Advance Rutgers Podcast: Our Changing Microbiome

Christine Fennessy

Welcome to Advance Rutgers, a podcast about the many ways that Rutgers, the State University of New Jersey, is addressing the critical issues of our day. At Rutgers, we believe a better tomorrow starts with bigger thinking today. Our talented and driven community is improving the human condition with transformative, multidisciplinary projects. This podcast will explore those groundbreaking initiatives: what they are, why they matter, and who they benefit.  

Today’s episode is Part One in a two-part series about the Rutgers University Microbiome Program. It features Dr. Martin Blaser and Professor Gloria Dominguez-Bello. They’re co-founders and co-leaders of the program. They help us understand what our microbiome does for us, why it’s changing, and the impact that change is having on our health — specifically on the health of kids. 

The second episode in this two-part series will feature the Rutgers University Microbiome Program’s third co-founder, Professor Liping Zhao. He’ll explain the importance of dietary fiber in maintaining a healthy gut microbiome and what you can do to improve your own nutrition. Thanks for joining us.  

Dr. Martin Blaser started looking at antibiotic resistance decades ago, when he was working as an epidemiologist at the Centers for Disease Control. At that time, he learned that antibiotics were primarily used not in human medicine, but in agriculture. 

Marty Blaser

Seventy years ago, farmers discovered that if they fed antibiotics to their livestock, they would grow bigger and faster. 

Christine Fennessy

It worked for chickens, cows, pigs. And the earlier in life farmers started the antibiotics, the bigger the effect. One day, Dr. Blaser was talking to a student about obesity. 

Marty Blaser

I said, “Well, farmers feed antibiotics to their farm animals to fatten them up. And just as I’m saying that, a light bulb went off in my mind and I thought to myself: Well, I wonder if that’s what we’re doing to our kids — that by giving our kids antibiotics early in life, we’re fattening them up also. That was almost 20 years ago, and I’ve been working on this problem ever since. 

Christine Fennessy

That problem: the relationship between the human microbiome and diseases like asthma, diabetes, and obesity. Today, Dr. Blaser is one of the founders of the Rutgers University Microbiome Program and…  

Marty Blaser

I’m a professor of medicine and pathology and laboratory medicine at RWJ Medical School at Rutgers. I’m also the director of the Center for Advanced Biotechnology and Medicine at Rutgers. 

Christine Fennessy

And for those who might not know, RWJ stands for Robert Wood Johnson Medical School. But what is a microbiome? It’s the collection of microbes that live on or inside us. And microbes are the smallest living things and the oldest form of life on earth. 

Marty Blaser

Bacteria got here first, and every plant and animal that evolved on Earth had to take microbes into account. 

Christine Fennessy

Which means every organism has a microbiome: animals, plants, humans. Soil has a microbiome. So does air, the oceans, forests, even cities have their own microbiome. And in our bodies, we have distinct microbiomes: on our skin, in our mouth, in our gut. To date, researchers know the most about our gut microbiome, because it’s been studied the most. But what do all these microbes do for us? Dr. Blaser says we live in cooperation and sometimes in conflict with them. And our understanding of microbes has evolved over time. 

Marty Blaser

What happened is that it became clear that many of the important illnesses of humans were due to microbes, like tuberculosis, cholera, typhoid fever, and smallpox, and we can go on and on. And so, microbes got a bad name. Everybody thinks of them as germs. 

Christine Fennessy

He says there definitely are bad microbes. 

Marty Blaser

But the overwhelming number of microbes in the world are either neutral to humans or beneficial. 

Christine Fennessy

For example, he says, our human microbiome… 

Marty Blaser

…helps us digest our food. It makes vitamins for us. It trains our immune system. It offers a line of protection against invaders. 

Christine Fennessy

So the healthier our microbiome is, the healthier we are. And a healthy microbiome needs a huge range of microbes. That diversity gives our system redundancy. If a lot of microbes can do the same thing, like protect us from invaders, we can afford to lose some. Say, if we take an antibiotic that kills a particular bacterium off. Diversity equals stability. But that diversity? It’s disappearing. To Dr. Blaser, this loss is an existential issue, like climate change. 

Marty Blaser

Climate change, we could say, is humanity’s activities that are affecting our macro-ecology. But I think that we’re doing the same kind of damage to our micro-ecology. But it’s only become obvious more recently. 

Christine Fennessy

He says there’s more and more evidence that we’re losing our microbial diversity. And that extinction, as he calls it, may be contributing to diseases like asthma, diabetes, and obesity. But what’s causing this decline in microbial diversity? Dr. Blaser says there are many factors, and they can begin at birth. 

Marty Blaser

If we don’t have the right organisms to start with, we’re at a deficit. 

Christine Fennessy

We first acquire our microbiome inside the birth canal. 

Gloria Dominguez-Bello

When the mother breaks waters and the baby starts its way out through the birth canal, unfortunately for women, it takes hours where the baby’s exposed to this microbiota of the mother, swallowing it, getting it in the skin, in the nose, everywhere. 

Christine Fennessy

That’s Professor Dominguez-Bello. 

Gloria Dominguez-Bello

My name is Gloria Dominguez-Bello. I’m a Henry Rutgers Professor for Microbiome and Health. I’m also the director of the Institute for Food, Nutrition, and Health at the School of Environmental and Biological Sciences at Rutgers. 

Christine Fennessy

Among many other things, Professor Dominguez-Bello researches microbiome development from birth. She says that when babies are born vaginally, they’re heavily inoculated with the bacteria that colonizes the birth canal. But babies born via a scheduled C-section are not. 

Gloria Dominguez-Bello

When a baby’s born by a scheduled C-section — I have to clarify. Because if it’s an emergency C-section with labor, the baby has been exposed, the baby’s born colonized. But if the C-section is scheduled, the doctors have to break the sac, suck the water, and then take the baby out. That baby’s sterile.  

Christine Fennessy

Meaning it missed out on its first exposure: the natural transmission of microbes from mother to baby from the birth canal. 

Gloria Dominguez-Bello

The first exposure is to the air of the operating room, which is loaded with skin flakes, microscopic skin flakes, which have skin bacteria. 

Christine Fennessy

C-sections affect a baby’s microbiome in other ways, too. Because it’s a surgery, it exposes the child to antibiotics. (More on antibiotics in a minute.) Scheduled C-sections also delay breast milk production. And breast milk not only feeds the baby… 

Gloria Dominguez-Bello

It also has indigestible components like fibers. Milk fibers, I call them. 

Christine Fennessy

These fibers, called human milk oligosaccharides, feed bacteria in the baby’s colon. So among many other things, breast milk is also food for the microbiome. But with a scheduled C-section, the mother’s body doesn’t immediately know that the baby’s been born. 

Gloria Dominguez-Bello

The body needs to learn that the baby’s out and then start preparing the breast and all that. So it takes about 24 hours for the mom to produce milk. 

Christine Fennessy

She says most mothers don’t want to wait that long to feed their newborn. So they give the baby formula, which she says can affect its microbiome and impair latching of the baby to the breast.  

Gloria Dominguez-Bello

So C-section, in general, impairs lactation, makes it more difficult, and makes mothers give up and bottle-feed formula. 

Christine Fennessy

So babies miss out on the microbial bath they get in the birth canal, get exposed to antibiotics, and may end up being formula-fed. And that’s why kids born via scheduled C-section start life at a deficit when it comes to those good microbes. 

Gloria Dominguez-Bello

So it’s a complex intervention that greatly alters the first microbiota that a baby gets. 

Christine Fennessy

Both Professor Dominguez-Bello and Dr. Blaser, who are married, say C-sections and formula feeding are two significant factors contributing to the decline in microbial diversity. Other factors include chlorinated water, excessive use of antimicrobials, eating a low-fiber diet, and antibiotics — especially when these drugs are used early in life. Dr. Blaser says that’s because our microbiome forms when we’re very young. 

Marty Blaser

And by the age of three or so, it largely has an adult profile. So those first three years of life are really the most critical time for the development of the microbiome. 

Christine Fennessy

Antibiotics can wipe out or suppress beneficial microbes or cause harmful microbes to proliferate. And he says anything that perturbs the microbiome is going to have an ill effect. 

Marty Blaser

The altered microbiome is not in the same kind of partnership that the normal microbiome should be. Remember, the microbiome instructs our immune system. 

Christine Fennessy

So if our microbiome is out of whack, our immune system will be, too. Which can have profound implications when it comes to the development of disease. 

Marty Blaser

If a person gets a disease when they’re five years old or 10 or 20 years old, the question is: When did it actually start? 

Christine Fennessy

He says, for example, we know an important precursor for adult obesity is childhood obesity or a child who’s overweight. 

Marty Blaser

So the roots of many of our really important diseases begin early in childhood. 

Christine Fennessy

So if a kid’s microbiome gets perturbed by, say a scheduled C-section or too many antibiotics early in life, the microbiome gets knocked off its normal course of development. And because the microbiome instructs the child’s immune system, the immune system gets what professor Dominguez-Bello calls a bad education. It overreacts to things that aren’t real threats and that causes inflammation. 

Gloria Dominguez-Bello

And the underlying thing behind asthma, obesity, Type 1 diabetes, allergies ⁠— there is one thing that is underlying them all. And that is inflammation. Inflammation is an excessive response of the immune system. 

Christine Fennessy

She says that inflammation can cause a vicious cycle, because it can harm the lining of organs, like our mouth and gut, opening them up to bacteria, which causes even more inflammation. 

Gloria Dominguez-Bello

So it’s a chronic state of high inflammation, which is very bad for health. 

Christine Fennessy

“Very bad,” because that chronic inflammation eventually leads to chronic disease.  

So when it comes to antibiotics, how much do young kids typically get? Dr. Blaser says, according to the Centers for Disease Control, on average, by the time a child is two, they’ve had nearly three courses. By the time they’re 10, they’ve had 10 courses. 

Marty Blaser

So the exposure is enormous. Now, we’ve known for a long time that we are overusing antibiotics. But no one really put a stop to it, because they thought, “Well, it might not help, but it won’t hurt you.” But there’s increasing evidence that it will hurt. 

Christine Fennessy

He says studies have found associations between antibiotic exposure in the first two years of a kid’s life and disorders like asthma, allergies, obesity, and autism. 

Marty Blaser

The question that always comes up is, “Yes, you have shown an association between A and B. But does A really cause B?” 

Christine Fennessy

To answer that question, his lab does experiments on mice. They take two groups of animals identical in every way, except one group gets antibiotics. Dr. Blaser and his colleagues have found that mice given antibiotics had more body fat, decreased immunity, and more food allergies. For kids born via scheduled C-section, Professor Dominguez-Bello says it’s a similar situation. Observational studies have found higher rates of diseases, like asthma and Type 1 diabetes, in children born via C-section. 

Gloria Dominguez-Bello

These are associations. We can’t say that C-sections and formula cause the disease, because all we are doing is making a correlation. 

Christine Fennessy

So again, researchers turn to the mice. 

Gloria Dominguez-Bello

We have germ-free animals. So if you have a germ-free animal, you can give them human microbes. And then you can use the animal to inform you which human microbes are pro-inflammatory, are making the disease worse, or which ones protect. 

Christine Fennessy

She says if a microbe is anti-inflammatory in humans, it’s likely to be anti-inflammatory in mice. Once they know what type of microbe does what, they can ask questions like: Did the child have low levels of this protective microbe before the onset of disease? Or, did the child have high levels of the microbe that increases the disease risk? 

Gloria Dominguez-Bello

So those kinds of studies which are showing causation are extremely important, because we can really learn which kinds of microbes cause the disease or protect. 

Christine Fennessy

Professor Dominguez-Bello has also studied the potential for restoring the microbiome in babies born via scheduled C-section. It’s called vaginal seeding. And just a quick heads up, if you’re at all squeamish or listening with kids, we’re going to get a little detailed over the next 30 seconds or so.  

They put gauze inside a tampon and inserted it into the mother’s vaginal canal for one hour before birth. After the baby was delivered, they swabbed its mouth, face, and body. 

Gloria Dominguez-Bello

We gave the babies born by C-section vaginal fluids of their mothers, and then followed those babies for a year and studied their microbiome. 

Christine Fennessy

They wanted to know if they could restore the microbes the baby would’ve gotten in a vaginal birth. And… 

Gloria Dominguez-Bello

Are we making the microbiome more normal, closer to babies born vaginally? And the answer was yes. 

Christine Fennessy

Closer to normal, yes. Not a hundred percent. That might be, she says, because the babies were exposed to antibiotics as part of the surgery. And just to be clear, vaginal seeding is not a standard practice. 

Gloria Dominguez-Bello

The FDA actually is treating this like a new drug for newborns. And they have asked us to repeat the tests the week of the C-section, again, so that we are sure that what we are applying on the baby doesn’t cause any harm. So far, no babies ⁠— neither restored or non-restored ⁠— have had any problems, but we will continue doing the study.  

Christine Fennessy

She says the next step is a randomized clinical trial with a five-year, follow-up period to see what effect, if any, vaginal seeding has on the health of the kids.  

So, scheduled C-sections and early antibiotic use are decreasing a child’s microbial diversity and perhaps increasing their risk for chronic disease. What can a parent do? First, if you do have a scheduled C-section, Professor Dominguez-Bello says breast milk can help normalize your baby’s microbiome. 

Gloria Dominguez-Bello

Breastfeeding is a great help. Breastfeeding is a good restorer. If a mom has to have a C-section and cannot breastfeed, can she get human milk and give human milk to that baby? At least that’s closer to the most natural. 

Christine Fennessy

She says, of course, lots of kisses and hugs will help transfer all those good microbes too. She also recommends waiting on giving real food until your baby has developed the motor skills to put something to its mouth. 

Gloria Dominguez-Bello

When I had my daughter 30 years ago, I was told that I should give her soup at four months. I realize now that’s force-feeding a baby. That baby is not ready. It’s not asking. 

Christine Fennessy

When it comes to antibiotics. Dr. Blaser says, there’s no question they are miraculous drugs. But they come with a cost, so they must be considered carefully. 

Marty Blaser

And the purpose of the doctor is not to give you an antibiotic. The purpose of going to the doctor is for the doctor to do a careful examination and say, “Your illness is severe. You need an antibiotic.” Or, “Your illness is mild. You do not need an antibiotic.” 

Christine Fennessy

He applies the same approach to his own health. 

Marty Blaser

I try to take antibiotics only when necessary. I try to take the shortest course of antibiotics and the lowest dose that I need to take, because all of the effects are dose-related. 

Christine Fennessy

It’s important to note here: This is research. It’s not meant to judge or shame. There are so many reasons why women have to have or choose to have C-sections. And the same goes for formula feeding and antibiotics. Researchers like Professor Dominguez-Bello and Dr. Blaser are not shaming parents for their choices. They’re trying to learn from them, so that one day all kids get the best possible start to a healthy life. Ultimately, researchers like Dr. Blaser and Professor Dominguez-Bello want to know if a degraded microbiome can be restored — if good, health-promoting microbes that are absent or have been wiped out can be brought back.  

Dr. Blaser has studied the potential for restoration in mice. His team showed that if they gave the animals antibiotics, they could accelerate the rate at which the mice developed Type 1 diabetes. 

Marty Blaser

We’ve also shown that we can reverse it by giving back poop from moms, and we can bring them back to their baseline. So, this is some evidence that we can actually restore. 

Christine Fennessy

He says the goal is to develop similar methods that could work in humans. 

Marty Blaser

It could be that in the future, every time someone takes an antibiotic, maybe they’ve been storing their poop or somebody’s been storing their poop for them. And they’ll get that poop back, for example. 

Christine Fennessy

That poop would be what he calls “normal,” meaning a sample taken from the person before that person was ever exposed to antibiotics. And that sample would restore the good microbes that were wiped out or suppressed by the drugs. 

Marty Blaser

Or maybe it won’t be poop, but we’ll know: What are the key organisms in the poop for that person? And the doctor of the future will reach on to their shelf and take out those organisms. Those are what we might call probiotics. 

Christine Fennessy

But doctors can’t reach for those key organisms if they no longer exist. And that’s why Dr. Blaser and Professor Dominguez-Bello are so worried about the decline of microbial diversity. We could be losing some of our best medicine. Collecting, preserving, and studying that microbial medicine will be part of the mission of the Rutgers University Microbiome Program, also known as RUMP. 

Marty Blaser

It’s a little facetious, but people remember the name. 

Christine Fennessy

The program will focus on research, education, clinical care, technology transfer, community outreach. And it will also focus on sustainability and conservation. Because according to Professor Dominguez-Bello, the greatest microbial diversity is found in traditional hunter-gatherer societies. She and her team have found that the more urban you are, the lower the microbial diversity, especially in your gut. 

Gloria Dominguez-Bello

When we compare U.S. people to people in the Amazon that have very little contact with Westerners, we have half of their diversity. 

Christine Fennessy

Westerners also have more chronic diseases. But urbanization is coming [to other areas of the world], she says. And as these societies integrate into urban areas with their C-sections, antibiotics, antimicrobials, and processed food diets, we may lose that diversity forever. 

Gloria Dominguez-Bello

So we started an initiative, called the Microbiota Vault, to preserve microbiomes — human and environmental microbiomes that are important for humanity. 

Christine Fennessy

Her inspiration for the initiative came from the Svalbard Global Seed Vault in Norway. It’s a long-term seed storage facility for every important crop on Earth. It’s an insurance policy of sorts for the world’s food supply. The Microbiota Vault will gather and preserve microbes from communities still untouched by urbanization. The vault will eventually contain microbes from both humans and environmental ecosystems. 

Gloria Dominguez-Bello

The system will have multiple local collections, where local scientists collect and have their own collections. And then they can deposit a safety backup in a central collection. We have two potential places, Switzerland or Norway. 

Christine Fennessy

And, she says, the project will empower researchers to grow their individual collections, learn which microbes protect against disease and which make disease worse, and share that knowledge. 

Gloria Dominguez-Bello

We want to preserve microbiomes of the world for the future health of humanity. So when we know what was the function of these microbes, we can use it and restore. 

Christine Fennessy

She envisions the Microbiota Vault becoming the most comprehensive, well researched source of probiotics, those beneficial organisms that support our health. The Microbiota Vault is a global nonprofit initiative. And its work is supported by Rutgers and by the Rutgers University Microbiome Program. 

Gloria Dominguez-Bello

This is a battle that the whole world needs to engage in, because we are all suffering. It’s not only developed countries that are now facing these new chronic diseases, but developing countries know it’s coming to them too. 

Christine Fennessy

But when it comes to restoring the microbiome, specifically of a child, Dr. Blaser says there’s another big unknown: Can it be restored in time? 

Marty Blaser

Because if there’s a critical developmental window — and maybe that window is the age of three or the age of five — if you restore it when you’re at the age of seven, you may have restored it, but it’s too late. The damage is done because it’s affected development.  

Christine Fennessy

One of the program’s research initiatives may help answer that question. It’s called the New Jersey Kid Study. 

Marty Blaser

We want to enroll 5,000 pregnant women and their babies. 

Christine Fennessy

He says those women will represent the cultural, ethnic, socioeconomic, and geographic diversity of the state. Researchers will use questionnaires to get information from the mothers. 

Marty Blaser

And we can get specimens from the moms and the kids. 

Christine Fennessy

And they’ll follow these kids for 10 years. 

Marty Blaser

And we know that during that time, some of the kids are going to develop asthma. Some will develop autism; some will become obese. And we will have specimens in the freezer from before they had asthma or autism or obesity. So we could see: Can we figure out what the predictors are? Why did this child develop autism and someone else didn’t? 

Christine Fennessy

He says it’s a major study, and they’re still in the early phases of it. But if they can better understand the early-life microbiome, Dr. Blaser and Professor Dominguez-Bello say, maybe they can develop good restoration approaches and ultimately improve the health of kids. 

Gloria Dominguez-Bello

Again, restoring… if we do it early enough, we can prevent. If we do it late, we cannot cure, because these are incurable diseases. But at least we can manage and improve diseases, improve symptoms. But for me, the crucial [factor] is to understand childhood and then prevent [disease from the outset]. 

Christine Fennessy

Dr. Blaser says one of the unique angles of the New Jersey Kids Study and of the Rutgers University Microbiome Program is the size of their team. 

Marty Blaser

We have more than a hundred faculty members from Rutgers. 

Christine Fennessy

And they not only come from the field of medicine, but fisheries and animal sciences, agriculture and engineering, biology, ecology, law, and ethics. 

Marty Blaser

So we’re going to take advantage of the intellectual brainpower of the Rutgers faculty. 

Christine Fennessy

He says this range of expertise is critical. 

Marty Blaser

Because the microbiome touches every aspect of life. It touches health. It touches agriculture, touches energy, environment — you name it.  

Christine Fennessy

Dr. Blaser says the program has many goals: Create new knowledge in the field of microbiome science. Train students to become the next generation of experts. License its knowledge to help companies develop products. And eventually, help communities better understand risks to their microbiome and how to counter them. He envisions RUMP evolving to include individual research programs, centers for study, degree programs, and startups. And ultimately… 

Marty Blaser

We will improve consciousness and thinking about the microbiome, both locally and globally. 

Christine Fennessy

He says the Rutgers University Microbiome Program has come about at just the right time. 

Marty Blaser

So in many ways, we are in the early days of the microbiome revolution. It is a scientific revolution. I liken it to electronics. If 50 years ago someone had said to you, “Well, I think electronics is really going to be a big field. It’s going to change the way we live.” It would’ve turned out to be correct. And I think that microbiome is that kind of field.  

Christine Fennessy

That’s it for today’s show. I’d like to thank Dr. Blaser and Professor Dominguez-Bello for their time and their insight. And remember, this episode is Part One in a two-part microbiome miniseries. In Part Two, Professor Liping Zhao will talk about the importance of dietary fiber in maintaining a healthy gut microbiome and what you can do to improve your own diet.  

Music in this episode is by Epidemic Sound. And you can subscribe to the show wherever you get your podcasts. Multidisciplinary projects, like the Rutgers University Microbiome Program, embody the innovative drive of Rutgers, New Jersey’s academic health and research powerhouse. I’m your host and producer, Christine Fennessy. Join us next time as we explore more initiatives that will better the world.