As to the precise identity 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 competitors. 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 assess the progress of my kraut, but the scent that wafted up from the fermenting pinkish mass 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 cucumbers 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 artisanal pickler, told me, “and let the microbes do their thing.” The fermenters I met cultivated a relaxed and genuinely humble attitude 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 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 b
efore 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 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 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 tis
sues, 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.