotics we're using in children are doing the same thing? And that's why we began to do studies in mice.

GROSS: Now, I thought the antibiotics in farm animals were being used to prevent them from getting sick because they're - in factory farming the animals are so close together, it's a very unhealthy situation, and it's easy to get sick, and then it's easy for disease to spread.

BLASER: Yes, that's true that it is - that just as you say, because they're close together, there's a lot of contagion. But the reason that the farmers are using the antibiotics is to promote growth. And again, there's a literature going back to the 1940s that shows that the use of sub-therapeutic antibiotics, these aren't therapeutic levels, these are sub-therapeutic levels, they're efficient at increasing growth.

And in reality the farmers and the farm scientists figured out a lot of this stuff years ago, and in one sense we're rediscovering it because the question is: Why should it work? Why does that work? And then it brings us back to the microbiome and the idea that 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 appear 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? And 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.

GROSS: You mentioned that the microbiome is developed during the first three years of life. And there's something you write about in the book that just, I hadn't heard this before, I found it so interesting, that when the baby passes through the birth canal that it develops some of its microbiome. I want you explain that.

BLASER: So as far as we know, when the baby is inside the womb, it is apparently sterile. There are some people who actually question this, too, but 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 are 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. There are a soup of these bacteria. That's their initial exposure to the world of bacteria.

GROSS: And you're saying that's a good thing, that's an important thing.

BLASER: Well, that's how mammals have been doing it for the last 150 million years, whether they're dolphins or elephants or humans. And that's how it's been done, and we know a little bit 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.

GROSS: And what - does the lactobacilli have a protective function?

BLASER: People have been studying lactobacilli and bifidobacteria, that's another class or organisms the baby gets from their mothers. But there's been a lot of study for many years showing many different beneficial effects, and these are the foundation of the microbiome that then gets later built on as babies experience more and more organisms.

And so you could project that if they didn't acquire these organisms, or if they didn't acquire them normally or at the normal time, then the foundations might be a little shaky, and that's exactly what - one of the points that I've proposed.

GROSS: So you're proposing that Caesarian births might compromise the microbiome of the baby?

BLASER: Well, actually, a very important study was done by Maria Gloria Dominguez and Rob Knight, and I think it's particularly important because Gloria is my wife. She did a study of moms who had C-sections or moms who gave birth vaginally, and shortly after birth, they compared the microbiomes in the babies that came out.

And 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.

GROSS: So it's different, but we don't know for sure what that difference means?

BLASER: We don't know what that means, but 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? We did a study in England, a cohort of more than 10,000 children was enrolled in the early 1990s in which the investigators followed these kids for a number of years, took lots of measurements, and we asked the question, was there a different in how - their rate of getting fat or getting obese when they were three, seven, 15, whether they were born by C-section or vaginally.

And our studies showed that kids born by C-section were more likely to have increased fat than the other kids. And this is one of four studies that has appeared in the last two years showing exactly the same thing: in Boston; our study in England; a study in Canada; a study in Brazil, all showing the same thing.

GROSS: So you mention a very do-it-yourself kind of compensatory procedure of using cotton gauze. Would you explain that?

BLASER: Well, this was actually - this was my wife Gloria's idea, and that is that if babies born by C-section are deprived of the natural microbiota that they would have gotten through birth canal delivery, why shouldn't we restore that? And so she's done - she's conducting an experiment, it's been approved by the Institutional Review Board, in which she has three groups of mothers: vaginal birth; C-section birth; and then C-section with a swab in the vagina. Now when the baby is born, the baby gets swabbed with this cotton swab with vaginal content so as to restore that which has been missed by the C-section.

GROSS: It's too soon to see what the results are, right?

BLASER: She's just analyzing the data now, and she's going to present this work at a big national meeting next month.

GROSS: If you're just joining us, my guest is Dr. Martin Blaser, and he studies the role of bacteria in human disease. He's the director of the Human Microbiome Program at NYU and the author of the new book "Missing Microbes," which is about the human microbiome and the microbiome is the collection of microorganisms - bacteria, fungi, viruses and other microorganisms - in our body, some of which are very helpful, some of them not so much.

Let's take a short break, and then we'll talk some more. This is FRESH AIR.

(SOUNDBITE OF MUSIC)

GROSS: This is FRESH AIR, and if you're just joining us, my guest is Dr. Martin Blaser, and we're talking about the human microbiome, and that's the collection of microorganisms - bacteria, viruses, fungi and other microorganisms - that live in the body and perform a lot of functions in the body and sometimes get invaded by not-so-good microorganisms. His new book is called "Missing Microbes," and he's the director of the Human Microbiome Program at NYU and the former president of the Infectious Diseases Society of America.

You're concerned that women who are delivering a baby are often prescribed antibiotics. I assume that's to prevent infection, which can be, you know, deadly. What's your concern?

BLASER: Well, I have to go back a couple steps and go back to the beginning of the age of antibiotics, when people were dying of very awful infections and antibiotics were miraculous. I mean they were one of the great miracles of the 20th century, and my specialty is infectious diseases. That's - we love antibiotics. But because they were so miraculous, people said, well, let's just start using them for this, and let's use them for that.

And everybody thought if there's even a tiny bit of benefit, it's worthwhile using them, because no one thought that there was any biological cost to antibiotics. There might be some short-term effects, people thought. We knew that people got an upset stomach, or maybe they'd get a skin rash, but then when you stopped the antibiotics, everybody assumed that everything would just bounce back for normal.

But in fact there was essentially no data that that was correct, and we now have more and more data that it is not correct, that things do not bounce back to normal, and in fact why should they, because an antibiotic is a powerful agent that its job is to inhibit or kill bacteria.

So the antibiotic changes the composition that's present in the body, and some of the organisms will go down. Others will go up in compensation. And some of them will go down to zero. And when they go to zero, they don't come back. They're extinct.

GROSS: So relate that to giving a woman in childbirth or just after childbirth antibiotics.

BLASER: So there's a very serious infection of children called infection by Group B Strep. It's an important infection of newborns. And it was found that if you give - if women have Group B Strep in the vagina, or they're carrying it in their vagina or their gastrointestinal tract, if you give them penicillin just before the moment of birth, you can pretty much prevent Group B Strep infection.

So that was considered to be a great breakthrough. One of the problems is that to prevent any single case of Group B Strep infection, we have to treat about 200 mothers, and thus their 200 children as well. And so the question is, if there was even a little biological cost in those 200 women, it's possible that that could outweigh some of or all of the benefit of - in that one child in which it's prevented.

So everybody was looking at the benefit of the antibiotic but not really calculating the cost. And once you assume that there might be a cost, then you can begin to more accurately decide should we do this procedure or not, or should we improve our diagnostics, so instead of treating one in 200, maybe we should only treat one in 10.

GROSS: So are you concerned that if a baby is born without a kind of full and varied microbiome, either because of antibiotics or because it was a Caesarian birth, and again a lot of this is still very speculative, that if they're born without that full, varied microbiome, that they will never be able to develop it?

BLASER: What we know about development is that there are developmental windows that you have to go through, various stages, that it's not random. And there are just times. We know that for the - how tall kids become, for example, and we know that about their development of intelligence. And so I'm concerned that the microbiome is part of our whole developmental process, and if we disrupt it early, there are potentially consequences.

These are difficult to study in humans. You can study them through big epidemiologic studies, such as I described, or you can study them in experimental animals. And that's why we do a lot of work with mice.

GROSS: So you were describing your concern that if a woman during childbirth or an infant is given antibiotics, that might affect the baby's microbiome, and who knows how long that would last, the effects of that would last, maybe a short time, maybe forever, we don't really know yet. But you're concerned about the imbalance it would create.

A lot of children get ear infections, and as a result of the ear infections they get antibiotics. And for some children it's recurrent ear infections, which means more doses of antibiotics. What are your concerns about the ear infections and the antibiotics?

BLASER: So that's a very important issue because as you point out, ear infections are very common in children, and in the United States we're giving a very high percentage of these kids antibiotics every time they have an ear infection. And that's not the only way to practice medicine.

First, we know that most of those ear infections are not caused by bacteria at all; they're caused by viruses. And antibiotics don't work against viral infections. That's very clear. So one of the problems is that the doctor can't really easily distinguish between viral infections and bacterial infections. But to some degree they can.

And I want to contrast what we're doing in the United States with Sweden, where they have just as good health care and maybe people live even longer. In the U.S. the average child is getting about four courses of antibiotics by the time they're three. That's across the entire United States. Some kids are more, some kids are less.

In Sweden, instead of four courses, it's 1.4 courses. And by the age of 10 in the U.S., the average child has gotten between 10 and 11 courses, and in Sweden it's about four courses. So at every age they're using fewer antibiotics. And Swedes are not that biologically different from us, but the practice of medicine is different, and culturally it's different.

And here in the U.S. we know that we're overusing antibiotics, but every parent with their screaming child and uncomfortable child isn't willing to bite the bullet because they think that maybe the antibiotics could help them. But if...

GROSS: Understandably, I might say, you know.

BLASER: Yes, understandably, but if the antibiotics have cost, if every time you took an antibiotic perhaps it raised the risk in a child that they would get obesity or asthma or diabetes by one percent, and the risk is cumulative - and I'm just making up these numbers just to give an example - then maybe the mom would say, well, in that case maybe I should just wait a day or two and see if the baby's going to get well. And of course in most cases the baby does get well.

So we've been giving antibiotics based on benefit without thinking that there might be long-term costs. And if there are costs, then the whole equation changes.

GROSS: Dr. Martin Blaser will be back in the second half of the show. His new book is called "Missing Microbes." I'm Terry Gross and this is FRESH AIR.

(SOUNDBITE OF MUSIC)

GROSS: This is FRESH AIR. I'm Terry Gross back with Dr. Martin Blaser, author of the new book "Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues." Blaser speculates that the rise in chronic conditions like obesity, asthma, Crohn's disease, eczema and juvenile diabetes is connected to changes in the human microbiome, the collection of microorganisms that live in and on our bodies. Most of the bacteria in the human microbiome - including bacteria essential to digestion and immunity - live in the gut, where they're vulnerable to antibiotics. Blaser directs the Human Microbiome Program at NYU.

You're also asking if changes in the human microbiome might be contributing to the rise in allergies, like food allergies.

BLASER: Yes. Yes. Well, so the question is: Why does someone become allergic to a food? And why has the rate of food allergies increased so dramatically? Peanut allergies, when I was growing up, were very rare. Now they're pretty common. And even if you say that there's some over-diagnosis, still at their nubbin, these have increased tremendously. So why should someone become sensitized to the food they eat? It all has to do with the formation of the immune system, how the immune system to differentiates between self and non-self. And what's training the immune system is the early life microbiome that is setting the context under which immune development occurs.

GROSS: Explain that a little more for me, like how the bacteria and other microorganisms in my gut are out of balance, that that might lead to a food allergy.

BLASER: Well, part of what I'm going to say is speculation, because I don't know the exact mechanisms. But what I can tell you is our own immune system is quite complex. There are many kinds of immune cells. There are cells that strongly recognized foreign substances. There are ones that try to damp it down 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. And that's what sets, in essence, immunological tone that will determine how allergic a person is, or how, let's say, stoical a person is in an immunologic sense. That's the idea.

GROSS: Part of your concern in general is the, you know, the overuse of antibiotics. And as you point out in the book, sometimes it's hard to tell. It's hard for a doctor to tell whether an infection is caused by a virus or bacteria. So I'm going to use myself as an example right now. I have a cold. My colds sometimes end in laryngitis. And my past history shows that sometimes - not always, but sometimes - like if I'm running a low-grade fever and I have a cold and I'm losing my voice, an antibiotic is really going to be helpful. But maybe that's just coincidence. Who knows? But the doctors don't seem to have a definitive way of knowing, you know, if my cold or your cold or anyone's cold is bacterial or viral unless they do a test that, you know, most doctors I think don't do.

I mean, I know they can - if you have the symptoms, they'll find out if you have strep throat or not, and strep is a bacteria. So that would be definitive. But I'm just wondering why - why isn't there like an easier test to determine, for instance, whether what I have is viral or bacterial?

BLASER: Yeah. So, a wonderful, important question...

GROSS: Especially for me now.

(LAUGHTER)

BLASER: Yeah, especially for you. But I want to first say that, as far as I know, you're not three years old. So there are two scenarios that are important. One is the infections of young children while they're developing, and the other is infection in adults, who are fully developed. And my biggest concern is about development.

GROSS: Mm-hmm.

BLASER: But now let's turn to you.

GROSS: OK.

BLASER: And that is that, actually, a lot of technology exists so that we could tell you what's the cause of your infection right now. But it's very expensive, and there's just no medical necessity or rationale for it, because in general, your cold is going to get better 95 times out of 100. And what you know is that when you take the antibiotic, the next day you feel better. But what you don't know is what would have happened if you didn't take the antibiotic. And in many - there have been studies of people with conditions like you, and in most cases, the antibiotic effect is zero or marginal. So, again, our custom is to treat with antibiotics.

I want to bring up a point that might be of interest to you that bears on this question. And that is that last year, the CDC published a survey of antibiotic use in the United States. And what they found is that in 2010, there were 258 million courses of antibiotics prescribed. And in our country, that comes out to 833 courses per thousand population, or about five courses for every six people. And from talking to the investigators at the CDC, this seems stable over a period of years. So our use of antibiotics is enormous. What was particularly interesting to me was the regional differences in antibiotic use. In the North and in the Midwest, it was about at the national average. In the West, it was way lower than the national average. It was about 630. And in the South, it was way higher. It was about 930. So between the West and the South, there was about a 50 percent difference in the prescribing of antibiotics.

And I can tell you, as a specialist in infectious diseases, there is not a 50 percent difference in the rate of serious bacterial infections. So this difference in usage is a difference in culture and practice and expectations. And I think that's part of what we're up against.

GROSS: So can you explain why it's so expensive to determine whether my cold is caused by a bacteria or a virus, or whether babies ear infection is caused by a bacteria or a virus? Considering the strides that we've made in medicine, it seems like that shouldn't be that big a deal. You know, you culture it. You look under the microscope and you see which it is. But apparently, it's not that simple.

BLASER: Well, the technology is there, it just hasn't been employed because it's never been a necessity. If you give every child - when a child comes in with some kind of upper respiratory infection, the chance that they'll walk out of the doctor's office with an antibiotic is 70 to 80 percent, and that's improved over what it used to be. So there's no economic necessity driving it, and so we haven't really employed the technologies that we have available and produce them on a mass level and try to get economies of scale. But I think we should. I think we need - we've been living under this antibiotic umbrella, which has many very positive effects. But I'm concerned about the hidden long-term effects. And once we start to accurately count them, then we're going to have to start cutting back on antibiotic use, and therefore, we're going to have to develop much better diagnostics and we're going to have to use those diagnostics.

And I think we're going to - the main thrust of antibiotic research in the last 50 years has been making broad spectrum antibiotics. So if somebody - if a child comes in with an ear infection, you can treat him with a certain antibiotic, and you know that it will cover all the important bacteria. But I think we should have diagnostics that will say, first, is it viral or bacterial? And if it's bacterial, which bacteria is it? And then the doctor can pull that agent off the shelf and say, OK, I'm with you treat your MafA(ph) infection just with a MafA-specific antibiotic so it won't do any collateral damage. We don't have those agents yet, but it wouldn't be that hard to develop them. The major issue right now is cost.

GROSS: If you're joining us, my guest is Dr. Martin Blaser, and he is an expert in the role of bacteria and human disease. He's the director of the Human Microbiome Program at NYU, the former president of the Infectious Diseases Society of America and author of the new book "Missing Microbes." And the book is about the human microbiome, and that is the collection of microorganisms, bacteria, viruses that live on or inside the body.

Let's take a short break, then we'll talk some more. This is FRESH AIR.

(SOUNDBITE OF MUSIC)

GROSS: This is FRESH AIR. And if you're joining us, my guest is Dr. Martin Blaser, and he studies the role of bacteria and human disease. His new book is about the human microbiome, and it's called "Missing Microbes." And the microbiome is the collection of bacteria, viruses and other microorganisms that live on or in the body.

So, Dr. Blaser, I have a cold right now, and I have been trying to use the antibacterial cleanser on my hands so I don't infect the people I work with. You're going to advise me not to do that?

(LAUGHTER)

BLASER: Yeah. You know, I don't know the specifics of your case, and that may not be a bad idea. It's a little hard for me to judge. But people who are perfectly healthy are using these antibacterial materials every day, and by the million. And we just don't know the consequences. Maybe the consequences are trivial. Maybe there are no consequences. But we're doing it on such a scale. We should know.

And my concern is that all the things we're doing are cumulative. We can't just look at them in isolation, but that kids are born by C-section. Moms get antibiotics during pregnancy. Kids are born by C-section. Kids are getting antibiotics when they're young. When they're older, they're in an antibacterial environment. My concern is that we are changing normal human development, development of our microbiome that has been going on since time immemorial. And in particular, we've been studying an organism that lives in the stomach called Helicobacter pylori - which we call HP just for short - which, as far as we know, has been present in humans since before we were humans, and over the course of the 20th century, it's almost completely disappeared.

GROSS: It's disappeared? Well, what is it, first of all?

BLASER: Helicobacter pylori is a bacteria that lives in the human stomach. And it's well known, because in the 1970s, two scientists in Australia found it in the stomach, and they tied the presence of this organism to ulcers. And they showed that if you treat people who have ulcers, to get rid of this bacteria, you can cure the ulcers. That was a huge breakthrough, and in fact, they won the Nobel Prize for their finding of the bacteria and its relationship to ulcers. And so, ever since then, we've been thinking about this organism as a bad organism, as a pathogen, and many doctors are trying to eliminate it from everybody. But, in fact, the bacteria has been disappearing over the course most of the 20th century, and we know this from a variety of different sources, even before the introduction of antibiotics. But antibiotics are certainly making it worse.

And as the organism is disappearing, ulcer disease is going down, stomach cancer is going down. That's all very good news. But other diseases are going up, like diseases of the esophagus, one disease that's called reflux or GERD, reflux esophagitis. And then there's a cancer of the esophagus, which is the fastest increasing cancer in the United States and other developed countries. So the loss of Helicobacter appears to be very good for the stomach, but it also appears that it's bad for the esophagus. So we can't have - at this point, we can't have it both ways. And there's evidence that the loss of Helicobacter may be fueling the rise in childhood onset asthma, as well, both from epidemiologic studies that we've conducted and others, and also from experimental studies in mice that show the same thing.

GROSS: What about the spread of MRSA, Methicillin-resistant Staphylococcus aureus? It's a resistant strain of bacteria that often lives in hospitals and other, you know, like nursing homes and medical institutions, C. difficile, which is also an increasingly resistant strain of bacteria that people often catch in hospitals and other health institutions, and it causes severe gastrointestinal upset that, in some cases, can even lead to death. What are your concerns about those resistant forms?

BLASER: Yeah. Yeah. So, I have a lot of concerns about them. I'm not the only one. The director of the CDC has issued a big report about this. The more you use antibiotics, the more likely you are to select for resistant organisms. MRSA is a staph aureus that is resistant to the common organisms. Clostridium difficile, or C. diff, is an organism that is resistant to many of the antibiotics that we use.

When they were first observed, they were found in the hospital, and which is not surprising, because that's where the greatest use of antibiotics are. But both of these infections have escaped the confines of the hospital. We're finding infections in people in the community who've never been to a hospital. They've lost their natural boundaries. So, you know, one of the questions is: why are they increasing so much? And part of it is all the antibiotics we're using that's selecting for them. But another possibility is that we're missing some of our Coast Guard, some of the organisms that help defend against them, and that's why they're spreading beyond their natural boundaries.

And these are two well-described examples, and I'm afraid of future examples, and especially ones that might be antibiotic resistant, so that when we need the antibiotics, they won't even be working, because there's so much resistance. The overuse of antibiotics has two very bad effects. One is that we're promoting resistance. The more we use, the more we're selecting for a resistant organism. We've seen this again and again, and this is not controversial. And, of course, the other is that we are depleting our normal organisms, which are part of our defense against invaders.

GROSS: So, this raises the question, you know, like we're so concerned about extinct animals, and even extinct insects in the environment causing imbalances in the, you know, ecological structure. Are you concerned, too, about extinction of bacteria in the human microbiome?

BLASER: I'm very concerned about extinction of bacteria in the human microbiome. I think this is a really critical issue. It's the microbiological equivalent of global warming, and that is that we are changing our microecology through practice, and that, I believe, is fueling the risk of these modern plagues, these epidemic diseases.

And I'm also afraid of something, which I've - in the book I've called antibiotic winter. That's a really very bleak scenario based on the knowledge that our normal organisms are protecting us against invaders. So if we've depleted our normal organisms, which there's more and more evidence is correct, and we're living in a smaller world where we're one or two days away from any village in the world, we are much more prone to epidemics and potentially very bad epidemics.

And without our normal resistance, without our coast guard to help guard our shores, and in this case our coast guard are our bacteria, that's in addition to all the chronic disease fears that I have, I'm also quite worried about, you know, a worldwide pandemic fueled by our lack of biodiversity.

We've seen it in cornfields. We've seen it in vineyards. We humans are not immune to that.

GROSS: You know, for animals who are endangered, there are animal refuges, and there are, you know, there are movements to protect endangered species and so on. Is there anything comparable going on with the microbiome, with bacteria that might be endangered?

BLASER: Yeah, so as you point out, we think that there are endangered bacterial species, that we have - that we people in the U.S. have much lower diversity than people who have not had the benefits of modern life. So my wife Maria Gloria Dominguez and myself and other investigators have been gradually studying peoples who have not been developed, people in the Amazon, people in the rainforest, people in different parts of Africa.

And we're obtaining specimens from these people to study them, and that's how we know that we have lost a lot of diversity in relation to them, but also to archive the organisms that they have so that perhaps we can use these as the way to reseed our human populations. And these people, of course, inevitably will modernize as well, and it will help reseed them as well. So we're trying to create an archive, a stockpile of these disappeared organisms, that is before it's too late.

GROSS: A lot of people now are taking probiotics, and probiotics are, you know, capsules or pills or liquids that have good guy bacteria in them, and the goal is to keep a healthy microbiome in the gut through the use of these probiotics, which is the opposite of antibiotics. Antibiotics kill bacteria. Probiotics are supposed to propagate good guy bacteria. How effective do you think they are?

BLASER: Well, of course there many different probiotics. If you go to the grocery store, the health food store or the drugstore, there are shelves and shelves full of probiotics; different names, different compositions. I think I could 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 about the important reasons even want to take probiotics, because they don't feel well, or they have particular symptoms.

There have been just a paucity of well-conducted studies of these. So 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.

I can imagine that there will be certain organisms that we'll give to most children. 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. Those will be the real probiotics.

GROSS: Well, let me ask you about something else, and that's fecal transplants, which we've been hearing more about lately, and that's the idea that if you want to create a more balanced microbiome in the gut of somebody who is totally out of balance and has gotten severely sick as a result, that you can take fecal matter from somebody with a healthy microbiome, transplant it into the person who's unhealthy, and the good-guy bacteria will start to take root. Thoughts?

BLASER: I'm really glad you brought this up. So as we discuss, there's this terrible infection caused by an organism that we call C. diff. It's also - the infection is also called antibiotic-associated colitis. What happens is that somebody takes antibiotics, and then this invader comes in, and it takes over, and in some cases you can remove it with antibiotics, but in other cases you can't, and it persists, and it persists, it relapses, and some people die from it. It can be a very severe infection.

And when we've studied the guts of such people, their intestinal microbiome is very disordered. And so doctors have found that if they can give the fecal materials from a normal person, they can cure these people from C. diff. So it's a very important proof of principle. It shows that if you have a very disordered microbiome, by bringing in a normal microbiome, you can cure them.

Now this is a very extreme condition, and it's very kind of circumscribed and well-defined, but it's a proof of principle that in other cases of disordered microbiome, we'll be able to introduce either fecal material or specific organisms. We would call those specific organisms probiotics. Those are the probiotics I'm talking about.

GROSS: My guest is Dr. Martin Blaser. His new book is called "Missing Microbes." More after a break; this is FRESH AIR.

(SOUNDBITE OF MUSIC)

GROSS: This is FRESH AIR. My guest is Dr. Martin Blaser. His new book, "Missing Microbes," is about how the overuse of antibiotics may be contributing to the rise of conditions like food allergies, asthma, obesity, Crohn's disease and eczema. He's an expert on the human microbiome, the collection of bacteria and other microorganisms that live in and on the human body but mostly in the gut.

So you've been very cautionary about the problems, long-term and short-term, individual and societal, that are being caused by the overuse of antibiotics and antibacterials. What are the two or three things you'd like us to do as individuals or as a culture to reverse that trend?

BLASER: Yeah, I mean, there's a whole list of things that we should do. Number one on the list is that we have to stop the overuse of antibiotics. We have to slow this down and try to use antibiotics more judiciously for when people really need them and not for convenience or for very marginal benefit. And it's clear that much of antibiotic use is for very marginal benefit.

And it's also clear that we could cut down on our antibiotic use dramatically and have no ill effects of health. But that means we have to take more time, perhaps we have to pay doctors so instead of seeing patients every eight minutes, they'd see patients every 15 minutes so they could have a little more time to think and to explain and to examine.

I think we need to develop narrow-spectrum antibiotics, not just broad-spectrum antibiotics, but really focused antibiotics. I think that the parent of the future, if you said, you know, we can give you broad-spectrum antibiotics, but it's going to cause a lot of collateral damage to our child's microbiome, or we can give you a narrow-spectrum one, it may cost you a little more, most parents will say I'll take the narrow-spectrum one if you know what the organism is.

So we're going to need to develop better diagnostics so we know exactly what it is. A lot of this technology is available, but it's not cost-effective. So we have to change the economics of health care for children in this country.

GROSS: When was the last time you took antibiotics?

BLASER: The last time I took antibiotics was about two years ago. I was in the Amazon, and I was in an area where there was a lot of malaria. And the prudent thing was to take antibiotics, and actually I only took it for part of the time because I have mixed feelings about antibiotics.

GROSS: Well, clearly you have mixed feelings about antibiotics. But I want to make sure we're leaving with the right message, which is that sometimes you really need antibiotics. You know, the goal is not to take them when you don't need them, but, like, take them when you need them, right?

BLASER: Yeah, well, so absolutely. When somebody's sick, there is nothing better than antibiotics. And actually in my book, I talk about when I got very sick after coming back from India, and I couldn't wait for the antibiotics because I was so sick. But it's not - the decision to take antibiotics isn't a person's decision. It should be the decision of their doctor, their health care provider.

They should make the decision who should take the antibiotic or not. And I'm speaking to doctors to talk to them about the cost of antibiotic overuse, as well, so that we can - by more careful evaluation, we could cut down on a lot of antibiotic use because the benefits are marginal. I'm not saying that people who are really sick shouldn't take antibiotics. In fact they must take antibiotics. But most of the cases are in that very gray area.

GROSS: Well, Dr. Martin Blaser, thank you.

BLASER: And thank you for having me on your show.

GROSS: Dr. Martin Blaser is the author of "Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues." You can read the first chapter on our website, freshair.npr.org. I'm Terry Gross. Transcript provided by NPR, Copyright NPR.