One intriguing recent study, done by Jan-Hendrik Hehemann from the University of Victoria in British Columbia, reported that a bacterium commonly found in the gut of Japanese people produces a rare enzyme capable of digesting seaweed, a trait seldom found in the same bacteria in other populations. The researchers demonstrated that the gene coding for this enzyme originally came from a marine bacterium commonly found on seaweed—Zobellia galactanivorans. The resident gut bacteria, called Bacteroides plebeius, had apparently picked up this useful gene from seaweed in the diet and incorporated it in its genome, where it has been preserved ever since, allowing most Japanese to make good use of the seaweed in their diet.* No doubt scientists will soon find other examples of our microbiota mediating our relationship to the rest of nature, speeding our ability to adapt. In effect, the microbiome vastly extends our genome, giving us access to a tremendous bag of tricks we did not need to evolve ourselves.
So it made very good sense, evolutionarily speaking, for us to join forces with the microbes, which are simply more skilled than we are at all the ways of biochemically contending. During the two billion years of natural selection that bacteria have undergone before more complex multicellular creatures arrived on the scene, they managed to invent virtually every important metabolic trick known to evolution, from fermentation to photosynthesis. (According to Lynn Margulis, who until her death in 2011 was the microbiome’s most eloquent human advocate, the only important biochemical innovations to come along in the billion years since then are snake venom, plant hallucinogens, and—this is a big one—cerebral cortices.) And one of bacteria’s greatest tricks of all is to combine forces with other creatures, taking up residence in or on their bodies, possibly even their cells, trading various metabolic services for their upkeep.*
Researchers have identified several, but surely not all, of the services that resident gut microbes supply to their hosts. Though we’ve tended to think of bacteria as agents of destruction, they are, like other fermenters, invaluable creators as well. In addition to producing organic acids, the gut bugs manufacture essential vitamins (including vitamin K as well as several B vitamins), enzymes necessary to digestion, and a great many other bioactive compounds scientists are only just beginning to recognize. Some of these compounds act on the central nervous system, moderating our appetite and the mechanisms that determine how we store fat.
Indeed, the microbiota may play an important role in regulating our weight. It has long been known that feeding antibiotics to livestock makes them gain more weight on the same amount of feed, and though the mechanism has not been identified, intriguing new clues are emerging. A group of researchers at Washington University in St. Louis discovered that the types of bacteria dominant in the gut of obese individuals (in both mice and humans) are very different from those found in slender people, and that the different species of gut bacteria metabolize food more or less efficiently. This suggests that the amount of energy we obtain from a given amount of food may vary depending on the kinds of microbes living in our gut. So might changing the composition of our gut bacteria in turn change our weight? Possibly: The researchers found that when they transferred bacteria from the gut of fat mice into germ-free mice, the germ-free mice gained nearly twice as much weight as when they received gut bacteria from skinny mice.* Other research has found that specific gut microbes, such as Helicobacter pylori, play a role in regulating the hormones that control appetite.
Could it be possible that the microbiota also affects mental function and mood, as some of the fermentos I met in Freestone claimed? The idea no longer seems preposterous. A recent study performed in Ireland found that introducing a certain probiotic species found in some fermented foods (Lactobacillus rhamnosus JB-1) to the diet of mice had a measurable effect on their stress levels and mood, altering the levels of certain neurotransmitters in the brain.† Precisely how the presence of a certain bacterium in the gut might affect mental function is unclear, yet the researchers found they could block the effect by severing the vagus nerve that links the gut to the brain. Studies like this one make you wonder if it might someday be possible to cultivate, or garden, our microbiota, altering its makeup to improve our physical and possibly also our mental well-being.*
Right now, of course, and for the last several decades at least, we have been assiduously doing exactly the opposite: disordering the community of microbes in our bodies without even realizing it, much less with any sense of what might be at stake. Under the pressures of broad-spectrum antibiotics, a Pasteurian regime of “good sanitation,” and a modern diet notably hostile to bacteria, the human microbiota has probably changed more in the last hundred years than in the previous ten thousand, when the shift to agriculture altered our diet and lifestyle. We are only just beginning to recognize the implications of these changes for our health.
For some of us, the deleterious changes to our gut microflora begin at birth, the moment when we are first inoculated with the microbes that will accompany us through life. In utero, our bodies are sterile, but the microbially messy process of vaginal birth exposes the baby to a set of bacteria that immediately begin to colonize its body. Children born by Cesarean section, a far more hygienic process, take much longer to populate their intestinal tract, and never acquire quite the same assortment of bugs. Some researchers believe this could help explain the higher rates of allergies, asthma, and obesity observed in children born by Cesarean.
The sanitized environment in which we try to surround our children is probably also taking its toll on their microbiota. Now widely accepted, the “hygiene hypothesis” holds that children need to be exposed to more bacteria, not fewer, in order to properly develop their immune system, so that it can learn to accurately distinguish between good and bad microbes. Without that training, the theory goes, the body is apt to mistake benign proteins, such as those in certain foods, for mortal threats, and react accordingly. The hypothesis explains escalating rates of allergy, asthma, and autoimmune disease in the developed world, as well as the curious fact that children reared in the microbially rich—some would say perilous—environment of a farm have fewer allergies and generally more robust immune systems.*
The average child in the developed world has also received between ten and twenty courses of antibiotics before his or her eighteenth birthday, an assault on the microflora the implications of which researchers are just beginning to reckon.* Like the pesticides applied to a farm field, antibiotics “work,” at least in the short term. Yet as soon as you widen the lens from a narrow focus on the “enemy species,” you see that that such blunt weapons inflict collateral damage to the larger environment, including, in the case of pesticides, the microbial community of the soil. Resistant bugs and various other health problems soon emerge; the soil’s ability to nourish plants and help them withstand disease is also compromised, because the toxins have reduced the community’s biodiversity and thereby compromised its resilience. As in the soil, so in the gut. The drive for control and order ends up leading to more disorder.†
And then of course there is the diet, perhaps the most important factor in first establishing and then maintaining the microbial community in our gut. The process begins with nursing, which shapes the gut flora in some unexpected ways. A mother’s nipple harbors a community of lactobacilli, and it was recently discovered that the milk itself contains bacteria that may play a role in colonizing the baby’s gut. But the most important contribution of mother’s milk to the infant microbiota may be in encouraging the “right” kinds of bacteria to dominate it from the start. For years nutritionists were mystified by the presence in mother’s milk of certain complex carbohydrates, called oligosaccharides, which the infant lacked the necess
ary enzymes to digest. Evolutionary theory argues that every component of mother’s milk should have some value to the developing baby, or else natural selection would be likely to discard it as a poor use of the mother’s precious resources. So why would she produce nutrients her baby can’t metabolize? It turns out the oligosaccharides are there to feed not the baby but certain of its intestinal microbes: Their presence in the diet ensures that certain optimal species of bacteria, and specifically Bifidobacterium infantis, proliferate and get established before less savory characters gain a toehold.*
As nature’s most perfect food—having been shaped entirely by natural selection—mother’s milk has much to teach us, and not least these two crucial facts: that bacteria is good food, and that feeding the bacteria is as important as feeding the baby. Put in a more scientific way, the diet should include both “probiotics”—beneficial bacteria—and “prebiotics”—something good for those bacteria to eat. But for most of the last century, those of us living in the developed world have heeded neither of these principles.
To the contrary: We are, literally, “anti-biotic.” We’ve worked hard to eliminate bacteria from the diet, by sterilizing our food, and, by processing it, we’ve removed much of the fiber—precisely that component of the diet of greatest value to the microbiota. With the exception of yogurt, live-culture foods have all but vanished from our plates. To take just one example, L. plantarum, the bacterium found in such abundance in most vegetable ferments, has been ubiquitous in the human diet since prehistoric times, along with all the vegetables it typically accompanied. But the so-called Western diet, with its refined carbohydrates, highly processed foods, and dearth of fresh vegetables, is downright hostile to fermentation: It preserves foods by killing bacteria rather than cultivating them, and then deprives our gut bacteria of much of anything good for it to ferment.
“The big problem with the Western diet,” Stephen O’Keefe, a gastroenterologist at the University of Pittsburgh, told me, “is that it doesn’t feed the gut, only the upper GI [gastrointestinal tract]. All the food has been processed to be readily absorbed, leaving nothing for the lower GI. But it turns out that one of the keys to health is fermentation in the large intestine.” A diet as rich in fats and refined carbohydrates as ours may supply our bodies with plenty of energy, but the lack of fiber in the diet is, in effect, starving our gut and its microbial residents. O’Keefe and many others are convinced that the myriad intestinal disorders that have become common among people eating a Western diet can be traced to this imbalance. We have changed the human diet in such a way that it no longer feeds the whole superorganism, as it were, only our human selves. We’re eating for one, when we need to be eating for, oh, a few trillion.
But intestinal problems may be the least of it. For more than a century now, medicine has recognized a link between this Western diet and the historically novel set of chronic diseases that now kill most of us in the West: heart disease and stroke, obesity, cancer, and type 2 diabetes. Populations that eat a Western diet consistently develop high rates of these diseases. What remains subject to debate is exactly what about this diet makes it so lethal: Is it the presence in it of some “bad” nutrient, such as saturated fat or refined carbohydrates or cholesterol? Or is it the absence from it of some essential “good” nutrient, like fiber or omega-3 fatty acids?
Any one of these nutrients, present or absent, might be the dietary culprit responsible for this or that chronic disease. But lately some researchers are beginning to suspect that the problem with the Western diet may be both less direct and more systemic, and that most if not all the important chronic diseases may have a similar etiology. Though none has yet dared use such an ambitious term, several scientists across several disciplines appear to be working toward what looks very much like a Grand Unified Theory of Diet and Chronic Disease. The theory turns on the concept of inflammation, something in which the human microbiota may turn out to play a crucial role.
A growing number of medical researchers are coming around to the idea that the common denominator of many, if not most, of the chronic diseases is inflammation—a persistent and heightened immune response by the body to a real or perceived threat. For example, the buildup of plaque in the arteries, once thought to be the result of saturated fat and cholesterol in the diet, now appears to be an inflammatory response, the arteries’ attempt to heal themselves. Various markers for inflammation are common in people with “metabolic syndrome,” the complex of abnormalities that predisposes people to cardiovascular disease, type 2 diabetes, and cancer, and which now afflicts 44 percent of Americans over the age of fifty. So what might be the source of these inflammatory responses, across so many organs and systems and people? One theory—and so far it is just a theory—is that the problem begins in the gut, with a disorder of the microbiota, and specifically of the gut wall. For when the integrity of the epithelium has been compromised, various bacteria, endotoxins, and proteins can slip into the bloodstream, causing the body’s immune system to mount a response. It is the resulting inflammation, which affects the entire organism and may never subside, that over time can lead to any number of the chronic diseases that have been linked to diet.
That, at least, is the theory. It no longer sounds even the least bit crazy to me, but, then, maybe I’ve been spending too much time among the fermentos, people who believe that the cure for diabetes and whatever else that ails you is kombucha. It obviously can’t be that simple. And yet the case for getting more live-culture foods in the diet (especially of our children) is already compelling and growing more so. Consider the research that has come out in just the past decade or so. Probiotics—beneficial bacteria ingested either in fermented foods or in supplements—have been shown to: calm the immune system and reduce inflammation;1 shorten the duration and severity of colds in children;2 relieve diarrhea3 and irritable bowel syndrome;4 reduce allergic responses, including asthma;5 stimulate the immune response;6 possibly reduce the risk of certain cancers;7 reduce anxiety;8 prevent yeast infections;9 diminish levels of E. coli 0157:H7 in cattle10 and salmonella in chickens;11 and improve the health and function of the gut epithelium.12
Much about the microbiota and fermented foods remains to be explored. Scientists still don’t understand exactly how the probiotics in fermented foods achieve their effects. Only occasionally do they actually take up permanent residence in the gut. Some of them, notably L. plantarum, move in and adhere to the epithelium, helping to crowd out various pathogens and strengthen the gut wall. But other probiotic species appear to be only transient members of the microbial community. And yet, like visitors often do, they seem to leave their mark, contributing things of value—a useful gene or plasmid, a bioactive chemical, some “news” of the microbial environment out there—to the biota. Somehow, they seem to stimulate the local residents to better resist invasion by pathogens. A series of recent papers has demonstrated that even bacteria that are just passing through can alter the genetic expression, and sometimes the genome, of resident gut bacteria, teaching them some new metabolic tricks.*
Taken together, the microflora may function as a kind of sensory organ, bringing the body the latest information from the environment, as well as the new tools needed to deal with it. “The bacteria in your gut are continually reading the environment and responding,” says Joel Kimmons, a nutrition scientist and epidemiologist at the Centers for Disease Control and Prevention, in Atlanta. “They’re a molecular mirror of the changing world. And because they can evolve so quickly, they help our bodies respond to changes in our environment.”
Mysteries remain, obviously, but the case for eating live-culture foods seems strong, and perhaps strongest for fermented vegetab
les.† For in addition to bringing large numbers of probiotic guests to the party (including such impressive characters as L. plantarum), the vegetables themselves also supply plenty of prebiotics—nourishment for the bacteria already there. So you won’t be surprised to learn I have been busy at my pickling, working to perfect my sauerkraut and kimchi. Since they have been in the human diet for thousands of years, it makes sense that these fermented foods would by now have become tightly woven into our biology. We have coevolved with them, not just the plants, but the microbial species these ferments contain in such abundance, especially ones such as L. plantarum, which for all we know might be one of the unsung heroes of human health.
And yet it’s not at all hard to see why it would take this long to recognize and appreciate the complexity of these foods and these relationships—because that complexity is, literally, so hard to see. As with the microbiota of the soil, another fermenting universe of biological complexity that it closely resembles, the complexity of the gut microbiota is supremely difficult to comprehend. So much more than the sum of its unprepossessing parts, it has been, until very recently, invisible to the reductive lens of Western science, which has always been better at understanding individuals (pathogens, variables, elements, whatever) than communities. And then there is the fact that it utterly fails to conform to our ideas—including our aesthetic ideas—of what a system or an organ should look like. Let’s face it, the kilogram mass of microbes living in our gut don’t look like much. It doesn’t help that we also find it disgusting.
Cooked: A Natural History of Transformation Page 33