Vital Sings: Microbiome

Premieres: June 15, 2020.

Dr. Sanjay Gupta: 00:23

You’ve probably heard that expression, you are what you eat, well there’s a lot more truth to that than you might think, and it all comes down to a few bacteria, 100 trillion of them to be exact. That makes up what is known as the microbiome. This is Vital Signs, I’m Dr. Sanjay Gupta. Microbes live in us and on us, in fact we have more bacteria than cells in our bodies, as many as 10 times more. These bacteria, specifically the ones in the stomach and intestines impact nearly every aspect of our health, from sleep, to disease, to diet, and it’s influenced not only by what we put into our bodies, but also by what’s around us.

Dr. Sanjay Gupta: 01:03

This diagram may look like a constellation chart, it’s actually a map of bacteria taken from people all over the globe, and you probably have some of these living in you right now.

Rob Knight: 01:14

There’s more bacteria in your gut than there are stars in the universe by long shot.

Dr. Sanjay Gupta: 01:20

Rob Knight is mapping the human microbiome.

Rob Knight: 01:24

The little dots are different kinds of bacteria, and we draw the line between two dots if that particular bacteria was found in  that particular sample, and when we zoom out we see some very clear patterns.

Dr. Sanjay Gupta: 01:36

What you see here is his brainchild; The American Gut Project. It’s a citizen science research compilation, meaning the data is donated by the general public, it’s also entirely crowdfunded. For 99 US dollars you can send your sample to the night lab at UC San Diego and see what makes up your microbiome.

Rob Knight: 01:58

By placing yourself on the map you’ll be able to diagnose particular conditions, and what we hope is ultimately we’ll be able to develop a kind of microbial GPS that helps you drive your microbiome around on this map, defining where you are at the moment, where you would like to go in order to optimize your health.

Dr. Sanjay Gupta: 02:17

This is the picture four years in, with over 10,000 samples collected from 43 countries and counting, and they’re only scratching the surface. So what do we know about these microbes?

Rob Knight: 02:28

We know a tremendous amount about the microbiome compared with what we did only a decade ago. Now, for a human stool sample usually 97-99% of the sequences are identifiable. On the other hand, we know very little about their functions. So it’s like we have the name tags for a lot of people at a party, but we don’t know what they do.

Dr. Sanjay Gupta: 02:49

What makes this particularly hard is the diversity of microbiomes, and that they change every day.

Rob Knight: 02:54

Each of us is changing our microbiomes right now through things like the foods we eat, the spaces that we live and work in, the people who we live and work with. While we’re all 99.99% identical in terms of the human genome, whereas you might be 90% different to the person you’re sitting next to in terms of your microbiome.

Dr. Sanjay Gupta: 03:16

No two microbiomes are the same, it’s unique to each of us. The microbiome is made up of all the microbes in and on our body; fungi, bacteria, viruses, for example. Most of these live in our gut, primarily in the large intestine. Researchers estimate that the total surface area of our gut is 3,000 square feet, that’s larger than a tennis court. All those microbes outnumber our human cells around 10 to 1, making us more bacteria than human. In fact, if you weighed the microbiome it would be as much as five pounds. Think of how many microscopic bacteria and fungi it would take to add up to that weight, it’s roughly 100 trillion of them if you were wondering, and while some might get grossed out by words like bacteria and fungi, the microbiome is the peacekeeper of our bodies helping us to digest food, fight disease, and regulate our immune system.

Rob Knight: 04:10

We ask a lot of questions of the participants in American Gut, so there’s an extensive questionnaire that covers everything from type of diet you have to how many hours sleep you get at night, to how much exercise you get, and all kinds of things that no one had any idea were linked to the microbiome when we started the project.

Dr. Sanjay Gupta: 04:29

Knight says that out of all these factors your diet has the biggest impact on your microbiome.

Rob Knight: 04:35

It really matters a lot what you ate over the last six months to a year. One exception to that though is the number of different kinds of plants people eat, and that seems to have a very big impact on the microbiome. That sort of points to the observational nature of these studies like American Gut, you really need to take it into more well defined experiments to find out what the connections are and whether the microbiome is driving the difference in health, or the difference in lifestyle, or whether the lifestyle is driving the microbiome.

Dr. Sanjay Gupta: 05:05

This project could be game changing, and potentially gut changing as well.

Embriette Hyde: 05:10

These microbes are involved in a number of diseases as varied as diabetes, autism, Parkinson’s, and so this is another avenue, or another piece to the puzzle and so I really think that as we unravel the mysteries and figure out exactly how the microbiome is associated with these different diseases we’ll be able to use that information to maybe improve diagnoses, but also treatment as well.

Dr. Sanjay Gupta: 05:38

Meet Embriette Hyde, self-proclaimed microbial enthusiast and three-time tester of her own microbiome. She also manages The American Gut Project at UC San Diego.

Embriette Hyde: 05:51

So when I took this sample it was actually just after thanksgiving in 2015 and I travelled to Michigan to visit my family. Diet certainly changed, but on top of that you can imagine that the weather in Michigan in November is a lot different from the weather in San Diego in Michigan, and so there’s a lot of different components affecting my microbiome.

Embriette Hyde: 06:10

This was collected in January 2016, after the holidays I was pretty much just in my normal daily routine schedule. If you look at the list of the bacteria that were present in my sample, the top four are still the top four, and so that started to indicate to me that my microbiome is pretty stable over time.

Embriette Hyde: 06:30

So this third sample was taken about 8 months after the second one, and this one is particularly interesting because this one was collected on day 7 of an antibiotic regimen. So I’d probably lost half of the bacteria present in my sample after this antibiotic regimen. But what I found even more impressive about this was that my top four were still my top four. Pretty stable across time, at least over this year time period, even though I’m doing different things daily to my microbiome that can have a big effect.

Embriette Hyde: 07:01

Being human isn’t necessarily what we thought it was. We are a super organism, we have our own cells, but we also have these microbial creatures living in us and on us and they have a bigger effect on us than we really thought about before.

Dr. Sanjay Gupta: 07:21

Deep inside Venezuela’s amazon exists a bacteria goldmine, the good kind, belonging to a remote, indigenous, semi-nomadic community.  Undiscovered until 2008, the Yanomami happened to host the most diverse human biome ever recorded.

Maria Gloria: 07:37

They have about twice the diversity westernized US population has.

Dr. Sanjay Gupta: 07:45

Pristine microbiomes, largely untouched by modern day medicine or members outside their community. Researchers wondered what have we lost and how?

Maria Gloria: 07:55

So these are extremely healthy people and we want to understand what they have, how they function with their microbes, how their microbes provide health, and compare their microbiota functions with ours. So we are trying to understand what’s their advantage. There is a lot of variation her but it’s-

Dr. Sanjay Gupta: 08:19

Microbial anthropologist, Maria Gloria Dominguez-Bello, who piloted this research tested fecal, oral, and skin samples from 34 members of the Yanomami community.  Her team found that the hunter gatherers harbored antibiotic resistant genes, suggesting it could be a natural feature of the human microbiome in an unaltered state.

Maria Gloria: 08:41

We also know and have tried to characterize very well what is different in their lifestyle in relation to ours, because many things change. Diet is a major driver of microbes, so we want to understand what is it that is modulated by diet or that may have disappeared with antibiotics that may not have been acquired from birth because of a C-section or because of antibiotics.

Dr. Sanjay Gupta: 09:12

The first microbes a newborn receives come from the mother’s fluids, if delivered vaginally, whereas infants born via caesarian section do not, some scientists theorize that these children may then miss out on important microbes that shape their immune systems and lifelong health.

Maria Gloria: 09:27

Both are the pioneer microbes that arrive in our mouth, nose, and they establish there and start talking to our immune system. Those will be considered friends. But every time we take an antibiotic, and especially during very early age, the assembly of these communities is disrupted by the antibiotics. It’s a tremendous effect because by definition antibiotics kill bacteria.

Dr. Sanjay Gupta: 09:55

It is thought that antibiotics, rigorous hygiene practices, and highly processed foods have decreased the diversity of microbiomes in the developed world.

Maria Gloria: 10:04

C-section and antibiotics we think are probably the more major drivers, but also water. We drink chlorinated water. What is the effect of chlorinated water? We don’t know that.

Dr. Sanjay Gupta: 10:19

Scientists are hopeful that the key to driving optimal health lies within the microbiome.

Maria Gloria: 10:24

That’s why I’m dedicating my life to this research. I think we have lost important microbes, our hypothesis is that we can restore them early in life and then once the immune system is educated and the metabolic system, the crucial stage of development is normalized, then those kids should have less allergies, asthma, celiac disease, type 1 diabetes, obesity, and keeping, of course, a healthy lifestyle. Eventually the whole world will converge into a single lifestyle. I think the window is closing. More and more we go back to places and in a year, we see that people have already been pretty much integrated. Of course, there is a big dilemma for them, they mostly want to remain in their lands, but they want technology and medicine. So is that achievable? I think so, but it’s a big challenge. So we want to save that biodiversity before it disappears.

Dr. Sanjay Gupta: 11:38

A snapshot of a culture suspected to have been left alone for some 11,000 years, these Amazonian samples can perhaps give us an insight into how our microbiomes have evolved, and possibly help treat chronic illnesses.

Dr. Sanjay Gupta: 11:53

The microbiome is such a fascinating window into our health and our environment. In fact, one laboratory in Boston has discovered that it can save lives as well, as my colleague, senior medical correspondent Elizabeth Cohen, explains, one man’s waste is another man’s medicine.

Eric: 12:10

Today is the big day.

Elizabeth Cohen: 12:12

For Eric, a 24-year-old research assistant at MIT, nature is calling. So he hops a train, and then a bus, he passes countless toilets but doesn’t use them, only stopping a full 30 minutes later inside this men’s room.

Eric: 12:30

I’m going to put this down first, and then this, and then I’m going to close the lid.

Elizabeth Cohen: 12:34

Eric is a poop donor and a pit stop here can save lives.

Elizabeth Cohen: 12:39

Eric, how’s it going in there?

Eric: 12:41

Things are going smoothly.

Elizabeth Cohen: 12:43

Good, good. So is this just like regular pooping or do you do something special?

Eric: 12:50

It is as normal as can be.

Elizabeth Cohen: 12:55

This I Open Biome. They’ve developed a way to turn poop into a treatment for clostridium difficile. The infection kills 15,000 Americans a year and sickens half a million.

Eric: 13:09

I have donated 29 times, which has resulted in 133 treatments, which is pretty great, and that has resulted in about 1000 dollars.

Elizabeth Cohen: 13:20

97% of people who want to donate poop are rejected, maybe because they’ve recently travelled to certain places, or used antibiotics, or gotten a tattoo.

Christina Kim: 13:31

This, I would say, is a bristle five. It has some inconsistency but it-

Elizabeth Cohen: 13:34

Lab technician Christina Kim demonstrates how they make the treatment. Poop that’s too hard or too soft won’t work.

Elizabeth Cohen: 13:41

It’s very descriptive, “like a dry cured sausage.”

Christina Kim: 13:45

Yes, it’s very descriptive.

Elizabeth Cohen: 13:45

“Soft logs, fluffy pieces.” Did you write this?

Christina Kim: 13:49

No, it’s actually an established medical chart.

Elizabeth Cohen: 13:52

A saline solution is added, then it gets sloshed around to filter out fiber. What’s left behind is a liquid teeming with healthy bacteria.

Elizabeth Cohen: 14:00

This is either administered bottom up, through a colonoscopy.

Christina Kim: 14:05

Yes.

Elizabeth Cohen: 14:05

Or top down through a tube in the nose.

Christina Kim: 14:08

Yes, a tube that travels all the way from your nose down to your intestines, our target area of delivery.

Elizabeth Cohen: 14:15

So, the healthy microbes from Eric’s poop will sort of chase out the sick microbes that the patient has.

Christina Kim: 14:22

Exactly.

Elizabeth Cohen: 14:23

It’s called a fecal transplant. Inside this freezer, the 133 treatments Eric’s provided. The bacteria inside them are still alive, cryogenically preserved at -112°.

Eric: 14:38

I never thought I would be staring at my poop frozen in a freezer, destined to help people across the country. It’s really cool.

Elizabeth Cohen: 14:46

Did you do all this for the money?

Eric: 14:49

No, no. The money was nice, for sure, but it’s about helping people.

Dr. Sanjay Gupta: 14:57

For Joe Cobucci every healthy day is a blessing. Joe has Crohn’s, an autoimmune disease that causes inflammation of the digestive tract. Crohn’s may slow Joe down from time to time, but he keeps on running, 58 half marathons and counting.

Joe Cobucci: 15:16

So here’s a few of my medals over the many years but there’s some ones that really stick out that mean a lot to me. This specific one right here is my first marathon.

Joe Cobucci: 15:29

So I was diagnosed at age 11 with Crohn’s disease, that was a little over 40 years ago, so I’ve lived this struggle for a long time, and the physician thought I had a mental illness. He thought I had extreme anxiety because he didn’t understand why I didn’t want to leave the home.

Dr. Sanjay Gupta: 15:53

Crohn’s is a type of inflammatory bowel disease, symptoms are debilitating, often embarrassing for sufferers.  They include severe diarrhea, abdominal pain, and fatigue.

Joe Cobucci: 16:04

I have to say I’m a GPS for restrooms. I always carry a change of clothes with me just in case, no matter where I’m going.

Dr. Sanjay Gupta: 16:12

But what really is Crohn’s disease, and what does it have to do with the microbiome?

Dr. Doug Wolf: 16:17

Crohn’s disease is a chronic inflammation of the intestines, and it’s a condition that can affect any segment of the intestine, though most commonly the small intestine.  Crohn’s disease and ulcerative colitis are really artificial names. Crohn’s disease was named after Burrill B. Crohn’s at Mount Sinai, and ulcerative colitis is simply called what it is, but really it’s IBD1, IBD2.

Dr. Sanjay Gupta: 16:46

Dr. Doug Wolf has been diagnosing inflammatory bowel diseases for 25 years, and he says some cases respond better to medicine and some by tweaking the microbiome.

Dr. Doug Wolf: 16:56

The challenge that lies ahead, to really be better at sorting out Crohn’s disease, ulcerative colitis, the IBD1 through 10 or 20, then better direct, personalize our care, target our treatments, and do a better job.

Dr. Sanjay Gupta: 17:15

How would you describe how well we understand Crohn’s disease, ulcerative colitis, where are we in our understanding of these diseases?

Dr. Doug Wolf: 17:25

We’re somewhere between the first inning and the ninth inning, but we’re not sure. We’re probably in the third or fourth inning, actually, so it’s still early in the game. Our understanding of genetics is great but very shallow, but it’s not all genetics, and then there is an environmental trigger that sets off a cascade of inflammation and immunologic dysfunction.

Dr. Sanjay Gupta: 17:56

Currently there is no cure for the chronic condition, and about 80% of patients will eventually need surgery.

Dr. Doug Wolf: 18:02

The best thing is to get an early diagnosis, early management, control the inflammation, and thereby really change the course of the disease.

Joe Cobucci: 18:10

Over the years it’s just been times where I’ve been very, very ill, then times when I’ve been really healthy. But with Crohn’s disease, or ulcerative colitis it can change in seconds. So it’s challenging because you can go to the restroom, it’s hard to say, about 20-30 times a day. Think about that, 20-30 times a day to use the restroom. The digestive issues and the pain for that is challenging, I mean it really is, it is just, your aches and your pains they’re all around. This disease dictates my life. I’ve built my life around it, which is one reason that working for the foundation is so important for me.

Dr. Sanjay Gupta: 18:51

Joe is a national team manager for Team Challenge, the Crohn’s and Colitis Foundation’s endurance training and fundraising program.

Joe Cobucci: 18:58

I found the foundation in a very odd way, I was getting a colonoscopy and saw a flyer for the Crohn’s and Colitis Foundation’s team challenge half marathon program. So I called the number on the back of the flyer and that changed my life forever. I went to a meeting, which was the following morning, and I was in a room with about 50 people, and I had never been around anybody who had Crohn’s or colitis and I got very emotional, I started to cry, and I fell in love with this program and found a new family.

Dr. Sanjay Gupta: 19:38

The exact cause of Crohn’s remains a mystery. Some have argued that bad microbes may prompt it, or that a missing microbe is the cause for the inflammation.

Dr. Sanjay Gupta: 19:47

How much does our personal microbiome play a role, could you predict if someone is more likely to develop inflammatory bowel disease based on their microbiome?

Dr. Doug Wolf: 19:57

Yeah, there is a pre-existing state. I think that we’re really, with trying to understand and certainly trying to manipulate the microbiome, we’re really at the tip of the iceberg, but I think that it’s pretty clear that there is importance to the microbiome, and there are things that we can do to tweak it.

Dr. Sanjay Gupta: 20:25

What do the treatment options look like now for someone who has Crohn’s disease?

Dr. Doug Wolf: 20:29

So now we’ve got at least seven biologics for Crohn’s disease, and also colitis, and now we have to figure out how to use them best. Should it be for an indefinite period, or for a few years? We’re not sure.

Dr. Sanjay Gupta: 20:44

When you meet a patient and they now have his diagnosis of inflammatory bowel disease, you’re having the first conversation with them and they want to know, “What’s my life going to be like?” What do you tell them?

Dr. Doug Wolf: 20:54

There truly are no limits because of the diagnosis. People typically have normal lives and normal life expectancies.

Dr. Sanjay Gupta: 21:04

Joe is the perfect example.

Joe Cobucci: 21:07

I love, love running. I can’t begin to describe it to you. Many, many races, it’s hard to believe 58 of them have happened. Crohn’s impacts me when I’m training or running, I’m always fearful of having to use the bathroom. I’m getting much better, I do proper nutrition and I eat certain things I know that work for me, but it is something that I constantly think about.  When I’m heading to the race, I’m making sure that I can find the restroom first, and I have to know on the course, where are the restrooms? Having Crohn’s disease used to be something that I didn’t want to discuss, now I’m open all the time to discussing it, because I know that by saying that I have Crohn’s disease, that I can make a difference.

Dr. Sanjay Gupta: 21:56

Because the microbiome is constantly changing and differs from person to person, it’s not yet clear how best to encourage and maintain a healthy gut. Research has potentially linked poor gut microbiomes with diseases as varied as Parkinson’s, autism, obesity, and as we just saw, Crohn’s and ulcerative colitis, and the key to treating illnesses and leading a healthy lifestyle may lie within the symbiotic relationship between microbes and humans.