Rob Knight: How our microbes make us who we are

Rob Knight is a pioneer in the study of microbes that live in the human body, tiny single-celled organisms that live inside us, but have a huge and largely unexplored effect on our health. “One and a half kilograms of microbes living inside you are much more important than each of the individual genes in your genome,” Knight said. And you'll know why.







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0:12

We humans have always cared about the health of the body, but we have not always been able to understand what is really important. Take for example the ancient Egyptians. They took great care of the parts of the body that were thought to be needed in the afterlife. They got rid of others.

For example, from this body. The Egyptians carefully preserved the stomach, lungs, liver and so on. But they liquefied the brain and pumped it through the nose and then threw it away. Surgery doesn't make sense, because why do you even need a brain?

But imagine that there is an organ in our body that is not paid attention, although it weighs as much and in some respects as the brain, and we know very little about it and treat it with little respect. Imagine that as a result of new research by scientists, we would begin to understand the role this organ plays in how we see ourselves. Would you like to know more about him?

1:06

Well, it turns out that we have such an organ: our gut, or rather, the microbes that live in it. But it's not just the microbes in our gut that matter. It turns out that microbes throughout the body are responsible for a range of differences that exist between people. Have you noticed that some people are bitten more often by mosquitoes than others?

1:30.

It turns out that everyone’s impressions of life in tents will really be different. For example, I'm rarely bitten by mosquitoes, and my girlfriend Amanda is chased by hordes; the reason is that we have different microbes on our skin that release different substances that mosquitoes catch.

1:47

Nowadays, microbes are important for medicine. For example, what microbes are found in your intestines depends on how toxic some painkillers will be to the liver. The effectiveness of drugs for the heart also depends on them. If you're a fruit fly, the microbes decide who you want to mate with. We haven't found it in humans yet, but maybe it's just a matter of time before we know all about sex. (Laughter)

2:14

Microbes have a number of functions. They help us digest food. They help to “train” our immune system. They help us resist disease and can even influence our behavior. So what would a map of the microscopic world look like? Well, it doesn't look exactly like this map, but it's suitable for understanding biodiversity.

Different parts of the world have different landscapes, different animals that are there, whether it's here or here or here. It's pretty much the same in microbiology, but I'm going to be honest with you: all microbes look alike under the microscope. So instead of recognizing them externally, we're actually looking at their DNA sequences.

In the framework of the project called "Human microbiome" The National Institutes of Health spent $173 million gathering hundreds of scientists to map adenines, thymines, guanine and cytosines and all the microbes in the human body. When we put all the data together, it looks like this. It's hard to tell who lives where, isn't it?

3:17

The challenge for my lab is to develop computer models that can turn terabytes of genome information into a kind of map that's easy to use. When we do the same thing with information about the microbiome of 250 healthy volunteers, the map looks like this.

Each dot on it represents the diverse microbes that make up the microbial community. I told you they looked alike. Therefore, at each point, one species of microflora is shown from the body area of one healthy volunteer. You can see that different parts of the map are colored differently, like different continents. It turned out that different parts of the body live different microbes.

The green is the oral microbiome. On the other side, blue is the skin microflora, the vaginal microflora is purple, and then at the bottom, we've browned the fecal microflora. In recent years, we've found that microbes from different parts of the body are very different from each other. Compare someone's mouth and gut microbes, and it turns out that the difference between these communities is very large.

It's even bigger than the differences between coral reef microbes and prairie microbes. When you think about it, it's breathtaking. This means that there are more differences between microbial ecosystems on a few tens of centimeters of the body than on hundreds of kilometers of the Earth.

4:45

However, you can not say that the microflora of the same parts of the body will be the same in two people. Your DNA is 99.99% the same as someone sitting next to you. But the same can’t be said for your microbes: chances are you and your neighbor will share only 10% of the microbes in your gut. They will be different in the same way that prairie bacteria are different from forest bacteria.

5:15

Different microbes have different functions, which I told you about, from digesting food to participating in various diseases, metabolizing drugs, and so on. So how do they perform all these functions?

Partly due to the fact that although our intestines contain only one and a half kilograms of microbes, they greatly outnumber us. How much? It depends on what you think the body is. Cells? While each of us consists of 10 trillion cells, our body contains about 100 trillion microbes. So there are 10 times more microbes.

Well, you think we're human because we have human DNA, but it turns out that each of us has about 20,000 genes, depending on how you think, and there are 2 to 20 million microbial genes in our bodies. So no matter what you look at, we're very much outnumbered by our microsymbionts. It turns out that in addition to human DNA, we also leave traces of our microbiological DNA, no matter what we touch.

Recently, we described in a study that the microbiological composition of the palm of your hand can reveal which mouse you normally use, with a probability of up to 95%. This study was published in a scientific journal recently, but more importantly, it was shown in C.S.I.: Miami Crime Scene. Now you know it's all true. (Laughter)





6:35

So where do our microbes come from in the first place? If you, like me, have kids or dogs, you've probably guessed this, by the way, it's completely true. Just as we know where your computer is from the microbes it shares, so we know where your dog is. But it's also found that in adults, microbial communities are relatively stable, and even if you live with someone, you retain your microbiological uniqueness for weeks, months, even years.

7:04

It turns out that our first microcommunities depend on how we are born. If babies are born in the normal way, all of their germs look like microbes living in the vagina. And if you did a cesarean section, then all the microbes of babies are similar to the microbes that inhabit the skin.

Therefore, babies born by cesarean section may have some health conditions: they are more prone to asthma, allergies and especially obesity – all those diseases that are associated with microbes. Think about it, because until recently, all mammals were born through the birth canal, so the lack of protective microbes that evolved with us may play a role in the development of various diseases associated with the microbiome.

7:47

When my daughter was born a couple of years ago, my wife had an emergency C-section, but we took everything into our hands and put a layer of vaginal microbes on her that she would have gotten naturally. It is difficult to say whether this has had any effect on her health.

With one child, as much as we love her, it's hard to draw conclusions about what happens normally, but she's two years old and hasn't contracted an ear infection, so we're hoping that's okay. We started clinical trials with other children to see if this method has any protective effect.

8:26

How we are born has a major impact on our primary microbiota, and what happens next? I'm going to show you again a map of the Human Microbiome Project, where the mugs are samples taken from one body area of each of the 250 volunteers. You have seen children develop physically. You've seen them develop mentally.

And now, for the first time, you're going to see my colleague's child develop microbiologically. What we're going to see is the baby's stool, its fecal microbiome, represented by samples taken weekly from the gut for almost two and a half years. We start with the first day of life.

At the beginning of the journey, the microflora of the child is represented by this yellow dot. You can see that the dot starts with the vaginal microbiome, which is expected because the baby was born naturally. Within two and a half years, the dot will move downward, and the composition of the microflora of the child will become closer to the fecal microflora of adult donors. I'll start and you'll see how it happens.

9:25

Remember that one step is equal to one week. You can see the microbial community in the feces changing week after week. These weekly changes far outweigh the differences between two healthy adults on the project, represented here by the brown dots below.

You can see the yellow dot approaching the adult fecal microbiome. All this up to the age of about 2 years. But here, something unusual is going to happen. He will be given antibiotics for an infection in his ear. You see a big change in the microbiome, followed by a rapid recovery. I'll rewind the video.

In just a couple of weeks, there were significant changes: first, a decline after many months of development, and then a relatively rapid recovery. By day 838, when the video ends, you can see that the stool microbiota has reached adult levels despite the intervention of antibiotics.

10:26

This experiment is interesting because it raises fundamental questions about interventions in child development at different stages. How important is it when the microbiome changes so quickly? Will this impact drop into the sea, will it pass unnoticed?

It turns out that if children are given antibiotics in the first six months of life, they are more likely to be overweight than children who do not receive antibiotics or receive them later. Therefore, how a child is treated early in life has implications for the microbiome and overall health at an older age. We are only now beginning to understand this.

This is very interesting, because in addition to the effect of antibiotics on resistant bacteria — which is very important — we will see their detrimental effects on the gut microflora. And then, perhaps, antibiotics will inspire us with the same horror as the metal devices of the ancient Egyptians, with which they shredded and extracted the brain before embalming.

11:26

I told you that microbes have important functions. In recent years, they have been associated with a number of different diseases, including inflammatory bowel disease, heart disease, colorectal cancer and even obesity. As it turns out, the link with obesity is particularly strong. Today, we are able to determine with 90% accuracy whether you are obese by examining the microbes in your gut.

The numbers are impressive, although this might seem like a strange test, because you can easily tell which of these two is obese without any microbial studies. But it turns out that even by deciphering their entire genome and getting all the information about their DNA, you can predict obesity with only 60 percent accuracy. Amazing, isn't it? This means that these kilograms and a half of microbes living in our bodies are more important to health than any gene in your genome.

12:22

With mice, we can experiment even more. In mice, microbes have been linked to a number of other diseases, including multiple sclerosis, depression, autism and again obesity. But how do we determine whether differences in the microbial mix are the cause of the disease or the consequence? You can grow a group of mice that do not have their own microbes in a sterile bubble. We can add microbes that we think we need and see what happens.

When we take microbes from an obese mouse and transplant them into a genetically normal mouse that grew up in a bubble with no microbes of its own, it gets fatter than if it got them from a normal mouse. This is happening for an incredible reason. Sometimes microbes help mice digest food from the same diet more efficiently, so they extract more energy from it. But sometimes microbes affect the behavior of mice. They eat more than normal mice and get fat if left unchecked.

13:23

Interesting, isn't it? This indicates the ability of microbes to influence mammalian behavior. You might wonder if this can happen between different species. As it turned out, if you take the microbes of a full person and transplant them into mice grown in a sterile environment, these mice will later become fatter than if they were transplanted microbes from the body of a thin person. However, you can “inoculate” mice with specially selected mycloflora, and it will not allow them to gain weight.

13:54

We can do the same with malnutrition. So we participated in a project funded by the Gates Foundation. We cared for children in Malawi who were suffering from kwashiorkor, a severe nutritional deficiency. Mice transplanted with kwashiorkor lost about 30% of their body weight in just three weeks.

However, they can be cured with a peanut paste supplement, which is used to treat children in the clinic. Mice transplanted with the microflora of two twins recovered from kwashiorkor also recovered. This is incredible because it means we can develop treatments by testing their effectiveness in mice by transplanting human gut microbiota into them. We may even be able to develop individualized treatments.

14:37

It is important to give everyone a chance to participate in this study. A few years ago, we launched the American Gut Project, which allows you to find your place on the microbiological map. This is the largest scientific project launched with the money raised by the participants. More than 8,000 people have already joined it! So the point is, people send in samples, we decode the DNA of microbes and send them the results.

We also anonymously publish the results of research for the needs of scientists, universities and everyone interested. Anyone can access the data. On the other hand, when our mobile BioFrontiers lab comes somewhere, and we talk about how we use robots and lasers to examine poop, the number of people who want to do it somehow decreases. (Laughter) I guess you're still interested, so I brought some sample kits for you to try.

15:34

Why would we do that? It turns out that microbes are important not only for health research, but for the treatment of diseases. This is one of the newest visualizations we've created with colleagues at the University of Minnesota. Here's a map of the human microbiome again. I'm going to add the microflora of patients with pseudomembranous enterocolitis.

This is the most severe form of diarrhea, when you go to the toilet up to 20 times a day. These patients were treated unsuccessfully with antibiotics for two years. So they were chosen for our experiment. What would happen if we transplanted stool samples from a healthy donor -- this is a star down here -- into our patients? Will the good germs fight the bad ones and the patients recover?

Let's see what happens. Four of these patients are transplanted from a healthy donor. You can see that there's an immediate shift in the gut microbiome. Within one day after the transplant, all symptoms will disappear, and the diarrhea will disappear, the patients are again healthy and no different from healthy donors, and their state of health is stable. (Applause)





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16:48

We're just getting started. We're just beginning to learn about the effects of microbes on a variety of diseases, from inflammatory bowel disease to obesity, and perhaps even autism and depression. We need to develop a kind of microbial navigator, so that we not only know where we are, but also where we are going or what to do to get there. It should be made as simple as possible so that even children can use it. (Laughter)

17:16

Thank you very much.

17:19

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