Exploring the Microcosm Within

Adventures and insights from the microbiome
April 1, 2016 Updated: April 10, 2016

You may not sense it, but many aspects of your life are controlled at the microscopic level. A number of intriguing studies from the last few decades have shown that we each possess a personal colony of bacteria that has a big influence on our weight, mood, metabolism, fertility, and propensity for disease.

This diverse microbial part of ourselves is called our microbiome. The majority of this bacteria—3 to 5 pounds worth— live in your intestines, but your other organs have their own set of microbes as well.

Humans are not the only ones living in concert with bacteria, every plant and animal on earth do. This is the new science of the hologenome—a concept in which all organisms are interlinked through a complex microbial network in ways we are only beginning to understand.

In his new book, “The Microcosm Within: Evolution and Extinction in the Homogenome,” Dr. Bill Miller looks at what recent research tells us about our relationship with microbial life, and how modern lifestyles could be changing it for the worse.

Epoch Times talked to Dr. Miller about what he’s learned from studying the microbiome, and why bacteria are just as much a part of who we are as our innate human cells.

Epoch Times Photo
Dr. William B. Miller.

Epoch Times: You say that research into the microbiome has changed the way we look at ourselves. How so?

Dr. Bill Miller: We used to think we were a singular living entity. I look in the mirror and see Bill Miller, and I’m just one thing, right? Well, that may be true with how I feel about myself. But if you actually examine what we are, metabolically, immunologically, under a microscope—we are a combination of microbes and our own innate cells. It is this combination that permits us to survive. We are dependent upon them.

So we’re a sort of confederacy of life that’s linked together in the way that we appraise ourselves as one thing.

The amount of this microbial life is astounding. It’s ten times the number of cells than that of our own. I know this sounds impossible but this is a strict truth. We don’t feel it. We don’t know it’s there. We don’t know it’s acting. But now, both in science and in medicine, we’re beginning to understand that we’re a combination of both of these things—this microbiome.

And furthermore this microbiome is different in every single part of our body. So our gut microbiome is different than our respiratory system microbiome. But the complicating factor is that they’re all linked together.

Epoch Times: One of the ideas that have emerged from our understanding of the microbiome is called the hygiene hypothesis. Could you explain what this is?

Dr. Miller: The hygiene hypothesis is this: We now live in a different type of association with microbes than we did in the past. We don’t have fewer microbes, we have different microbes.

For example, people used to live on farms. They lived with an intimate association with the earth and with dirt. They played with farm animals, and they slept five to a bed. This is a different experience than we have now. Our culture of cleanliness is changing the populations of microbes that we experience. We’re only learning now the nuances of this balance.

Secondly, we’re using antibiotics. That’s a modern human phenomenon. Never before in our evolutionary history did we administer antibiotic drugs into our self and into the food chain as we do now. Now, antibiotics are one of the great discoveries in all of human history, but they have a negative side, too.

I was trained not to give out antibiotics unless they were necessary. But I will tell you as a front line physician, you’re always under pressure to give out antibiotics. Your patients demand it because antibiotics cure. Physicians in general give in because even if the patient doesn’t need it, they figure it’s not doing any real harm.

The problem is that it is doing subtle forms of harm. It upsets the bacterial balance. These are broad spectrum antibiotics. They don’t act against just one bacteria. They act across differing strains of bacteria, and the balance gets upset.

According to the hygiene hypothesis, our modern sense of hygiene and antibiotic drug use has changed the types of bacteria that we’re coming into contact with. Over time, we’re going to determine that many of the things we thought were effective treatments were not, and other things that didn’t seem likely to be good treatments, are.

I’ll give you an explicit example: cruise ships and norovirus. This gets people’s GI systems upset. The crew is miserable because they have to go back to port early, and they have to sanitize the ship.  So if you go on a ship you’ll see that there are Purell dispensers all over the place. The problem is that not only is Purell not useful, the lab research shows that it actually spreads norovirus.

Epoch Times: How has our understanding of the microbiome changing how we treat disease?

Dr. Miller: We’re going into a new era of medicine where we will be treating some infections by administering different microbes so we can bring back the balance. This is already being done with – it-

This is not science fiction— it is already being done, and we will be doing more and more of it as we understand it in the future. For example, the treatment for allergy and asthma may be a set of probiotics.

We’re not there yet, but that’s the line of reasoning that we’re beginning to follow.  We know now that we have to look at things in a different way than we did before.

Currently, medicine is all about pills and surgical procedures. It’s all about action. Take it out. Give them a pill that will block it. This has served us for a long time. But now we’re going to have more nuance in medicine. It’s going to be kind of like an Eastern philosophy—a balance of forces. We’re going to restore balances that we didn’t know were there before.

Epoch Times: One of the modern diseases you discuss in regard to the microbiome is the rise of food allergies. How does a change in the balance of bacteria influence this?

Dr. Miller:  Our experience with asthma and allergies of all kinds is linked to this critical balance of bacteria. The incidents of allergies and asthma is higher in industrialized countries than in non-industrialized countries, and there’s pretty good evidence that the actual amount of allergy, and food allergy in particular, are much larger than they were in the past.

You can talk to anyone my age (I’m in my 60s), I never knew anyone with an allergy growing up. People had allergies to pollen and things like that, but there was no kid with a peanut allergy that I ever knew. But now, you have a dinner party, and your guests will tell you, “I’m allergic to tomatoes, mushrooms, and cucumbers.” Their kids can’t eat this and they can’t eat that.

Our sense of hygiene is changing the types of microbes that we’re coming into contact with. Some of these microbes are vital to us. Others aren’t exactly vital, but they change how we experience stress. Allergies are a response to immunological stresses. People don’t think of that in those terms, but that’s exactly what it is. You have a stress, your immune system reacts. You have an allergic reaction. Your body is saying that there is something foreign here that you don’t want.

One of the things that most people don’t realize about the microbiome is the constant transfer of information. Most people don’t think of their cells as a transfer agent of microbial life.

We are shedding microbes all the time. When we shed our microbes, they’re picked up by plants. And in turn, when we ingest plants, we’re ingesting their microbes. There’s a very complex ecological cycle that’s going on in which we are both participant and recipient. So in the case of peanut allergies, peanuts are a product of holobiomic life—they can only exist because they own a set of microbes that permit nitrogen fixation and other things that a legume needs. They have their microbial fraction and we have ours.

The microbes in your gut are part of your ecology. It’s the fraction of you that’s getting your immune system to react negatively to it by giving off antigens that the immune system senses.

The microbes in the gut give off other signals, too. For example, we only learned recently that 90 percent of the brain chemical serotonin—a mood chemical—is produced by microbes in your gut. You absorb the microbial fraction. Your microbes control your mood much more than you could imagine. It’s kind of frightening actually, but it’s still the truth as we understand it today.

What we’re finding out is that are associations between allergic reactions and the microbial populations that are part of us. And we’re only beginning to tease these out. There are more questions now than there were before and new avenues in research. The answers are only beginning to come in.

There are going to be experiments in which people are going to be given probiotics and fermented foods such as kim chi, sauerkraut, things like that. Lots of things are going to be tried to see if by manipulating the gut microbiome you change the incidents of food allergies. We don’t know whether or not those experiments will prove successful, but there are tantalizing ideas out there that it is likely to be true. In three or four years we’ll know a lot more.

Epoch Times: So when someone says that science hasn’t proven the hygiene hypothesis, it doesn’t necessarily mean that it isn’t true. It just means that it has not been examined in enough detail to determine if it’s true.

Dr. Miller: That’s correct, or it is true in the cases that we understand, but there are other cases that we did not know to look for. For example, it is true that antibiotics cure pneumonia. But it is also true that antibiotics create problems. So at one point we would say, “Well, we know the truth is that the best treatments for all pneumonias are antibiotics.” That’s true up to a point, but in a future time, the best treatments for pneumonia might be an aerosol of another microbe that restores a balance to the respiratory microbiome.

This is actually being researched, by the way. There are people who are beginning to think that in COPD (chronic obstructed pulmonary disease) part of the problem is not only the fibrosis that’s going on in the lungs, but a critical change in the microbiome of the respiratory system. If you adjust that, you won’t cure the COPD but the patient won’t get pneumonia like they normally do.

Epoch Times: Based on what we know now, are there ways to influence our microbiome so that we can lead a healthier life?

Dr. Miller: With something as complicated as these balance of forces, you know who becomes the best scientist of the bunch? The individual. Each of us is highly individualized. Not merely because of the innate personal selves that we see with our eyes. We have extremely detailed individual differences of our microbiome. We share as humans certain obligatory microbes—these are ones we must have in order to survive. Our immune system and metabolism will not work properly without them. And we must gather them quickly to survive.

You know, fetuses used to be thought of as sterile. When I was taught in medical school it was just obvious that every fetus, the womb, the amniotic fluid that surrounds the baby is sterile. But that is dead wrong. Why didn’t we know it? Because we used cultures and the cultures were negative. But what we didn’t know was that culturing only demonstrated fewer than 10 percent of the total amount of microbes that were there. It was a horribly inefficient technique, we just never knew it.

So when someone has a urinary tract infection and their urinalysis comes back sterile. Well, it’s culture negative, but it’s not sterile. There is no such thing as sterility. You know NASA’s sterile rooms? They sent probes out to space because they’re sterile. No not even close. They were culture negative. Now with a new technique called metagenomics, which basically enables us to look at gene sequences, there’s a whole enormous world of microbes that we didn’t know existed. We’ve seeded space with microbes, we just didn’t know it. We thought we were being good but we weren’t.

Epoch Times: This makes me think that we don’t even know what we don’t know.

Dr. Miller: That’s exactly right. Good scientists are humble in the sense that they reflect on the fact that the best they can do is know a little bit more than what we knew before, and we don’t know very much. But we’re filled with hubris. Humans are not a humble group. We have a very large sense of our selves. But science is humbling. When you start along a pathway of learning and thinking about science you see how little we yet understand. We do remarkable things. Humans have accomplished some very remarkable things and many more are coming.

Epoch Times: The microbiome concept is very humbling. The fact that I’m made up of 10 times more microbes than actual human cells is huge.

Dr. Miller: Here’s an interesting fact that was just uncovered by a group of French researchers: You know who decides when you’re full? Your microbes. You feed your microbes and they give off different chemicals. When the microbes in your stomach reach a point where they’re satisfied with the nutrition they receive, they start putting out a satiety protein. It goes to your brain 20 minutes after you start eating these chemicals circulate and tell you, “Okay we’ve had enough.”

We used to think this was coming from the cells of our stomach, and these made the proteins which told our brain it was full. Some of the cells of our stomach are participants, but the greatest majority of those chemicals are coming from the microbes in your stomach, and when they’re full you’re full.

Epoch Times: You mentioned before how our microbes also dictate our mood. It made me wonder: what other aspects of us are really our microbiome in action?

Dr. Miller: Well, we need to change our frame of reference. When you say, “my microbes,” they are you too. We have to get over this them and us aspect. That’s the old way of thinking. It is not a host and guest relationship. It’s a consensual we. My microbes are part of me. You are a confederacy of all these combined things.

So what aspects do they influence? All of you. What aspects do your innate cells influence? All of you.

Let me give you illustration. I use this with my physician friends and this helps them start to think about things differently. If someone has his spleen or appendix taken out he will be fine. But if I remove all the microbes from your gut you’re dead in a day. So which is the more important fraction? Which is the organ?

So the proper way to think of the microbiome is it’s a system of accessory organs that are as much of you as your liver, your spleen, or your lung is of you. It’s a hard concept, but that is a reality of all animal and plant life in this world. This is the hologenome. This is what we are, we just didn’t know it before.

Epoch Times: So when I say, “human cells,” that’s a limiting definition of what’s actually essential to me.

Dr. Miller: That’s correct, but I’ll make it even more complicated.

For example, you’re born, you become a child, and then an adult. You’re always you but your manifestation—your physical you—is different at every point in time. We accept that our hormonal system changes. I’m different before puberty than I am after puberty and as I get older testosterone levels drop and so on. People understand that there are hormonal markers of life. They go through developmental stages, they develop hormonal surges, women go through menopause.

We accept that our innate cells go through a life arc. So does our microbiome. There are parts that have to be there consistently. There are parts that can come and go. It’s the fraction of balance that changes. All this research requires an understanding that all of this is a simultaneous overlapping arc of life in motion. It’s always in motion. There’s never any stasis or stand still. It’s a very beautiful concept.

The microbiome is as much of you as your liver is, but it’s in flux. Just like your personal hormonal levels are in flux, and your moods are in flux. We’re basically a flux agency of this conjoined life.

It’s a difficult concept, but once your mind starts to wrap around it, it’s a very beautiful thing. Even when you die, you just change. It’s part of the arc. When you die, your cells aren’t all gone. They are being consumed. They are being transmuted. You have been shedding them your entire life. How do bloodhounds follow scent? Shed cells. These things are invisible to us but you are a flux agency and you’re participating in this great diversity experiment. You’re contributing all the time. You’re in service to the outward ecology even when you can’t see what you are.

Epoch Times: It seems that so much of our life takes place at a level that we can’t see.

Dr. Miller: Most of it. It took me a lifetime to learn that our physical embodiment is a very subtle and pleasing illusion. We are not what we think we are. Not even close. But what a lovely thing we’re granted to believe we are as we are. It’s a miracle.

Follow Conan on Twitter: @ConanMilner