Cooked: A Natural History of Transformation (48 page)

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
necessary 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.