The Essential Book of Fermentation (10 page)

I can lose any number of body parts—a finger, an eye, a leg—and still be me and be healthy. But I can’t lose my intestinal flora. Without it, my immune system is compromised, my ability to digest plants is compromised. I wouldn’t last long. So what and who am I?

CHAPTER 5

New Findings About the Ecosystems Within Us

In nature, there are various ecosystems that we can see with our naked eyes, organized by the kinds of environmental conditions that exist in their habitats. From New England across the northern tier of states to the Pacific Northwest, you can find long-abandoned field ecosystems, with grasses and tall weeds growing in the sunlight, with old apple trees in decline, left over from a time when the field was an orchard, all abutting woodland. Where water ponds and flows, you will find a riparian ecosystem that’s quite different from the old field, with almost completely different weeds and shrubs, water plants, and fauna. Forests and mountains in the Rockies and desert ecosystems in the Great Basin are all very different, with different players participating.

There are also ecosystems that we can’t see, including those in our intestines. And if you examine people’s gut ecosystems closely, as researchers at the European Molecular Biology Laboratory in Heidelberg, Germany, have done, you will find something astonishing. The scientists have discovered that people’s gut ecosystems fall into three distinct types, which they call enterotypes. And the three categories hold up despite differences in ethnicity, sex, weight, height, health, or age. The scientific team is now exploring possible reasons why the three enterotypes exist. It’s all speculation at this point, but it may be because the intestines of newborn infants are randomly colonized by certain collections of pioneering bacteria, and these microbes change the gut so that only certain species can follow or elaborate on them. We will surely find the answer in coming years.

As we know, gut bacteria help in food digestion, work with the immune system, help prevent disease-causing bacteria from gaining a toehold in the gut, and synthesize vitamins by producing enzymes that our bodies can’t produce. Dr. Peer Bork, the leader of the Heidelberg group, and his fellow scientists have found that each of the three enterotypes makes a different balance of these enzymes, and thus produces a different mix of vitamins. For example, the ecosystem they call Enterotype 1 (ET1) has high levels of bacteroides that produce enzymes for manufacturing vitamin B
₇
, also known as biotin. Bacteroides in Enterotype 2 (ET2) were fairly rare, while the genus
Prevotella
was very common and produced enzymes that make vitamin B
₁
, called thiamine.

I found no mention of the predominant bacteria or their function in Enterotype 3, so I asked Dr. Bork about it. In an e-mail, he replied, “With more than six hundred samples analyzed, Methanobrevibacter seems the major driver of Enterotype 3, but also Ruminococcus is associated with ET3. Haem biosynthesis seems over-represented in ET3.” Rather than producing enzymes that allow the synthesis of vitamins, Enterotype 3 bacteria are evidently involved in heme (“heme” is the American spelling; “haem” is the European) biosynthesis—the production of hemoproteins, the most familiar of which to most people is hemoglobin. There are many other heme proteins with various important functions in the body.
Methanobrevibacter
smithii
is the dominant archaeon (a class of microbes with no nucleus) in the human gut. It is important for the efficient digestion of complex sugars because it consumes end products of bacterial fermentation, helping to transform nutrients into calories.
Ruminococcus
is an anaerobic, gram-positive microbe. One or more species in this genus are found in significant numbers in the human gut.

Dr. Bork told Carl Zimmer of the
New York Times
that doctors might be able to use knowledge of the enterotypes to find alternatives to antibiotics. Instead of trying to kill disease-causing pathogens that have disrupted the ecological balance of the gut, Zimmer wrote, they could try to provide reinforcements for the good bacteria by attempting to restore the enterotype you had before. This provides probiotics with a new wrinkle.

Dr. Bork said his team had no hypothesis when they started comparing ecosystems of gut bacteria among people both healthy and sick, obese and slender, Asian and European, and so on—four hundred people in all. They just wanted to see what was happening, and they were startled to find that the gut ecosystems all fell neatly into the three categories. These findings concern gut bacterial ecosystems—broad, overall categories of microbes that have a dominant type of bacteria for each category and specific functions within our bodies. If you compared these gut ecosystems to life at the macro level where human beings live, it would be like saying beavers and trout dominate the streams and lakes ecosystem of Maine, while alpine wildflowers and eagles dominate the Rocky Mountains’ higher elevations, and deer, bear, and hickory trees dominate central Pennsylvania. All these systems are healthy, they all share some of the same flora and fauna, but each is different from the others.

This is just the beginning of our understanding of the universe of microbes on us and in us. For every person on earth, there are almost 100 trillion cells on or in his or her body, only 10 trillion of which are human body cells.

From our understanding of how health develops in natural ecosystems, whether garden or body, we can see why the surest way to develop an unpleasant body odor is to use harsh deodorants and antiperspirants. By cleansing yourself of microbes with antibacterial soaps, you are dismantling their healthy ecosystem on your skin. The sterile skin breathes and exudes sweat and other natural compounds, and the first microbes to recolonize the skin start to metabolize the sweat and other compounds. The process develops as an unpleasant body odor. The answer is to let the skin’s healthy ecosystem of microbes reestablish itself by using pure soap without antiseptic chemicals or detergents daily and putting away the harsh deodorants.

TRUST YOUR GUT

Most people don’t think much about their intestines—their guts—unless they are speaking metaphorically.

Think of the way people talk about guts:

“They have guts,” meaning they’re brave, stand up for what they believe, show courage, do the right thing even though it’s difficult. Some corollaries have become clichés: “No guts, no glory.” “It’s hard, but he’s going to gut it out.” And so on.

Other metaphorical uses describe intuition: “Trust your gut.” “I had a gut feeling.” “I just felt in my gut it was the right thing to do.”

And those gut feelings are also where you measure something against reality. To make a “gut check” is to see how you really feel about something, not with your head, or even with your emotional heart, but with the integrated whole being of who you actually are.

In other words, the gut is where you confront your personal feelings, priorities, and desires, even more than with your head and your heart. And it’s where you act from those feelings without, or despite, fear of the consequences. Could it be that the biological systems within us, without which we couldn’t function as human beings, and on which we depend for life itself, are so integral to who we are that when we need to check in on who we really are and make crucial decisions—even life-and-death decisions—we take the gut into account?

Most of us would like to think of ourselves as just the hominid portion of our being and the intestinal flora as something else. But it may be that those two seemingly separate entities are one, and that we reveal that when we speak of our guts.

A recent
New York Times
editorial, titled “A Universe of Us,” declared that “we think of ourselves as individuals . . . but whatever else we are, we are also a complex ecosystem, a habitat.” Scientists have now discovered another realm within that habitat that they call the virome—a large community of viruses. Far from making us sick, these viruses are a part of the human biome that makes us healthy.

Microbiologist Jeffrey Gordon reported in a study published in
Nature
that each of us has a pattern of viral DNA that is highly stable and highly distinct, even among closely related humans. This differs from our bacterial communities, which tend to evolve over time and are similar among family members.

That means you and I are not just the expression of our individual human genome and the DNA in our human cells, but rather we are a genetic landscape with the DNA of hundreds of different species working together to keep us healthy so we have time for wondering what’s for lunch.

CHAPTER 6

The Intelligent Intestine

It appears that the old saying “The way to a man’s heart is through his stomach” is scientifically accurate as well as metaphorically true—if by heart you mean the place where his thoughts and desires originate; that is, his brain.

The human gut communicates with the brain, recent studies show. Now there’s evidence that it’s the gut microbes that communicate directly with the brain. A healthy ecosystem of friendly gut bacteria not only keeps the gut happy, it evidently may help keep their hosts happy, too,
Science
News
reports.

Certain parts of the brains of mice fed a nutritious broth containing
Lactobacillus rhamnosus
developed more of a protein that senses an important chemical messenger called GABA than mice fed a sterile broth. The result was that the mice fed the gut bacteria were less anxious than mice fed sterile broth. In stress tests, the probiotic mice had fewer stress hormones than the sterile-fed mice. Further research showed that the chemical messengers leading to reduced feelings of stress and anxiety most likely traveled from the gut to the brain via the vagus nerve. In humans as well as mice, the vagus nerve connects the brain to the viscera, regulating gut function and reporting the state of the gut to the brain.