Ten years ago, a retired Cornell microbiologist and fermentation expert by the name of K. H. Steinkraus conducted a global survey of fermented food products, organized by type. Here is a very small sample of what he found:

LACTIC-ACID FERMENTS: sauerkraut, olives, pickled vegetables, Chinese hum choy, Malaysian tempoyak, Korean kimchi, Russian kefir, Indian dahi, Middle Eastern yogurts, Egyptian laban rayeb and laban zeer, Malaysian tairu, Western cheeses, Egyptian kishk, Greek trahanas and Turkish tarhanas, Mexican pozole, Ghanaian kenkey, Nigerian gari, Philippine balao balao and burong dalag, sourdough bread, Sri Lankan hoppers, Indian idli, dhokla, and khaman, Ethiopian injera, Sudanese kisra, Philippine puto, Western sausages, and Thai nham.

ALKALINE FERMENTS: Nigerian dawadawa, Ivory Coast soumbara, African iru, ogiri, Indian kenima, j.a.panese natto, Thai thua nao ...

On and on it goes, through the savory amino-acid ferments (soy sauce, fish sauce, ketchup); the fermented vegetable proteins (tempeh and ontjom); the acetic-acid ferments (vinegar, kombucha, nata de coco); and of course the numberless alcoholic ferments practiced in almost every culture (preconquest Australia and North America are thought to be the rule-proving exceptions), including South American Indian chicha, Egyptian bouza, Ethiopian tej, Kenyan busaa, Chinese lao-chao, and j.a.panese rice wine. To read Steinkraus's vast exotic catalog is to begin to appreciate the deep links between human and microbial cultural diversity, and how through history each has fed and so sustained the other. To read him is also to worry about the survival of this biocultural diversity, since the industrialization of the world's food strongly favors both h.o.m.ogenization and sterilization.

Important as fermentation has been to human culture, we can't take credit for inventing it. It is, like fire, a natural process, nature's primary way of breaking down organic matter and recycling energy. Without it, as Steinkraus points out, "the earth would be a gigantic, permanent waste dump"-the dead would pile up and there would be no food for the living. Humans are also not the only animal that has learned to exploit fermentation for its own purposes: Think of the squirrel burying acorns (a kind of pit fermentation) or the bird souring seeds in its craw. Some animals also enjoy one of the most important by-products of fermentation: alcohol. And though few animals can be said to actually make alcohol (though it's been reported that monkeys in eastern China will h.o.a.rd flowers and fruits and patiently wait days for the c.o.c.ktail to ferment before imbibing), some have it prepared for them by plants. The pen-tailed tree shrew (Ptilocercus lowii) of Malaysia enjoys a daily nip, drinking from a reservoir of alcohol prepared for its enjoyment by the bertram palm (Eugeissona tristis) in "specialized flower buds that harbor a fermenting yeast community." The palm serves wine to the shrew that, in exchange for this kindness, pollinates the palm in the course of his barhopping through the jungle. Plant, animal, and yeast all benefit from this clever coevolutionary arrangement.

As the example of alcohol suggests, the uses of fermentation extend well beyond preservation, though it seems likely that preservation was humanity's original impetus for mastering the process. (Alcohol-a strong antiseptic-is itself an important preservative.) Archaeologists believe that, until there were reliable methods to preserve food, humanity could not have moved from hunting and gathering to a more settled, agricultural pattern of life. Fermentation (along with other preservation techniques, such as salting, smoking, and drying) provided a critical measure of food security, allowing agriculturists to survive the long months between harvests and to withstand the inevitable crop failures. Though, as I would discover when I started to brew beer (because brewers can always be counted on to mention it), there is a school of archaeological thought that contends that the reason humanity turned to agriculture was to secure a more reliable supply of alcohol, not food. Either way, the mastery of fermentation and the advent of agriculture (and civilization in turn) appear to go hand in hand.

As so often happens, the original purpose of an invention or adaptation doesn't turn out to be the ultimate or even highest use to which it is put. Humans soon recognized that fermenting various foodstuffs did a lot more than extend their shelf life, important as that was. Fermenting the juices of fruit not only sterilized the beverage, but also turned it into a powerful intoxicant. A great many foodstuffs become significantly more nutritious after fermentation. In some cases, the process creates entirely new nutrients-several B vitamins are synthesized in the fermentation of beer, soy sauce, and various grains. Natto, the slimy odiferous ferment of soybeans beloved by the j.a.panese, produces a unique therapeutic compound called nattokinase. Many grain ferments yield important amino acids, such as lysine. Sauerkraut contains breakdown products believed to fight cancer, including isothiocyanates such as sulforaphane. (It also contains goodly amounts of vitamin C: Captain Cook kept his crew free from scurvy during a twenty-seven-month journey by forcing them to eat sauerkraut.) As I learned when I was baking bread, the fermentation process renders grain more nutritious by breaking down chemical compounds that interfere with nutrient absorption, such as phytate. Fermentation also breaks down toxic compounds in certain plants. That shark I tasted in Iceland? It would have sickened me (well, even more than it did) had it not been fermented. This particular species of shark has no kidneys, so toxic levels of uric acid acc.u.mulate in its flesh; the fermentation renders it harmless. Oxalic acid, another antinutrient, found in certain vegetables, is also broken down during fermentation.

To ferment food is to predigest it, in effect, breaking long chains of proteins, fats, and carbohydrates our bodies might not be able to make good use of into simpler, safer compounds that they can. Think of the kraut crock as a burbling auxiliary stomach, doing much of the work of digestion before your body has to. As with cooking, it offers your body an energy savings. Unlike cooking, however, the energy required to ferment food does not need to come from burning wood or fossil fuel. It is self-generated, by the metabolism of microbes breaking down the substrate. Fermentation can easily be done off the grid, a quality that commends it to the enviros, anarchists, and peak-oil types who help make up the subculture. "The historical bubble of refrigeration may not last," Katz likes to point out. When that particular bubble bursts, you're going to want to know people like Sandor Katz and microbes like L. plantarum.

Fermenting foods also intensifies their flavors, a particular boon to agricultural humans. The advent of agriculture dramatically narrowed the human diet, in many cases down to a small handful of bland staples, most of them carbohydrates. All the year long, fermented foods allowed people to enliven a monotonous diet with strong flavors, while supplementing it with vitamins, minerals, and phytochemicals that staple foods often lack.

People tend to feel very strongly about the flavors of fermentation, one way or the other. "Between fresh and rotten," Katz has written, "there is a creative s.p.a.ce in which some of the most compelling flavors arise." In the same way that the process of ripening fruits imbues them with deeper, richer flavors and scents, many other foods acquire powerful new sensory qualities just as they begin to decompose. Why should this be? Perhaps for the same reason that our taste buds respond more strongly to simple sugars than to complex carbohydrates, or to amino acids rather than long protein chains. We've evolved specific taste receptors for these basic molecular building blocks (umami) and simple packets of energy (sweetness), so respond favorably to foods that have been broken down to those indispensable elements, whether by cooking or fermentation.

Yet many of the flavor molecules created by fermentation are not so simple or universal in their appeal. Could it be that, like ripening fruits, the microbes that decompose foods produce powerfully aromatic compounds for their own purposes? The reason fruits produce strong scents and flavors when ripe is to attract animals that can transport their seeds. The microbes that rot fruit or other foods also emit signaling chemicals. Some are designed to repel compet.i.tors. But others are attractants. Like the seeds of plants, fermentation microbes sometimes need help with transportation, especially after they've exhausted a food source. Some scientists believe that bacteria and fungi produce their own taxi-hailing scent compounds, in order to attract the insects and other animals they need to transport them to the next feast of putrefaction.

What's curious is how culturally specific so many of the flavors of fermentation turn out to be. Unlike sweetness or umami, these are not the kinds of simple flavors humans are hardwired to like. To the contrary, these are "acquired tastes," by which we mean that to enjoy them we often must overcome a hardwired aversion, something it usually takes the force of culture, and probably repeated exposure as a child, to achieve. The most common term children and adults alike will use to describe the fermented foods of another culture is some variation on the word "rotten." A wrinkle of the nose is how we react to both rottenness and foreignness. Many of these foods occupy a biological frontier-on the edge of decomposition-that turns out to be a well-patrolled cultural frontier as well.

Considered as a method, or set of methods, for food processing-for turning the stuff of nature into safe, nutritious, durable, and delicious things to eat-the ancient arts of fermentation have yet to be improved on. For what has modern food science given us that can compare? Vacuum-sealed cans. Frozen foods. Microwavable entrees. Mock meats made from soy. Baby formula. Irradiated food. Vitamin-fortified breakfast cereal in colors. Energy bars. Powdered Jell-O. Marshmallow fluff. Cryovacking. Freeze-drying. Artificial sweeteners. Artificial sweeteners with fiber. Margarine. High-fructose corn syrup. Low-fat and no-fat cheese. Quorn. Cake mix. Frozen peanut b.u.t.ter and jelly sandwiches. The countless simulations of real foods and real flavors that line the center aisles of the supermarket. Stack any of these inventions up against such achievements as wine or beer, against cheese, against chocolate, soy sauce, coffee, yogurt, cured olives, vinegar, pickled vegetables of all kinds, cured meats, and the conclusion is inescapable: Thousands of years on, we still haven't discovered techniques for processing food as powerful, versatile, safe, or nutritious as microbial fermentation.

And yet these latter-day industrial methods of food preservation and processing have pushed most live-culture foods out of our diet. Yogurt is the exception that proves the rule, which is that very few of our foods any longer contain living bacteria or fungi. Vegetables are far more likely to be canned or frozen (or eaten fresh) than pickled. Meats are cured with chemicals rather than microbes and salt. Bread is still leavened with yeast, but seldom with a wild culture. Even the sauerkraut and kimchi are now pasteurized and vacuum packed-their cultures killed off long before the jar hits the supermarket shelf. These days most pickles are no longer truly pickled: They're soured with pasteurized vinegar, no lactobacilli involved. Open virtually any modern recipe book for putting up or pickling food and you will be hard pressed to find a recipe for lactofermentation: What once was pickling has been reduced to marinating in vinegar. And though it's true that vinegar is itself the product of fermentation, it is frequently pasteurized, a finished, lifeless product, and far too acidic to support most live cultures.

The modern food industry has a problem with bacteria, which it works a.s.siduously to expunge from everything it sells, except for the yogurt. Wild fermentation is probably a little too wild for the supermarket, which has become yet another sterile battlefield in the war on bacteria. Worries about food safety are very real, of course, which is why it's probably easier for the industry to stand staunchly behind Pasteur than to try to tell a more nuanced story about good and bad bugs in your food. With the result that live-culture foods, which used to make up a large part of the human diet, have been relegated to the handful of artisa.n.a.l producers and do-it-yourselfers signing up for Sandor Katz's "cultural revival."

This might not matter to much of anyone but a confirmed Slow Foodie, eager to save and sample endangered food traditions, except for one notable fact: Medical researchers are coming around to the startling conclusion that, in order to be healthy, people need more exposure to microbes, not less; and that one of the problems with the so-called Western diet-besides all the refined carbohydrates and fats and novel chemicals in it-is the absence from it of live-culture foods. The theory is that these foods have a crucial role to play in nourishing the vast community of microbes living inside us, which in turn plays a much larger role in our overall health and well-being than we ever realized. Bacteria-free food may be making us sick.

My first solo expedition into the wilds of the post-Pasteurian world came last summer, when I tested a few of Sandor Katz's pickling recipes at home. I decided to begin my education with vegetable ferments because they seemed the easiest and, which is important, the safest. No less an authority than Steinkraus had written that the safety record of fermented vegetables was very good even when "the foods are manufactured by people without training in microbiology or chemistry in unhygienic, contaminated environments." (That would be me.) One USDA scientist went so far as to claim that there has never been a doc.u.mented case of food-borne illness from eating fermented vegetables.

Suitably rea.s.sured, I bought a case of quart-sized Mason jars at the hardware store. I did not sterilize them, just rinsed them out with some hot tap water. I also ordered online a 7.5-liter German sauerkraut crock. The perimeter of this ceramic crock has a deep circular well into which the lid fits; filling this moat with an inch or two of water creates an airlock that prevents oxygen from getting in while allowing the carbon dioxide emitted during fermentation to bubble out. Note: I discovered when it arrived that 7.5 liters is a much bigger crock than anyone needs, unless you're planning to feed a small German village. It took no fewer than six large heads of cabbage to fill my crock. That represents easily a few years' worth of sauerkraut in my house.

Fermentation vessels at the ready, I paid a visit to the farmers' market and bought a bunch of pickle-able vegetables: cabbages of course (both Napa and regular), cuc.u.mbers, carrots, cauliflower, sweet and hot peppers, beets, radishes, turnips, etc. At the supermarket, I loaded up on bulbs of garlic, ginger roots, and various pickling spices-juniper berries; dill, coriander, and caraway seeds; star anise; and black pepper-and a big box of sea salt.

According to Katz, there are two basic approaches to fermenting vegetables: leafy ones, like cabbage, are best fermented in their own juices, whereas others require the addition of a brine to keep them fully submerged in liquid. The saltiness of the brine is a matter of personal preference, but several of the sources I consulted recommended 5 percent, so I started with that. I dissolved the salt in a pot of hot water (roughly an ounce of salt for every three cups of water), to which I added various combinations of spices.* While the mixture cooled on the stovetop, I packed the vegetables into a Mason jar (usually with cloves of garlic, sometimes with sliced ginger as well) and then poured the brine over them. Katz had said the vegetables should be completely submerged, but invariably some insist on floating to the top, exposing themselves to oxygen-and the possibility of rot. I tried a variety of tricks to force them back underwater, including a saucer, some Ping-Pong b.a.l.l.s, a plastic bag filled with pebbles, and some weighted grape leaves. I had read that grape leaves, which contain tannins, help keep the vegetables crisp by suppressing certain fungi. (Oak, cherry, or horseradish leaves, do the same thing.)

The procedure for making sauerkraut is slightly more involved. After quartering the cabbages and cutting out their hard cores, you can either shred the resulting chunks on a mandoline or cut them with a knife. I found shredding made life easier and produced more liquid more quickly than cutting with a sharp knife, probably because the knife doesn't leave as much surface area for the salt to go to work on. Put the shredded cabbage in the biggest bowl you own, sprinkling as you go with salt, and then, with all your fingers, press and squeeze and generally bruise the cabbage leaves without mercy until your hands begin to cramp. Now put something heavy on top of the heap to force the water from the leaves-a second bowl full of rocks will work, or use the crock itself. Within twenty minutes or so, the shredded cabbage will be awash in cabbage juice, magically beckoned out of the leaves by the salt.

Pack handfuls of shredded cabbage, with its liquid, into the crock as tightly as you can, a layer at a time. Add garlic and spices (for my first batch I used juniper berries, dill, and coriander) after each layer, pushing the mixture down and squeezing out air as you work. If you're using a sauerkraut crock, it probably came with a heavy inner lid made from fired clay or brick. Place this on top of the kraut and force it down until liquid rises high enough to cover everything. Then fit the outer lid into the lip and fill with water to create the seal. Keep the crock in the kitchen, where you can watch (and listen to) it for the first few days.

The procedure for making kimchi is either only slightly different, according to Sandor Katz and other American fermentos I consulted, or substantially different, according to actual Korean people. Aware of, but unperturbed by, the authenticity issue, Sandor calls his version "kraut-chi," and that's what I tried to make first. With a sharp knife, I cut heads of Napa cabbage into one-inch rounds. In addition to the salt, I added enough red chili powder to turn the cabbage red, along with as much garlic and ginger as I could stand to grate, and some fresh hot peppers. I also added slices of daikon radish and apple, as well as a bunch of spring onions. You can pack this into a kraut crock or an ordinary gla.s.s jar, making sure there's some way for gases to escape. But I found that an airlock is not critical when making kimchi, probably because the peppers and garlic, both vigorously antimicrobial, keep fungi from getting established. (In Korea, as I would learn, kimchi is made by soaking Napa cabbage in a brine overnight; the heads are then rinsed before the leaves are individually rubbed with a paste of ground-up red peppers, garlic, and ginger.)

Within a few days, and straight through that fall, my kitchen counters were lined with an a.s.sortment of jars, bowls, bottles, and crocks of various fermenting vegetables. In addition to the sauerkraut and kimchi, I pickled cauliflower, carrots, cuc.u.mbers, chard stems, beets, ramp bulbs, garlic cloves, turnips, and radishes. As the colors of the vegetables grew more vivid in their brines, and the brines themselves took on the pigments of the vegetables, the jars and bottles grew more exotically beautiful. I was reminded of tanks of tropical fish. And just like fish tanks, some of the crocks bubbled. Three days after filling it, the big crock of kraut began to stir, every few minutes emitting a bubble of gas with a resonant cartoony-sounding baritone burble. Fermentation had begun, which meant it was time to move the crock to a cooler location in the bas.e.m.e.nt, so that it wouldn't proceed too fast.

So what was going on in there, deep within those thick brown ceramic walls? This sort of microbial cooking is invisible and gradual-not much drama to observe, apart from the occasional bubble or bulging of lids on the Mason jars. Yet there was a kind of drama unfolding in these containers, a microscaled drama I had set in motion simply by shredding and salting some dead plant parts. In doing so, I had created a very particular environment-an ecological niche that was in the process of being colonized by new life. (In this respect, too, the crock resembled a fish tank-only this was a microbe tank.) But what was uncanny was how the niche had populated itself-spontaneously. I had done nothing to inoculate it,* and yet on the evidence of the increasingly insistent bubbling, the kraut was now very much alive. The necessary bacteria had been there from the start, dormant but lurking on the cabbage leaves, waiting patiently for conditions to be exactly right-wet, airless, saline, the leaves too badly wounded to keep them out-to set about their methodical work of destruction and creation.

As to the precise ident.i.ty of the microbes at work in my crock, it was hard to know for certain; temperature, place, and chance play a role in selecting them. But according to the microbiologists I consulted, my first fermenters were probably Enterobacteriaceae, a ubiquitous and rather cosmopolitan family of bacteria that can survive in a great many different environments, including in the soil and on plants. I was alarmed to learn that one of the environments in which Enterobacteriaceae do well is (as the name suggests) the gut of animals, and some of them (like salmonella and E. coli) are pathogens. This seemed a good argument for not sampling my sauerkraut too soon.

The Enterobacteriaceae, which begin the process of acidification, are soon succeeded by Leuconostoc mesenteroides, the first of several lactobacilli that will dominate the natural history of my sauerkraut. Like the weedy species that initially colonize a disturbed patch of land, the L. mesenteroides thrive under a wide range of conditions, including the salty, sugary, partially aerobic, low-acid conditions typically present at the beginning of a fermentation. Like many lactobacilli, these characters turn sugars into lactic acid, acetic acid, and carbon dioxide-the gas bubbling out from my crock. The CO2 flushes any remaining oxygen from the ecosystem, preparing the ground for the strict anaerobes, as well as preventing the plant matter from getting mushy and preserving its color.

The objective of all these bugs is to render the environment safe for themselves and inhospitable to compet.i.tors. In the case of the lactobacilli, this is accomplished by producing copious amounts of acid, rapidly lowering the pH of the environment. But the L. mesenteroides eventually go overboard, acidifying the environment to the point where they have, in effect, fouled their own nest. (Remind you of anyone?) Yet what is foul to one microbial fermenter is fair to another: the L. mesenteroides inadvertently create the perfect conditions for another, hardier lactobacillus to succeed them, a more acid-tolerant species such as Lactobacillus plantarum.

I'm not sure exactly which of these characters were ascendant when, after three weeks, I first opened my crock to a.s.sess the progress of my kraut, but the scent that wafted up from the fermenting pinkish ma.s.s put me back on my heels. It was nasty. "Note of septic tank" would be a generous descriptor. In view of the off-putting scent, I wasn't sure whether sampling the sauerkraut was a good idea, but, trying my best to channel Sandor Katz's nonchalance, I held my nose and tasted. It wasn't terrible and I didn't get sick. That was a relief, but ... well, this seemed kind of a low bar for a food. Judith compounded my disappointment by requesting that I get the crock out of the house as soon as possible. I wondered if I should throw out the whole batch and start over.

But before doing anything rash, I decided to check in with Sandor Katz. He advised me to stick with my kraut a little longer. He explained that some ferments seem to go through "a funky period," during which certain unpleasant-smelling microbes temporarily predominate. Some of the bacteria that show up to ferment vegetables are "sulfate reducers": they obtain their energy by turning sulfur into hydrogen sulfide-the odor of rotten eggs. I definitely had a few of those bugs. But my sulfate reducers would eventually be succeeded by other, more benign microbes, he suggested. In all likelihood my ferment was just going through an awkward stage.

Sandor was right. A month later, when I dared to open the crock again, the stink was gone. Whichever the bad bug had been, by now it had been supplanted by the acid-loving climax species that ultimately dominates nearly all vegetable ferments, L. plantarum. When L. plantarum arrives on the scene, you're out of the woods. The ferment is sufficiently acidic to kill off any pathological or otherwise undesirable microbes. L. plantarum establishes a bacteriological regime so stable and low in pH that it can endure more or less unchanged for months, even years.

Yet, truth be told, the sauerkraut wasn't very good. The septic stench may have left, but a disconcerting beard of gray mold had sprouted along the perimeter of the cabbage. I heeded Sandor's advice, carefully shaving it off while trying to override the visceral, possibly instinctual, disgust rising in me. But the mold had obviously been there for while, because my kraut had lost most of its crunchiness. Some filamentous fungus had sent its fine tendrils deep into the kraut, dispatching enzymes to decompose the plant cell walls, turning them nearly to mush. I had been warned that summer sauerkrauts often suffered this fate, which is why Germans traditionally make kraut from cabbages harvested late in the fall.

I had much better luck with my kimchi, or kraut-chi, which after a month of fermentation was still crunchy, its spiciness bright with acid and ginger. As for the dill pickles, the cuc.u.mbers tasted just right but had a slightly grayish cast and suboptimal crunch. The carrots and cauliflower pickled with Indian spices were excellent, the carrots marred only slightly by a thin, barely noticeable slime coat. (Probably a bloom of yeast, another challenge of fermenting in warm weather.) But by far my favorite pickle was the chard stems, which after two weeks were crunchy and a brilliant ruby red, lightly inflected with coriander and juniper. They were delicious, particularly with eggs.

As a mode of cooking, pickling plants was at once remarkably straightforward-cut, salt, and season vegetables, then wait a few weeks-and yet borderline magical: the way these common microbes just show up and utterly transform the vegetables, creating whole new flavors and qualities. And yet it wasn't so easy to pickle really well. To an extent you can guide or manage the microbes, by adjusting the temperature and salinity of their environment, but in the end you can't control them. That's why most of the serious picklers I talked to agreed this was not a craft for the control freak or obsessive.

"You do your best preparing the ferment, but finally you have to be able to let go," Alex Hozven, a local artisa.n.a.l pickler, told me, "and let the microbes do their thing." The fermenters I met cultivated a relaxed and genuinely humble att.i.tude to their work, which they regarded as a collaboration between species. It helped to have the kind of temperament that could tolerate mystery, doubt, and uncertainty without reaching for rule or reason. Instead of the pH meter, they trusted their senses. And they were willing, with a shrug and a rueful smile, to throw out a bad batch every now and then.

The phrase "live-culture foods" is of course a euphemism: for fermented foods teeming with living bacteria and fungi. "Live-culture" sounds a lot more appetizing than, say, "bacteria" for breakfast, in the same way that calling a cheese "washed rind" goes down more easily than "coated with a biofilm of bacteria and mold," which is what a washed-rind cheese is. Enjoying my "live-culture" pickles and kimchi, I gave some thought to the billions of microbes I was ingesting along with the vegetables, wondering what in the world they might be doing down there. But somewhere deep in the coils of my intestines one community of microbes was presumably encountering another. I hoped for the best. At the time, I had no idea what that best might be.

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 ma.s.s of fungi and bacteria used to ferment this ancient Chinese tea soda-or the cultures to make your own tempeh, natto, kva.s.s, 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 t.i.tled, refreshingly noneuphemistically, 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 n.o.bel 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-a.s.sociated 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 pa.s.s 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 const.i.tutes 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.