Cooked: A Natural History of Transformation (47 page)

I began to get some strong and surprising
hints when I
accompanied Sandor Katz to the third annual Fermentation
Festival, in Freestone, California. Held over the course of a sparkling spring weekend,
on the grounds of an elementary school that had temporarily sprouted tents and stages
and booths, a thousand or so people had gathered to celebrate the tastes, wonders, and
putative health benefits of fermentation. In this crowd, which had more than its share
of hippies both old and young, Sandor Katz was a major celebrity, unable to cross a room
or field without stopping to sign an autograph or pose for a picture. This was the place
to be if you wanted to buy a “kombucha mother”—the slimy mass of fungi and
bacteria used to ferment this ancient Chinese tea soda—or the cultures to make your own
tempeh, natto, kvass, or kefir, all of which were available for sampling. Never before
had I knowingly ingested so many different kinds of fungi and bacteria. And except for
the natto, a filamentous soybean-and-mucus treat that gave off a nauseating whiff of
putrefaction, it all went down the hatch without a hitch.

While cruising the book tables, I spotted
and purchased a thick self-published volume titled, refreshingly
non
euphemistically,
Bacteria for Breakfast: Probiotics for Good
Health
. The author, a pharmacist living in Pennsylvania, patiently laid out the
case for the myriad health benefits of fermented foods and “probiotics”—the
beneficial bacteria, most of them lactobacilli, often found in those foods. These
“good bugs” and their by-products were credited with all kinds of good
works, from improving digestion, reducing inflammation, and “educating” the
immune system, to preventing cancers of the gastrointestinal tract.

It turns out there is a substantial body of
peer-reviewed science to back up all these claims, and more generally give credence to
the age-old belief, shared by many cultures, that fermented foods confer special
benefits on our health. (The Romans treated various ailments with live-culture foods,
and Confucius insisted the key to long life
and good health was to eat
a fermented condiment, called a
jiang
, with every meal.) Yet some hard-core
fermentos go much, much further, claiming live-culture foods as a panacea for a range of
ailments that would seem to have nothing whatever to do with “gut health,”
from AIDS and diabetes to various disorders of the mind. At the Festival I talked to a
woman who claimed to have cured her child’s autism with raw milk and sauerkraut. I
learned about the GAPS (gut and psychology syndrome) Diet, recommended for everything
from autism to attention deficit disorder, and took in a lecture about “leaky gut
syndrome,” a condition caused by the “overgrowth” of bad bugs in the
colon that undermines the integrity of the epithelial barrier, allowing various toxins
to seep into the bloodstream and wreak all kinds of havoc. Talking to these people, and
listening to their fervent monologues, I was reminded of Dr. Casaubon, the character in
Middlemarch
who is convinced he has discovered “the key to all
mythologies.” Here among the fermentos, the key to all health, in body as well as
mind, was a lactofermented pickle.

At first I figured I had wandered into a
hothouse of pseudoscientific quackery that could be easily dismissed. Sandor Katz
himself is careful to distance himself from the more extreme claims of the fermentation
underground. “I don’t believe kombucha can cure diabetes,” he told the
audience at one point. After he wrote in
Wild Fermentation
, his first book,
that a diet rich in fermented foods was an important part of his self-treatment for HIV,
so many patients took his prescription to heart that he felt compelled to add a
disclaimer in his new book,
The Art of Fermentation:
“While I wish it
were so, live-culture foods are not a cure for AIDS.” But Katz also urged me to
look into the rapidly growing body of scientific research on the role of fermented foods
in gut health, and in turn the role of a healthy gut in our well-being overall. “I
think you’ll be surprised.”

I did, and I was. Following up on some leads
from Sandor, I began reading around in the subject, and speaking to scientists who study
the “gut microbiota”
^*
or
“microflora”—basically, the vast community of organisms (bacteria, fungi,
archaea, viruses, and protozoa) that reside in our intestines and exert far more
influence on our lives than was recognized until very recently. Sometimes the scientists
working in a particular field come across as just plain more
excited
than
scientists working in another area. Radical hypotheses and incipient breakthroughs and
Nobel Prizes are in the professional air, creating a bracing ozone of possibility. The
scientists working today on “microbial ecology” are as excited as any
I’ve ever interviewed, convinced, as one of them put it, that they “stand on
the verge of a paradigm shift in our understanding of health as well as our relationship
to other species.” And fermentation—as it unfolds both inside and outside the
body—is at the heart of this new understanding.

In the decades since Louis Pasteur
discovered bacteria, medical research has focused mainly on their role in causing
disease. The bacteria that reside in and on our bodies were generally regarded as either
harmless “commensals”—freeloaders, basically—or pathogens to be defended
against. Scientists tended to study these bugs one at a time, rather than as
communities. This was partly a deeply ingrained habit of reductive science, and partly a
function of the available tools. Scientists naturally focused their attention on the
bacteria they could see, which meant the handful of individual bugs that could be
cultured in a petri dish. There, they found some good guys and some
bad guys. But the general stance toward the bacteria we had discovered all around us
was shaped by metaphors of war, and in that war, antibiotics became the weapons of
choice.

But it turns out that the overwhelming
majority of bacteria residing in the gut simply refuse to grow on a petri dish—a
phenomenon now known among researchers as “the great plate anomaly.” Without
realizing it, they were practicing what is sometimes called parking-lot science—named
for the human tendency to search for lost keys under the streetlights not because
that’s where we lost them but because that is where we can best see. The petri
dish was a streetlight. But when, in the early 2000s, researchers developed genetic
“batch” sequencing techniques allowing them to catalog
all
the DNA
in a sample of soil, say, or seawater or feces, science suddenly acquired a broad and
powerful beam of light that could illuminate the entire parking lot. When it did, we
discovered hundreds of new species in the human gut doing all sorts of unexpected
things.

To their surprise, microbiologists
discovered that nine of every ten cells in our bodies belong not to us, but to these
microbial species (most of them residents of our gut), and that 99 percent of the DNA
we’re carrying around belongs to those microbes. Some scientists, trained in
evolutionary biology, began looking at the human individual in a humbling new light: as
a kind of superorganism, a community of several hundred coevolved and interdependent
species. War metaphors no longer made much sense. So the microbiologists began borrowing
new metaphors from the ecologists.

It’s important to keep in mind that,
despite the powerful new exploratory tools, the microbial world within our body remains
very much a terra incognita—its age of exploration has only just begun. But already
scientists have established that the microbiota of the human gut is in fact an
ecosystem, a complex community of species
doing a whole lot more than
just hanging out or helping us break down foods or making us sick.

So what exactly
are
the five
hundred or so distinct species and countless different strains of those species that
make up the kilogram or so of microbes in our gut doing there? Evolutionary theory
supplied the first big clue. For most of these microbes, their survival depends on our
own, and so they do all sorts of things to keep their host—us—alive and well. Indeed,
even speaking of “us” and “them” may soon seem quaint; as a
group of microbiologists recently wrote in
Microbiology and Molecular Biology
Reviews,
^*
we need to begin thinking of
health “as a collective property of the human-associated microbiota”—that
is, as a function of the community, not the individual.

Perhaps the most important function of the
microbes in our gut is to maintain the health of the gut wall, or epithelium. This is
the tennis-court-sized membrane that, like our skin or respiratory system, mediates our
relationship to the world outside our bodies. In the course of a lifetime, sixty tons of
food pass through the gastrointestinal tract, an exposure to the world that is fraught
with risk. It appears that much of that risk is managed, most of the time brilliantly,
by the gut microbiota. So, for example, the microbial fermenters living in the colon
break down the indigestible carbohydrates in our food—that is, the fiber—into the
organic acids that are the most important source of nourishment for the gut wall.
(Unlike most other tissues, which obtain nutrients from the bloodstream, the gut wall
gets most of its nutrients from the by-products of fermentation in the colon.) Some of
these organic acids, like butyrate, are such a good fuel for the cells of the intestines
that it is believed to help prevent cancers of the digestive tract.

Meanwhile, other gut bacteria have evolved the
ability to adhere to the inner surface of the epithelium, where they crowd out
pathogenic strains of such microbes as
E. coli
and salmonella, and keep them
from breaching the gut wall. Many such pathogens can be found within the gut but
don’t make us sick unless they manage to get out and into the bloodstream. The
reason some people are more susceptible to food poisoning than others may owe less to
their ingestion of bad bugs than to the failure of their epithelium to keep those bugs
from escaping (as well as to the overall health of their immune system). Helping to
maintain the health and integrity of the gut wall is one of the most valuable services
gut bacteria provide.

As a more or less stable ecological
community, the microbes in the gut share our interest in resisting invasion and
colonizations by microbial interlopers. Some of them produce antibiotic compounds for
this purpose, whereas others help manage and train our body’s immune system, by
dispatching chemical signals that activate or calm various defenses. Though to speak of
“our” immune system or self-interest no longer makes much sense. Taken as a
whole, the microbiota constitutes the largest and one of the human body’s most
important organs of defense.
^*

An interesting question is why the body
would enlist bacteria in all these critical functions, rather than evolve its own
systems to do this work. One theory is that, because microbes can evolve so much more
rapidly than the “higher animals,” they can respond with much greater speed
and agility to changes in the environment—to threats as well as opportunities.
Exquisitely reactive and fungible, bacteria
can swap genes and pieces
of DNA among themselves, picking them up and dropping them almost as if they were tools.
This capability is especially handy when a new toxin or food source appears in the
environment. The microbiota can swiftly find precisely the right gene needed to fight
it—or eat it.

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.
^*