The Rutgers University Microbiome Program

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.

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. And 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 two in a two-part series about the Rutgers University Microbiome Program. It features professor Liping Zhao. He’s the Eveleigh-Fenton chair of applied microbiology in the department of biochemistry and microbiology at Rutgers and director of the Center for Microbiome, Nutrition, and Health at the New Jersey Institute for Food, Nutrition, and Health.

In this episode, he talks about how feeding the microbes in his gut helped him overcome obesity, why dietary fiber is so critical to our health, the simple steps we can all take to improve the health of our own microbiome, and why he plans to do this work until he is 120.

Thanks for joining us.

Christine Fennessy:
Professor Liping Zhao is a trim, fit-looking guy. But in the early 2000s, he was in pretty bad shape.

Professor Liping Zhao:
I was about 45 pounds heavier. BMI over 30.

Christine Fennessy:
He also had metabolic syndrome, which includes things like high blood pressure and excess belly fat. And it can lead to heart disease and Type 2 diabetes. But professor Zhao was also a microbiologist who studied gut health.

Professor Liping Zhao:
And then in 2004, Professor Jeff Gordon at the University of Washington, St. Louis published a seminal paper in mice models to show that gut bacteria can actually regulate fat storage.

Christine Fennessy:
That paper? It got him thinking …

Professor Liping Zhao:
My gut microbiome may somehow be related with my own obesity problem.

Christine Fennessy:
For two years, he experimented with different foods. He believed that if he improved his gut health, his overall health would get better.

Professor Liping Zhao:
I used myself as a guinea pig to try this diet. And eventually it worked.

Christine Fennessy:
He ate fermented foods like Chinese yam and bitter melon. And just to clarify, fermentation is the controlled growth of good bacteria, and it can give food and beverages a range of health benefits. So fermented foods would be things like kombucha, kimchi, sauerkraut, sourdough bread.

So anyway, professor Zhao combined fermented foods with a diet based on whole grains. After making these changes to his diet, he lost 45 pounds over two years and lowered his blood pressure, cholesterol, and heart rate.

Professor Liping Zhao:
I eventually developed a dietary scheme. I call it the “Feed me, feed my microbiome” diet.

Christine Fennessy:
“Feed me, feed my microbiome.” When it comes to maintaining our health and lowering our risk for disease, we’re all, in a sense, eating for two. But, says Professor Zhao…

Professor Liping Zhao:
We need to make the distinction between human nutrition and microbiome nutrition.

Christine Fennessy:
But why does our microbiome need its own nutrition? He says our gut microbiota co-evolved with us. And for thousands of years, we humans ate a lot of fiber.

Professor Liping Zhao:
Our ancestors had a much higher fiber intake. On average, 200 to 400 grams of fiber…

Christine Fennessy:
Every day. But now …

Professor Liping Zhao:
On average, American people now take 15 grams of dietary fiber every day.

Christine Fennessy:
He says this shift from a high-fiber diet to a low-fiber diet has disrupted our gut microbiota. And that disruption can lead to the inflammation that causes disease.

Professor Liping Zhao:
So that is why dietary fiber is so important. If you look at the literature, almost the only nutrient which has consistent results on its beneficial effects is dietary fiber.

Christine Fennessy:
And by beneficial effects, he means dietary fiber cannot only help prevent disease; it can help alleviate the symptoms of disease.

Professor Liping Zhao:
That means it’s a fundamentally important nutrition to humans. But it’s actually targeting the gut microbiome.

Christine Fennessy:
We’ll talk about sources of dietary fiber in a minute. But first, how exactly does fiber nourish our gut? Professor Zhao says we all have a huge number of bacteria and other microbes living in our guts, but we lose a massive number of them every time we have a bowel movement. So, to make up for that loss, microbes have to grow constantly. And all that growth requires a lot of food.

Professor Liping Zhao:
And so the nutrition that our bacteria need to grow can come from two primary sources. One is anything non-digestible or undigested in our diet.

Christine Fennessy:
Our bodies can’t digest dietary fiber, and that makes it the best energy source for certain bacteria: the bacteria that tend to be health-promoting. The more fiber these beneficial microbes get, the faster they grow. The faster they grow, the more they take over the ecosystem. And a gut dominated by beneficial microbes is a healthy gut.

He says the second source of nutrition comes from the gut itself—from mucus and dead cells. But the microbes that rely on this energy source …

Professor Liping Zhao:
They tend to be pathogenic or detrimental. And so that’s why dietary fiber can be very important for microbiome nutrition.

Christine Fennessy:
But what makes beneficial gut bacteria so beneficial? When these microbes eat dietary fiber, they release short-chain fatty acids.

Professor Liping Zhao:
These short-chain fatty acids, they are not in our diet. Vinegar is an exception. And also, we cannot synthesize or produce [these fatty acids] by ourselves. But they are very, very important.

Christine Fennessy:
They’re important because short-chain fatty acids help maintain a healthy gut surface, regulate our appetite, and reduce inflammation.

Professor Liping Zhao:
We know inflammation is damaging to our healthy organs and cells.

Christine Fennessy:
So, reducing inflammation is critical in preventing or alleviating disease—but like he says, [short-chain fatty acids] don’t exist in our food and we can’t synthesize them. And that’s why we need to feed the bacteria that can.

Professor Liping Zhao:
This would be the best example for the so-called the symbiotic relationship—the mutual beneficial relationship between humans and some important gut bacteria. I think this is the most well understood, well studied, and also one of the most important mutual relationships between humans and gut bacteria.

Christine Fennessy:
But in general, we humans aren’t doing a great job of holding up our end of this relationship. Among other things, we don’t eat nearly enough dietary fiber to keep these good microbes at high enough population levels.

Professor Liping Zhao:
And most people, when I talk about the importance of high-fiber and how they nurture gut bacteria, say, “Oh, it’s fiber, okay. Have more fruits and vegetables. Problem solved.”

Christine Fennessy:
He says it’s not that simple—because there’s fermentable fiber and there’s non-fermentable fiber. Beneficial bacteria can only digest fermentable fiber.

Professor Liping Zhao:
Surprisingly, if you look at fibers in fruits and vegetables, they are mostly non-fermentable.

Christine Fennessy:
Now, he does not mean that fruits and veggies aren’t important. Far from it. They have loads of vitamins, minerals, antioxidants, and they are good sources of dietary fiber.

Although, as he says, most of that is non-fermentable fiber. But that non-fermentable fiber is important. It absorbs water, which makes our gut content bulkier. And that bulk increases the gut pressure that helps with transit and alleviates constipation.

Professor Liping Zhao:
But that’s it. That’s the physical benefits. In order to get the physiological, immunological, and psychological benefits that we talk about from short-chain fatty acids, dietary fiber should be fermentable.

Christine Fennessy:
Because the bacteria that produces these short-chain fatty acids needs fermentable fiber. And that comes in large part from whole grains.

Professor Liping Zhao:
The general advice is whole grains contain much more fermentable fiber than vegetable and the fruits.

Christine Fennessy:
Whole grains include quinoa, oats, barley, brown rice. But he says you have to be careful how you cook them. Because if you cook whole grains too long, they become too digestible and can release a lot of glucose into your body, which can cause your blood sugar to spike. And over time, repeated blood sugar spikes can increase your risk for conditions like Type 2 diabetes and heart disease.

Professor Liping Zhao:
So that’s why I’m very careful in giving across-the-board very general advice to people. It’s just because our microbiome nutrition research has advanced to a level where we can use a data-driven approach to help people.

Christine Fennessy:
The research behind this data-driven approach began when Professor Zhao was obese and using himself as a guinea pig. He and his team learned that a diet high in fermentable fiber fed beneficial bacteria. But what they didn’t know was which of the hundreds of species of bacteria in our guts were the good ones.

They developed the WTP diet, which stands for whole grains, traditional Chinese medicinal foods, and prebiotics. And then they conducted numerous clinical trials giving the diet to those with adult obesity, childhood genetic obesity, and Type 2 diabetes.

Professor Liping Zhao:
We identified a very specific group of bacteria. Before we gave the WTB diet, they were very low in numbers. And when we provide the WTB diet, after about four weeks they become predominant. And they regain their ecological dominance.

Christine Fennessy:
This group of bacteria produces the short-chain fatty acids that nurture our guts, regulate our appetite, and reduce inflammation. His team also found that when it comes to Type 2 diabetes, these short-chain fatty acids stimulate production of a hormone that promotes the secretion of insulin. Professor Zhao says that after patients were on this high-fiber diet, they had much better glycemic control.

Professor Liping Zhao:
So, this is one side of the story.

Christine Fennessy:
The other side? This group of good bacteria lowers the pH of the gut. And that makes it a lot harder for disease-causing bacteria to grow. On top of that, these good microbes …

Professor Liping Zhao:
They themselves actually are also antimicrobial. These short-chain fatty acids also can kill or inhibit other pathogenic bacteria. Eventually, disease-related pathogens are reduced and then beneficial bacteria promoted. You’ll have a much healthier gut ecosystem.

Christine Fennessy:
Professor Zhao calls this group of good bacteria “the Foundation Guild”…

Professor Liping Zhao:
Because they are not one species. They are actually many different species, but they work together as a guild. That’s why we call them instead of foundation species, we call them a Foundation Guild. And this is a very important finding.

Christine Fennessy:
Very important, because the Foundation Guild is the key to a healthy gut. If the average American doesn’t get enough fiber and a lot of the fiber that we do eat isn’t the right kind, why can’t we all just eat some version of the WTP diet? The whole grains, traditional Chinese medicinal foods, and prebiotics dietary scheme.

Professor Zhao says that diet was designed to test the hypothesis that a high-fiber diet could promote good bacteria. It wasn’t meant to go mainstream for a lot of reasons.

Professor Liping Zhao:
Because different ethnic groups, different geographic regions, different families, different individuals, they have their own dietary habits, preferences, and the local produce they prefer. So, we cannot provide a diet which across the board, everybody should [eat].

Christine Fennessy:
But all of this research has led to where we are right now: at a point where he says we can use a data-driven approach to help people. For example, once they identified the Foundation Guild bacteria, they could sequence their genome to understand why the bacteria thrive on such a high-fiber diet.

Professor Liping Zhao:
Then we look at their genome. Now we realize, ‘Okay, so they are very good at using several different kinds of plant fibers.’ And you know the chemical structure, properties of those fibers. And so now we no longer need the whole diet.

Christine Fennessy:
Professor Zhao and his team at Rutgers have developed a high-fiber formula specifically designed to promote Foundation Guild bacteria. The FDA has granted the formula investigational new drug status. They used it in a recent feasibility study on a patient who had COVID-19 in 2020 and was suffering from Long COVID.

Professor Liping Zhao:
She developed very severe GI symptoms, like nausea and bowel refluxes, and almost could not have a regular meal for over a year.

Christine Fennessy:
She also had anxiety and palpitations and couldn’t work. Professor Zhao and his team gave the patient the high-fiber formula for two months, and…

Professor Liping Zhao:
She recovered. Not completely, but she started to have regular meals.

Christine Fennessy:
And he says her GI symptoms and anxiety improved significantly. It was the first study to show the potential of treating [Long COVID] by targeting the gut microbiota. The next step is a randomized, controlled, phase two trial. The formula that Professor Zhao developed is a product of a Rutgers startup.

Professor Liping Zhao:
And so I’m the scientific co-founder of a microbiome company called Notitia Biotechnologies Company.

Christine Fennessy:
The company has a clinical program for patients and a wellness program for the general public. If you’re wondering about the state of your gut, you can send in a fecal sample and they’ll analyze it to measure the level of your Foundation Guild bacteria. And if it’s low, they have a product that can help restore it.

Professor Liping Zhao:
And this company is now producing a nutrition formula—our microbiome formula, which is high in fermentable fiber—for the general public.

Christine Fennessy:
It’s a powder you can mix in water, add to smoothies or to muffin, pancake, or waffle mixes. And there’s a third step to the wellness program, too. Once your Foundation Guild is restored, you can send in another sample.

The company will isolate your bacteria and store it. And if you ever lose those good microbes completely, which can happen with certain infections or treatments, they’ll help you regain your original Foundation Guild.

Okay. But we all want to know: What can we do right now?

Professor Liping Zhao:
In general, my advice would be not much different from what a nutritionist would give you: Have more fiber. But when it comes to using various fiber-rich ingredients, we know that you need to balance the intake between fruits and vegetable fiber and the green fiber and the whole grains fiber.

Christine Fennessy:
But remember: Don’t overcook your whole grains.

Professor Liping Zhao:
For the whole grains… I also roast it. So that means after you roast the seed, the starch inside the seeds become much less digestible, so you can get even more benefits. But there is a balance between how much you roast and how much you still keep the necessary “mouth feel” that you like. If it’s too dry, then nobody likes it.

Christine Fennessy:
He says in general, ethnic foods tend to be more beneficial to their respective ethnic groups.

Professor Liping Zhao:
That makes sense. Why? Because your ancestors and your ancient microbiome has been relying on those ingredients. And so if you want to nurture your Foundation Guild, the first place to turn to is your ethnic food.

Christine Fennessy:
But a lot of us want to know about the supplements that we see on the shelves and all the foods that say they contain prebiotics or probiotics. He says they can be helpful.
And just a refresher, prebiotics are nutrients for beneficial bacteria, and probiotics are the beneficial bacteria themselves. But he says, you need to do your research. First, read the label. Professor Zhao says you’ll usually see two Latin words.

Professor Liping Zhao:
The first word is the genus name. And the second word is a species name. That’s not enough.

Christine Fennessy:
He says you also need the strain ID of the bacteria. So, whether you’re reaching for yogurt or a supplement, look for the bacterium that’s included on the label.

Professor Liping Zhao:
By taking this name and putting it in Google search, you can pull out all the patent application, clinical trial papers, all centered on that strain. So if you see, ‘Okay, I can pull quite a number of clinical trial papers showing the benefits of this particular strain or products containing this particular strain,’ that might be a product worth trying.

Christine Fennessy:
There’s another simple thing that you can do on a daily basis. And just a heads up here: We’re going to get very blunt about bowel movements.

Professor Liping Zhao:
Well, I know in the West people don’t talk about bowel movement in public, right? Some people have never looked at their poop before. But you need to monitor the so-called stool quality, because that’s a very immediate sign of your gut health and then your overall health.

Christine Fennessy:
So, what comprises stool quality? First: shape.

Professor Liping Zhao:
And I actually have a chart on the wall beside every toilet in my home.

Christine Fennessy:
He’s referring to the Bristol Stool Chart, which lists seven shapes ranging from too dry (constipation) to too loose (diarrhea).

Professor Liping Zhao:
So even my three-year-old granddaughter, after each poop, she will look at the chart and say, “Okay, it’s type four. Normal, normal.”

Christine Fennessy:
The second indicator is color.

Professor Liping Zhao:
If you have a very dark color, that’s not a good sign. A yellow golden color, light color, usually is better than a very dark color.

Christine Fennessy:
The third is odor. He says a strong odor usually means an unhealthy gut. And finally, stickiness. It’s exactly what you think.

So, while it may take some getting used to, monitoring your bowel movements can reveal a lot about your gut health. And if the indicators aren’t good, he says, fix your diet first.

Professor Liping Zhao:
It’s just because there’s nothing more powerful than your own diet.

Christine Fennessy:
Take a minute to look at your plate, and remember: You’re eating for two.

Professor Liping Zhao:
Every time I look at my meal, I’ll have a very quick estimation of whether I have enough protein and fat for myself. And also how much microbiome nutrition I [have on the plate]. It almost becomes automatic.

Christine Fennessy:
He’s not saying give up all those treats you love. Just don’t forget those microbes need a lot of love too.

Professor Liping Zhao:
We indulge from time to time, right? We enjoy life. But then I would say, ‘Okay, next day,’ and the next two or three days I need to make it back. You know, to become balanced.

Christine Fennessy:
Professor Zhao has been working in the fields of nutritional health and gut ecology for 30 years. And he plans to keep doing it for quite a few more.

Professor Liping Zhao:
I joke that I’m going to retire at 120.

Christine Fennessy:
And that’s because he’s got a lot to do.

Professor Liping Zhao:
I actually have a goal: I hope at least 10 million people can either restore and recover or maintain their health by using what I found in my scientific research. And that will be very fulfilling.

Christine Fennessy:
One way he plans to reach that goal is through the Rutgers University Microbiome Program. Professor Zhao is a co-founder and co-leader of the program. And as part of it, he’ll soon be launching the Family Microbiome Project.

Professor Liping Zhao:
We know that the Foundation Guild bacteria are essential to human health—so that’s why we need to get them very early in our life.

Christine Fennessy:
He says the Foundation Guild bacteria are transmitted from mother to baby through the reproductive tract and through breast milk.

Professor Liping Zhao:
But they can also be picked up from interactions with other family members. From a father, from grandparents.

Christine Fennessy:
He wants to recruit 1,000 families to identify the Foundation Guild bacteria unique to each one and to each family member. They’re hoping to learn more about how this essential bacteria is transmitted among families and among ethnic groups.

Professor Liping Zhao:
New Jersey is the best place to start this project, because we have the highest ethnic diversity not only in the U.S., but also in the world.

Christine Fennessy:
He says the goal is to better understand how modern-day practices are affecting the transfer of Foundation Guild bacteria—practices like scheduled C-sections, bottle feeding, and antibiotic use early in life. And if that transfer is severed, can it be restored?

Professor Liping Zhao:
We need to identify and understand this. And hopefully we can find such bacteria, identify them, and isolate them so that we can have a bank. And then they can be used to develop drugs and to help those who have permanently lost them.

Christine Fennessy:
The Family Microbiome Project will be a very long-term study, but he sees real change coming in the not-so-distant future.

Professor Liping Zhao:
Probably the generation who’s going to be born 10 years from now will be the microbiome babies. Because their microbiome will be taken care of from even before they were born. Their [parents] will manage and test and optimize their microbiome to prepare for the new baby.

Christine Fennessy:
But really, when it comes to making our microbiome healthier, we don’t have to wait that long. Professor Zhao says that’s the beauty of this research: so much of it can be applied today.

Professor Liping Zhao:
Sometimes I joke that before you listen to my talk, you are you. After you listen to my talk, you are no longer you, but you and your microbiome, right?

When you realize there is a gut microbiome living inside your gut, you need to respect it. You need to nurture… it so that it can keep you healthy. This will fundamentally change your behavior in many ways.

Christine Fennessy:
That’s it for today’s show. I’d like to thank Professor Zhao for being so generous with his time. And remember, this episode is part two in our two-part microbiome miniseries.
In part one, Dr. Martin Blazer and professor Maria Gloria Dominguez-Bello 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.

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.