12
THE FLAVOR OF BIODIVERSITY
I can’t recommend anything about life indoors.
—JIM HARRISON, A Really Big Lunch
Tell me about a complicated man. Muse, tell me how he wandered and was lost.
—HOMER, The Odyssey, as translated by Emily Wilson
It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us.
—CHARLES DARWIN, On the Origin of Species
ONE DAY WE HUMANS may garden exactly the species we need on our homes and in our bodies. We may be able to perfectly manage the species we most need in ways that yield a daily harvest that is, at once, healthful, beautiful, and sublime. Doing so will require extraordinary cleverness and a good understanding of the biology of most (if not all) of the species on our bodies and in our homes. I wouldn’t hold my breath. This doesn’t mean people won’t soon be selling solutions in a bottle, jars of bacteria that you can spread around your home. They will. We just won’t have very much understanding of whether such bacteria are actually beneficial. Instead of gardening, we need to rewild our homes; we need to let the wilderness back in, albeit a little selectively.
What I am advocating is not a return to a life in which we exert no control over the species that live with us. Instead, I am more humbly advocating moderation. We need drinking water in which the concentration of pathogens is low. We need effective hand washing to control the spread of pathogens person to person. We need everyone to be vaccinated for those pathogens for which vaccines exist. We also need the availability of antibiotics to treat bacterial infections when they arise. Nowhere is all of this clearer than in the many parts of the world where clean water, good hygiene and sanitation systems, vaccines, and antibiotics are lacking. But once and where we have done these things, once and where we have tamed the most dangerous beasts, we also need to find ways to allow the rest of biodiversity to flourish around us. We need, like Antony van Leeuwenhoek, to find joy and wonder in the bacteria, fungi, and insects in our daily lives.
If we do it right, inviting biodiversity back into our lives simultaneously helps to conserve biodiversity and allows us to avail ourselves of more of its services. The biodiversity of plants and soil can help our immune systems function properly. The biodiversity in our water systems can help keep pathogens in the water in check. If we pay attention to it, the biodiversity in and around our homes can help inspire wonder in children, as it did for Leeuwenhoek, as it does for me. The biodiversity of spiders, parasitoid wasps, and centipedes can help control pests. The biodiversity in our houses provides the opportunity, too, for discovery of enzymes, genes, and species useful to all of us, whether to make new kinds of beers or to transform waste into energy. Favoring biodiversity while at the same time dissuading dangerous species isn’t rocket science and so is unlikely to ever be advocated by those who envy rockets. Instead, it is far more like making bread or kimchi, a reality I was reminded of recently when I sat down with Joe Kwon and Joe’s mom, Soo Hee Kwon (aka Mama Kwon), to have lunch.
Joe, Soo Hee, and I had gotten together to talk about Korean cooking. Internationally, Joe is best known as the cellist for the popular band the Avett Brothers. The Avett Brothers play bluegrass-inspired rock, and Joe plays the low notes that hold the music up. But, at least in Raleigh, Joe is also known for his love of food. The unusual schedule created by touring with the band gives Joe long periods during which he can spend a day, say, roasting a pig. Joe and his pigs are well regarded enough that people search him out just to be able to sit with him during a long day of cooking. Roasting a pig well takes time, time enough to consider both the loveliness of pig and the grandeur of the universe.
But on this particular day, I was sitting with Joe not because of his music, or because of his cooking, but instead because of his mother’s cooking. Joe’s mother, Soo Hee, grew up in Korea, where she learned to cook traditional Korean dishes such as Haemul Pajeon (a kind of seafood pancake), Jajangmyeon (noodles in black bean sauce), and Tteokbokk (spicy stir-fried rice cakes). She learned the techniques necessary to make those dishes. She learned to make food that was, in and of itself, a kind of love. She made that food with her hands. Korean food is often made with heavy involvement of the hands. The hands roll cabbage. The hands cover fish in brine. The hands touch and maneuver each ingredient and do so with a subtlety and specificity that is both somehow deeply Korean and incredibly individual.
Making Korean food wouldn’t have anything to do with houses but for one important concept, sson mhat (
), where sson means “hand” and mhat means “taste.” Sson mhat refers not to the food itself but instead to the flavor given to food by the person who makes it—literally by their hands, but figuratively by everything about who they are and how they touch, walk around, and work with food. Inspired by this idea, I wanted to explore a hypothesis with Joe and his mother, namely, that the microbes from the body of a Korean chef (traditionally a Korean woman) are precisely what gives her food a flavor different from that of her sister’s or cousin’s food.
Joe, Soo Hee, and I ordered some drinks and lunch. We started to eat and talk. I wanted to understand what Joe’s mother thinks about sson mhat and what the word means to her. In Korean cooking, more than almost any other cuisine, foods are often fermented (meaning that sugars are chemically broken down by bacteria or fungi in a way that produces gas, acid, alcohol, or some mix thereof). The by-products of this fermentation add flavor and aromas to the food, such as the acidity and sour notes of yogurts. They make food intoxicating (when alcohol is the by-product). They also make the food toxic to other microbes. Alcohol kills most pathogens; so too, acidity. During the days when cholera was common in London, those who drank beer tended to be less likely to die of cholera than were those who drank water. The alcohol in the beer made that liquid safer to drink. Yogurt is safe to eat because the acidity in the yogurt prevents other microbes from colonizing. Acidity is measured on a scale from 0 to 14. Substances that have a pH of 7 are neutral, those with values higher than 7 are basic, and those with pH values lower than 7 are acidic. The pH of yogurt is typically around 4, similar to the pH of the stomach of a baboon.1 The acidity of sourdough starters, kimchi, and sauerkraut is similar. The fermenting microbes that produce the acid (often species of the genus Lactobacillus) are tolerant of this acid, whereas most other species are not. Some fermented foods, such as Japanese natto, are alkaline, and this alkalinity has an effect similar to that of acidity. It keeps pathogens at bay. Species with the genes necessary to grow (typically slowly) in the presence of alcohol, high acidity, or high alkalinity almost never have the genes required of pathogens, genes that tend to entail fast growth. Fermentation, then, is not only a way of gardening species with favorable effects on our food; it is also a means of warding off pathogens. Fermented foods are ecosystems that weed themselves.
Because of the many benefits of fermentation, most human cultures have fermented foods. On my desk sits a compendium of thousands and thousands of different fermented foods of the world, most of them unstudied.2 Some fermented foods, be they fermented shark or fermented seal stuffed with fermented auk, require a little getting used to. Many, though, are more familiar to the Western palate. Bread, vinegar, cheese, wine, beer, coffee, chocolate, and sauerkraut are all fermented. We eat fermented foods all the time, whether or not we realize we are doing so.
Among the most complex and biodiverse fermented foods is Korean kimchi. Kimchi is a Korean staple. The average South Korean eats eighty pounds of this good stuff a year. In making kimchi, the first step is to split, salt, and wilt cabbage. After several hours, the salt is washed off and the cabbage is further split or cut and mixed, by hand, with a pasty slurry of sweet rice, fish paste (itself fermented), shrimp paste (also previously fermented), ginger, garlic, and onions and radishes. The paste must be pushed into and around each cabbage leaf, with fingers and thumbs. It is massaged. It is worked. It is brushed and pushed anew. The result is then put into jars (sometimes small, more often enormous) and left to ferment. This is the basic plan, but the details vary greatly. Hundreds of kinds of kimchis are made, kimchis using different spices, different vegetables, and different steps. As it turns out, there may be as many different kinds of kimchi as there are people who make kimchi.
To my senses, kimchi is a delight. All humans have taste receptors for sweet, sour, salty, bitter, and umami. The umami taste receptor was discovered most recently (so you might not have learned about it in school). It detects flavors such as those found in some savory foods, including many meat dishes. The food additive MSG (monosodium glutamate) is so delicious because it tickles our umami taste receptor. Kimchi is one of the few vegetable-based foods that best satisfies the umami taste receptor (sun-dried tomatoes are another). I think of kimchi and joy, hand in hand; if I am eating kimchi, odds are that I am experiencing joy. But kimchi, Soo Hee told us, was not all joy when she was a little girl. It was hard work. The cabbage was ready in November. So too the radish that would be used along with the cabbage. The cabbage and radish needed to be harvested in huge quantities and then mixed in with the chili peppers and other ingredients. The kimchi made from the Napa cabbage and radish was important because it would be a key source of nutrients—the vegetable and protein that would accompany rice—for the entire winter. When Soo Hee was young, the winter in Korea was long and cold. Kimchi was delicious, but it was also part of survival, of getting through the winter. Kimchi, like other fermentations, was a means of storing food. It was a way to preserve vegetables so that they would last and last. And kimchi was also, as Joe’s mom told me, among the foods with the strongest sson mhat. Each person’s kimchi had a unique hand flavor.
Soo Hee sometimes leads kimchi cooking classes. In one of these classes, she said, she had cut up the ingredients for many people to work alongside her and make kimchi. They all made the kimchi. They did it in exactly the same way. They used the same ingredients. They followed the general motions of Joe’s mom’s hands. She was the instructor. She led, they copied. But the motions were not identical. So much about how a hand moves, about how it holds and works with a vegetable, is unique and gestural.
Weeks later, when the kimchis were all done, Soo Hee told me, each one tasted different. Each one, each person’s kimchi, had a different hand flavor. Some were more sweet, others more sour. Some smelled a little fruity, others less. Some were delicious, others, well, Soo Hee said, less so. With this, I leaned in further. I ignored the food in front of me. I was becoming convinced that this hand flavor is due in part to the microbes on the bodies of the people making the kimchi, on their bodies and in their homes. The microbes in kimchi are of many species. Some of those species are likely to come from the cabbage itself, or from the radish. But they also include microbes known to be human bodily microbes. Lactobacillus species, for instance, are key to kimchi, as can be, even, Staphylococcus.3 Lactobacillus species are common bodily microbes. Some species and strains are known to be gut microbes; others are vaginal. Staphylococcus, on the other hand, is a human skin microbe. Each one of these species and genera produces different enzymes, proteins, and flavors. Each one contributes something different to the final food.
When Joe’s mom helped to make kimchi in the winter as a girl, the air was cold. The water in which the cabbage was soaked and wilted was also cold. Everything was cold. But making the kimchi was necessary. She labored over the giant buckets, again and again. It was certainly not, she conveyed, an unambiguous pleasure. And yet, it was part of who she was, this creation and fermentation.
Winter kimchi was one of many kinds of fermentation in Soo Hee Kwon’s house when she was a little girl. Other kinds of vegetables were also fermented into summer kimchi. Crabs were fermented when they could be caught or afforded. Fish, too. If a food was not fermented in Joe’s mom’s house, it was fermented somewhere nearby. Soybeans were sometimes fermented with their own microbes into a paste (Doenjang) or a sauce (Ganjang) and in other cases with a special bacterium (Chongkukjang).4 Red peppers were fermented, too, into a paste to be used as a flavoring (Gochujang). Fermented food could keep until the most desperate seasons. When such foods were fermented, the microbes from those foods must have spilled over onto each and every surface of the house. They must have risen up into the air. It is easy to imagine that the microbes of Joe’s mom’s house, the microbes of Joe’s mom (and the rest of her family members), and the microbes of the foods themselves were part of one continuous story. Perhaps kimchi was flavored not just by some microbial hand taste but also by something for which there is not a Korean word, “house taste.” And perhaps microbial hand taste and house taste come together to change the daily experience and well-being of everyone living in houses in which kimchi and other foods are regularly being fermented. I had been trying to find ways to favor a diversity of beneficial species in our homes and in and on our bodies, and here, in the form of kimchi, was one, maybe.
After talking to Joe Kwon and his mom, I wanted to launch a new project to understand the biology of hand taste, house taste, and whatever other sorts of tastes might be found. Kimchi is as good an example as we have for how the microbes around us and on us influence our food. But kimchi didn’t seem like an ideal candidate for our first large-scale study of food. It is an acquired taste, one bound up in culture, history, and context. We could study instead some cheeses. Like kimchi, cheeses depend on many species. French Mimolette cheese, for example, depends on both bacteria from human bodies and those from cheese mites (Tyrophagus putrescentiae).5 Or we could study the famous Sardinian cheese casu marzu made using body microbes and the wriggling, transparent larvae of household cheese flies (Piophila casei).6 But these cheeses, like kimchi, are biologically very complex, foods for which more is understood by chefs and bakers than by scientists. They are also foods that don’t appeal to everyone (casu marzu is actually illegal to produce and sell, though one can still find it). We needed to start with a food that was potentially interesting to bodily and household microbes, simple enough to be experimentally tractable, and appealing to nearly everyone. We needed to start with bread.
Leavened bread rises because microbes in the dough produce carbon dioxide that becomes trapped in air pockets in the bread. If you cut a loaf of leavened bread in half, each hole and opening is the result of the exhalation of a group of yeasts contained inside a kind of gluten dome. Without microbes, bread dough does not produce carbon dioxide. Without gluten, bread dough cannot catch the carbon dioxide produced by microbes. The very first breads were made with barley, which lacks enough gluten to make leavened bread, and so were unleavened.7 By no later than 2000 BCE, Egyptian bakers had figured out how to make bread using emmer wheat. Emmer wheat contains gluten. Doughs made with emmer wheat can rise so long as the right microbes are present.8 The switch from unleavened to leavened bread can be seen in Egyptian art. Early Egyptian art shows flat loaves, but later loaves in similar scenes are round and risen. The microbes in those breads that enabled them to rise were yeasts. Yeasts in traditional bread produce carbon dioxide. Meanwhile, bacteria in those early breads would have made them taste sour. Nearly all traditional leavened bread is at least a little bit sour and this sourness (with very few exceptions) is often due to the same kinds of bacteria found in yogurt, species of Lactobacillus. We don’t know how the ancient Egyptians controlled the yeasts and bacteria used in their breads, 9 but thanks to the depictions of risen bread in Egyptian art, we can be sure they did.
Today, the community of microbes used to make leavened bread is called a starter. To make a starter, one takes simple ingredients, often just flour and water, and leaves them out in a vessel.10 Microbes ferment the starches in the flour.11 Fed again and again with water and flour, the starter reaches a kind of steady state in which a relatively simple community of species survives in the bubbly, sticky, acidic mix. Just as with kombucha, sauerkraut, or kimchi, the more acidic the starter becomes, the less likely any pathogens are able to survive.12 This is what we might hope for more generally in managing the life around us: simple ways of favoring species that benefit us and, at the same time, keeping troublesome species in check.13 Starters, then, would be the ideal microbial communities for us to study; they are biologically diverse and, through their diversity, keep pathogens at bay.
A hundred years ago, essentially all leavened bread was made using a starter containing a mix of bacteria and yeast. Not anymore. In 1876, French scientist Louis Pasteur, progenitor of the germ theory (the idea that individual pathogen species can cause disease), discovered that some of the microbes that made beer and wine could also make bread rise. Not long thereafter, Emil Christian Hansen, a Danish fungus biologist, figured out that the key microbe in the fermentation of beer was a species of Saccharomyces. Saccharomyces cerevisiae was later shown to be sufficient to making a new kind of bread, one that was never sour, did not depend on any bacteria, and yet still rose. Scientists found ways to grow Saccharomyces cerevisiae in monoculture, in the lab, in enormous quantities, and then send it, freeze dried, around the world. The freeze-dried yeast allowed the production of bread to be scaled up. Today, the vast majority of bread you buy in the store is made using one of a handful of kinds of wheat and a single species of yeast, grown at large scales and then sold to the companies that make the bread.14 This yeast goes by a variety of names, names that suggest diversity where there is none to be found. You don’t have to be a nutritionist to know that, in the switch from homemade sourdough to a bag of mushy white bread, what has occurred is not exactly progress in terms of either nutrition or flavor. Industrial-scale breads don’t have to be produced in this way, but most are. We have lost the richness of our daily bread, a richness of texture, flavor, nutrition, and microbes.
Fortunately, many home bakers and bakeries continue to make new starters as well as keep old ones alive. Much like their antecedents working a hundred or even a thousand years ago, these bakers mix flour and water, and then they wait.15 In some cases, they repeat, exactly, what their ancestors did in making starters, step for step, gesture for gesture. In other cases, they make their own starters from instructions they found online. Either way, they must wait for microbes to begin to colonize the mix. They then take care of those microbes. The starters found in different bakeries and homes can be very different, but no one really knows why. More than sixty different lactic acid–producing bacterial species and a half dozen species of yeasts have been found in one or another starter. To understand why starters differ so much, we decided to conduct a study. The study would have two parts. In the first part, a true experiment, we would have each of fifteen bakers from fourteen countries make the same starter, using the same ingredients, where the only factors not controlled would be the bodies of the bakers and the air in their homes or bakeries. The bakers’ bodies would be the treatment. We’d test the hypothesis inspired by my conversation with Soo Hee Kwon, namely, that the microbes on the bodies of the bakers and in their homes and bakeries would influence the microbes in the starters. In the second part of the study, a survey, we would characterize the microbes in starters from around the world.
For the first part of the study, the experiment, we teamed up with the Puratos Center for Bread Flavour in Saint Vith, Belgium. In the spring of 2017, Puratos helped us send out identical sourdough starter ingredients to each of the fifteen bakers in each of fourteen different countries. Each baker then mixed the flour and water and waited. Once the bakers had a living, functioning starter, they continued to feed it with flour we had sent. Later in the summer, we identified the microbes in each of these starters and whether they were contributed by the flour, the water, or the bakers’ hands and homes. The “we” in this case was Anne Madden, an expert on the ecology and evolution of yeasts, and me.
Simultaneous with sending the starter ingredients to the bakers, we also began the second part of the project, a global survey of starters around the world. We invited people from Israel, Australia, Thailand, France, the United States, and anywhere else to share their starters with us. We reasoned that in the global sample we’d encounter new kinds of starter microbes, species present in just one region or even just one family. The experiment in Saint Vith enabled us to focus on how much starters varied when we held everything but the bakers constant. The global survey held nothing constant. In the global survey, we’d characterize the diversity of starters in all their glory. The participants in the global survey were people who, through making sourdough starters and bread, were helping to keep both tradition and microbes alive. They were curators of the beneficial biodiversity of bread microbes. The scientific team required to carry out the global part of the experiment would be huge and interdisciplinary. It would include, once more, Noah Fierer, but also Anne Madden, Liz Landis, Ben Wolfe, and Erin McKenney as food microbe experts, Lori Shapiro as an expert on the microbes of grains, with Angela Oliveira in charge of sequencing and analysis, Matthew Booker in charge of helping to record people’s stories of food, Lea Shell and Lauren Nichols helping with everything, and many more people, not least of whom were the bakers who shared their sourdough starters. The home bakers and professional bakers who sent their sourdough guided every step of the work, more so than in any other project we have ever done.
In the global survey, when we talked to people about their starters, the number of questions we had grew and grew. Many of the starters had histories that were known to go back hundreds of years. Most starters had names. People talked about the starters like they were pets, but the attachment was even deeper. A mother could push her hands into the same starter her mother had cared for, which might be the same one her grandfather cared for or even her great-great-grandfather. And when people told stories about the starters, they did so as if describing a near immortal participant in their family’s history. One starter, for instance, was called Herman. The woman who sent the starter called Herman included this note:
In 1978, my parents went to Alaska. Because they knew I was a huge fan of sourdough, they brought back for me… [a] sourdough starter. This starter was over 100 years old. I rehydrated the starter, fed it, expanded it and began to use it. Because this starter was a living organism, we named him Herman and put him in our refrigerator, where he has lived for many years. We have used Herman to bake bread, rolls, waffles, etc. ever since. However, there is still more to my story. In 1994, two things happened that impacted our family. The first was the Northridge Earthquake, which caused a tremendous amount of damage in our area. The second was that just before the earthquake—and for the first time—Herman turned pink!16 That was disastrous because it indicated a bacteria had invaded our dear Herman and I had to toss him out. However, I was not overly concerned because my friend also had some Herman. Sometime after the earthquake, I finally got around to asking my friend for some Herman. When I did, her face dropped. It turned out that after the earthquake, as her husband was trying to clean things up, he noticed a jar of whitish grey somewhat sticky stuff in the back of the refrigerator. Thinking it was something old and bad—he threw it out! Disaster strikes again! My family was disconsolate. It was as if we had lost a well-loved family member. I tried buying and creating new starters, but they just did not have the same aroma or taste as Herman. In late 1993, my Mother had passed away. My Mom loved to entertain and, shortly before she died, she had been planning on having a party at their summer home. The following August, in 1994, my father, my siblings and I and our spouses decided to go to their summer home and give the party my Mom had been planning. When we got there, I realized that they had left precipitously when she was sick and that the refrigerator was in great need of cleaning. As I sat on the ground in front of the refrigerator sorting thru items, I began to laugh. And then cry. I knew as soon as I saw him, in all his gooey, sticky beauty. My Mom had a jar of Herman that I had given her at some point in time! Our kids doubted it could truly be Herman, but when we unscrewed the lid, Herman’s pungent and unique aroma hit us right in the face. It was as though my Mom had reached down and given Herman back to us! Now, I have 4 jars of Herman. My kids and various friends also have him—just for insurance. I expect our story will continue to grow thru the generations of our family.
Participants, including Herman’s owner, had questions. They wanted to know whether starters changed over time. They wanted to know whether their starter contained the same kinds of microbes it did a hundred years ago. They wanted to know whether the temperature at which the starter is kept really makes a difference. They wanted to know how to make starters that produced bread that was more sour or less sour.
In studying the starters from the global survey, we would try to answer as many of these questions as possible. We might be able to use the identity of the microbes present in these families of starters to trace their history genealogically (or, conversely, to find out that individual bacterial or yeast species die in or colonize starters so often that “Grandma’s starter” no longer has very much to do with Grandma). We could and would try to identify the extent to which geography, climate, age, ingredients, and many other factors influenced which species were found in the starter. The microbes that colonize starters might be different in different regions. It was even possible that in some regions the local microbes might simply be unable to make starters. It had been speculated, for instance, that a traditional sourdough starter could not be made in the tropics, but no one seems to have ever studied whether this is true (no one except bakers in the tropics).
Meanwhile, we continued to obsess over the question we hoped to answer with the experiment in Saint Vith: Where do the sourdough microbes come from in the first place? To make sourdough, one mixes together flour and water, whether it’s the cheap flour that comes in a paper bag at the store and tap water, or flour made from wheat hand-ground by a baker and mixed with the dew on dandelion leaves after the first full moon. Somehow, the right mix of bacteria and fungi appears. Poof!
In August 2017, the fifteen bakers, along with their fifteen experimental starters, all came to Saint Vith. Some bakers were younger, some were older. One worked at a bakery that supplies baguettes to thousands of stores a day. Another sold a few hundred loaves of bread a day, sometimes fewer, and made high-priced, well-known, and delicious toast. Some of the bakers used many starters while baking, each to suit a particular bread. Others used just one, a single starter to which they attributed a personality and gave a name. What all of the bakers shared was a deep, passionate, obsessive love for great bread. We met them all at the Puratos Center for Bread Flavour. The building was locked. The bakers gathered outside the center and waited to get in. The conversation was nervous and multilingual. It was nervous because the bakers were going to bake bread the next day, but they would do so using the experimental starters they had just made. These were not their ordinary starters. The bakers didn’t want to bake bad bread. They didn’t want to have made bad starters.
The door to the Center for Bread Flavour opened. We all walked in. After some introductions, Anne and I put the starters on the table and got ready to swab them. As we did, the bakers (who we imagined might just step back and watch) gathered around. They hunched in. They were used to being in control, used to being judged not for their starter but instead for what they could use a starter to make. The bakers wanted to care for their starters right away; they wanted to feed them.17 They didn’t want to wait. The bakers talked about what each of them thought would have been a better, more perfect way to make a starter. While these opinions were being voiced, Anne Madden put on gloves, I put on gloves and took out a notebook, and we began to sample. One by one, I opened the containers in which the starters were living. I inserted a cotton swab deep into each one, and then put the swab in a sterile case. Already, while carrying out this procedure, we could tell that the sourdoughs were different from each other. Some smelled extremely sour, others fruity, others a little bland. When Anne and I were done swabbing, we allowed the bakers to feed their starters. The bakers looked relieved; the starters, too. The starters bubbled gratefully and began, visibly, to rise.
The next morning, after the bakers had spent a night drinking Belgian beer (brewed by monks using a mix of bacteria and yeast) and singing songs about bread (really), and the starters spent a night luxuriating in a new dose of food, Anne and I came in to swab the bakers’ hands. Anne did the swabbing. She took the work slowly, one hand at a time. She was careful to exhaustively sample all the cracks and crevices.
Finally, once each hand was swabbed, we let the bakers make dough with their starters. Each baker made the dough the same way. Or, rather, each baker made the dough according to the same written steps. So much about the relationship between baker and dough is unwritten and intimate that some of what happened next varied more from one baker to another than we would have liked. Some bakers were gentle with their dough, rolling it with a kind of tenderness. Others were aggressive. Some breads were coddled, others smacked. Some bakers used spoons, others wouldn’t dare.18 In the end, the experiment was also subject to the differences in the details of the traditions and styles of the bakers.
On the last night, Puratos hosted a bread and beer tasting. Each bread was set out. One by one, we sniffed the crust. We squeezed the bread and sniffed the insides, the crumb. We put the bread up to our ears and listened to the sound it made (or didn’t make) when squeezed. We poked the bread to examine its elasticity. We chewed the bread on its own and then with a sip of beer. We savored the flavors of the slightly different microbes present in each loaf.
By this time, we had begun to believe that breads, like kimchi, are one way in which we experience the subtle biology of our homes. Our studies of homes and bodies have revealed the ways in which the microbes of each person and home are different. Such microbes must, we imagined, fall into starters. If and when they do, we taste bread and, whether we realize it or not, savor some of the species floating around us every day. Even species that can’t be seen with the naked eye can be savored. In a single loaf of bread, glass of beer, or bite of kimchi or cheese, we find hints of the work the species around us do on our behalf. In French, the flavors associated with the soil, biodiversity, and history of a place are called terroir. When we bite or sip, we savor the terroir. Ecologists, more blandly, call the experiences that result from biodiversity the result of “ecosystem services.” The ecosystem services of biodiversity in and around our home include the wonder biodiversity can inspire. They include the benefits biodiversity offers to our immune systems. They include the potential for new technologies, such as the use of camel cricket gut microbes to rid ourselves of industrial waste. They even include the local manifestations of distant services, such as the filtering of our tap water by the biodiversity in aquifers. I thought about this as we tried another bread, and another beer, and then another bread, and then yet another beer. I thought about this as we toasted “to bread” and “to microbes.” I thought about it as I considered what the data from the Saint Vith study would show and the bakers started to sing again. “To bread, and to microbes!” And to a house in which both are delicious. “To bread and to microbes!” And houses in which we are all healthy. “To bread and to microbes!” And to lives filled with wild species we have yet to study or understand, species that float like mysteries all around us and offer services we are only beginning to measure. To bread and to microbes and our one wild life.
For a while, that was the end of the story of the Saint Vith experiment. The sourdoughs were made, breads baked, and samples shipped to the lab of my microbiological collaborator, Noah Fierer, at the University of Colorado, where their DNA would be sequenced, their species identified. In Colorado, the Saint Vith samples sat alongside the global samples. I thought this would be all I’d be able to say at the time of the publication of this book, all we would know. But just in case, I hounded Noah to hurry. Noah hounded Jessica Henley, his technician. Jessica hounded Angela Oliveira, a new student in Noah’s lab. In December 2017, Angela sent us the results for both the Saint Vith and the global study. Usually, it takes months to fully make sense of results. But Anne Madden and I were so excited that we couldn’t resist. We started to do analysis. I was in Germany. It was late at night. Anne Madden was in Boston. She still had a longer day ahead of her. We dug in.
When we had talked to the bakers about the Saint Vith project, we emphasized that the science that would be done on the samples of their starters would be hard. That wasn’t totally accurate. It was better to say that parts of the Saint Vith experiment, like the global survey, could just fail. If they failed, we wouldn’t have results we could believe and the whole effort would have been, though fun (really fun), scientifically useless. One way the project could have failed was if we didn’t get enough DNA from the samples. There are a bunch of ways this might have happened. Fortunately, it didn’t. Another way it could have failed was if the samples were contaminated, whether with microbes from my skin, microbes from Anne’s skin, or even microbes that ended up inside the “sterile” swab containers when they were manufactured. But, when we checked our controls, we could see (and show) that we did not have contamination. There were even more boring ways this type of experiment could fail: a shipment could have failed to arrive (it happens all the time with scientific samples). The DNA could have degraded during shipping. Or an individual effort at sequencing the samples might have failed for reasons that were part bad magic, part technical, part human. None of these things happened either. The samples arrived. The box was not crushed. The samples were not spilled. The sequencing runs worked. We were able to process the data without trouble. We had, it seemed, the right mix of luck, hard work, and some more luck. But none of those things was what we were most worried about. What we were most worried about was that the results, particularly those of the Saint Vith study, would be inconclusive. This is what we didn’t tell the bakers—that we might get the results but that we might not be able to tell whether their hands, lives, and bakeries had influenced their starters at all. It might simply be the case, even if the bakers’ hands strongly influenced the starters, that amid all the other sources of variation, we wouldn’t be able to say for sure. Fortunately, that isn’t what happened.
As we started to consider the data, we discovered that the bacteria and fungi found in the Saint Vith starters were a subset of those we encountered in the global survey of starters. In the global survey, we found several hundred species of yeast and several hundred species of Lactobacillus and related bacteria. The starters weren’t diverse compared to soil, homes, or even human skin, but they were more diverse than food scientists or bakers had previously understood. Different microbes were present in different regions. One fungus, for example, was confined nearly exclusively to Australia. Does it give Australian breads a unique taste? It might.
Among the starters made by the fifteen bakers who traveled to Saint Vith we found seventeen different species of yeast in the starters and twenty-two species of Lactobacillus bacteria. The diversity of bacteria and fungi in the Saint Vith starters was more or less what we might have expected given that we had sampled a relatively small number of starters and controlled the ingredients used to make them. We then looked at the results from the hands of the bakers.
On the basis of previous studies, we knew that all hands (just like noses, belly buttons, lungs, guts, and every other external surface of the body) are covered in a layer of microbes, a sheath. It is easy to imagine that in washing our hands, we remove all of the microbes. We don’t. If you sample the microbes on someone’s hands, have them wash and scrub their hands, and then sample the microbes again, no change in the overall composition of the microbes occurs. Noah Fierer was the first person to do a version of this experiment. The results were unambiguous and remain uncontested. Hand washing prevents the spread of pathogens and saves many lives a year, but it doesn’t do so by sterilizing your hands. Instead, hand washing appears to remove microbes that have newly arrived, but not yet established on the hands. For example, when scientists experimentally put nonpathogenic E. coli on peoples’ hands, washing with soap and water removed much of the E. coli. It didn’t matter if the water was cold or hot. It didn’t matter for how long people washed (so long as it was at least twenty seconds). Also, ordinary bar soap was more effective than antimicrobial soap at getting rid of the E. coli.19 Keep washing your hands and do so with soap and water.
The most common microbes on hands in studies by Noah and researchers in other labs tended to be species of Staphylococcus (which dominates on the skin in general and is common in some cheeses, but not in bread), Corynebacterium (which cause armpit odors), and Propionibacterium.20 Lactobacillus was also present on the hands. It was this Lactobacillus, along with its relatives, that we thought might be helping to inoculate sourdough. But Lactobacillus is usually relatively rare on hands—about 2 percent of the microbes on men and 6 percent on women in Noah’s study.21 Fungi can be present on hands, but are neither abundant nor diverse. This is what we expected on the bakers. We hadn’t imagined there was any reason to expect differently. Hands are hands. Then, we looked at the results.
The first surprise was that the bakers’ hands were totally different from any hands we had ever seen before. On average, 25 percent and up to 80 percent of all of the bacteria on the hands of the bakers were Lactobacillus and related species. Similarly, nearly all of the fungi on the bakers’ hands were yeasts that can be found in sourdough starters, such as species of Saccharomyces. We had no idea this was even possible, and we don’t yet fully understand it. My suspicion is that because the bakers spend so much time with their hands in flour (and starters), their hands become colonized by the bacteria and fungi they work around. One can even imagine a scenario wherein the Lactobacillus bacteria and Saccharomyces yeasts on bakers’ hands outcompete other microbes by producing acid and alcohol, respectively. Such a community of microbes might make the bakers less likely to get sick than are other people. I’m speculating, but this result is really very novel and leads us down many new paths. I wonder whether all people who work with food develop unusual hand microbes. I wonder whether when more people cooked, a hundred years ago, or five thousand years ago, the continuity between food and hand microbes wasn’t much greater in general than it is today. I wonder many things. We will have to do more experiments. And this wasn’t the only exciting result.
When we looked at which bacteria were in which starters, we found that nearly all of the bacteria in the flour were also in the starters. No starter contained all of the bacteria from the flour, but most of the flour species were present in at least one of the starters. The species seeded into the starters by the flour included microbes from inside the grain seeds themselves that help the seed to grow (when the grain was milled, these microbes survived). They included soil microbes from wherever the grain was grown. But they were dominated by species able to live on the sugars of the grain and flour itself, including species of Lactobacillus bacteria. Results were similar for yeasts, with about half of the kinds of yeasts we found in starters coming from the flour. None of the bacteria nor the yeasts in the starters appeared to be those from the water. By now, we know the kinds of microbes that tend to be found in water, and they were absent from the growing starters. No Delftia, for example, the bacteria that can precipitate gold. Nor any Mycobacterium. The starters were not different because they used different sources of water. Why then were the different starters different?
In part, these differences were due to chance, which species from the flour happened to establish. In part, these differences were due to the bakers’ hands. As we had hypothesized, the hands and lives of the bakers influenced the starters they made. The bacteria in each starter matched the bacteria from the hands of the baker who made the starter more than they matched the hands of other bakers. The same was true of the fungi, though to a lesser extent. The hands of the bakers were contributing bacteria and fungi (and, we presume, bacterial and fungal “hand flavor”) to the starter. What is more, as we dug in to the details, the anecdotes were also telling. One of the bakers in our group is somewhat renowned for having a relatively unusual kind of fungus in his starter, Wickerhamomyces. That same baker had that same fungus in the starter he made in our experiment, and it was on his hands. His was the only starter with that fungus, and his hands were the only hands with that fungus. We also found yeasts and some bacteria in starters that didn’t come from the flour, the water, or the bakers’ hands—microbes that are most likely to have come from the life in the bakeries themselves.
When breads were baked using the starters, with identical ingredients (except for the microbes), the differences among starters influenced the flavor of the bread. Some starters made breads that were more sour, others that were more creamy, as judged by an expert panel of bread tasters. Each bread had a unique “microbe flavor,” influenced by chance, and the microbes in the flour, on the bakers’ hands, and in their bakeries. Once we consider in more detail the results and starters from our global survey, it is likely those starters, which are even more variable than those in the study of the bakers’ breads, are able to create even more unique breads. Stay tuned. Meanwhile, everything we have learned so far suggests both that the species of microbes in a starter matter and that everyone is, to some extent, right about where the microbes are coming from. But we need to rethink this all a little bit. The way we initially asked our questions about the relationship between houses, bodies, and breads misses something important about what now seems to be going on, both with our food and our lives more generally. In bread making, the microbes on our bodies and in our houses are shaping the starter. But the starter is also shaping the microbes on our hands (and, potentially, in our homes). The action of making bread then is a kind of restoration, a restoration of certain kinds of biodiversity into our food, onto our bodies, and throughout our houses in such a way that all of these processes are connected. When we make sourdough starters, our bodies and homes flavor our daily bread. In making sourdough starters, the flour, starter, and bread enrich our bodies and homes. Nor should we imagine sourdough starters to be unique. The stories of cheeses, sauerkraut, kimchi, and many of the other foods we can ferment at home are likely to be similar.
AT THIS POINT in our work, I estimate my colleagues and I have found roughly two hundred thousand species in homes. It is hard to accurately tally species from studies done at different times and with different methods (and the definition of a species depends on subfields, methods, and so on), but two hundred thousand is a reasonable estimate. Perhaps three-quarters of those have been bacteria found in dust, bodies, water, food, and guts. One-quarter is fungi. The arthropods, plants, and other taxa make up the rest. We haven’t even started counting the viruses. But some houses are very diverse and other houses much less so, some houses full of species that seem mostly beneficial, other houses more likely to contain problem species. I imagined I’d get to the end of this book and conclude with the stories of architects, building engineers, and the like who had figured out how to build a healthy house full of the subset of these species that benefit us. I’ve spent thousands of hours researching this book. I did not find those people. Nor did I find their buildings. Sure, some new and innovative houses and cities do a better job than others of favoring biodiversity and beneficial species, but they do so not in their future-savvy sophistication but instead through their Paleo return to simplicity. They build houses with more open designs, out of more sustainable materials. This is great, but not yet a panacea.
I should have known at the beginning. One trouble with considering architecture as a solution is that much of what is offered to us by the most innovative architects is offered in small numbers, a house, a neighborhood, and at expensive prices. Such innovations are less likely to be offered to the big, collective “us.” I won’t be able to go and build a new house any day soon that perfectly favors biodiversity, much as I might want to. Also, the truth is, what people asked about when I told them about this book was not how they could build the perfect house. It was, instead, “Has studying the life in houses changed how you live?”
To that question there are some easy answers. I leave the windows open more often. I try to avoid turning on the central air-conditioning for as long as I can. If I’ve got the time, I wash dishes by hand to avoid spraying the fungus that lives in dishwashers everywhere around the house.22 If water gets in my house, I get whatever got wet out. I considered getting a dog, but didn’t (we travel too much). I begrudged my cat slightly more and spent a fair amount of time late at night wondering if she had given me Toxoplasma gondii. I planted a garden of fruit trees. I spent more time watching the insects in my home, and in other peoples’ homes. I started sitting with my son to draw them, too, and of course wondered what new value each one might have (at the moment I’m pretty fascinated by the potential of silverfish). I started, too, to appreciate the magical services performed by the water from ancient, untreated aquifers. I savor the terroir of biologically diverse tap water. I buy more fresh food from local farmers, food that has some chance of still being covered in the microbes from the farm. All of those things. I didn’t change my showerhead, but I do now eye the water coming out of it slightly suspiciously.
I was also inspired by the bakers. I started making more sourdough bread with my children. We also started experimenting more with different starters (I’ve got one going outside to see whether I can catch some interesting outdoor fungi with it). I was inspired by the lesson from the starter, namely, that there may be simple ways to favor beneficial biodiversity while keeping pathogens at bay, tricks of balance and moderation. That insight hasn’t changed my life yet, but it changes how I think about my life. The biggest impact of the bakers came from the unexpected observation that the bakers’ hands were covered in sourdough bacteria and fungi. The skin of the bakers reflects their daily actions. The truth is, all of our skin reflects our daily actions, so too do the species in our homes. In the Dark Ages, it was sometimes believed that God lived inside peoples’ hearts and recorded on the heart’s interior each good deed as well as each sin. The heart, we now know, is an unsentimental pump. But the biodiversity of your body and home is, indeed, a kind of record of your life, much as the bacteria on the bakers’ hands are a measure of how much time they spend baking. I’ll note here that once the bakers found out that some among them had hands covered in starter bacteria, each one wanted to know who had the most. Who, among them, had lived the life most fully submerged in bread?
This to me is the biggest lesson. The species in our homes are a measure of our lives. The early cave paintings of our ancestors documented the species they watched, stalked, and feared. The dust on our walls, in turn, documents the species with which we wake up each day. It is a measure of the species to which we are exposed and fail to be exposed. It is a measure of how we spend our moments. I know what I want my dust to say about me—that I am living a life embedded in biodiversity, a life in which I spend as much time outside with my family as I do indoors, a life exposed to biodiversity’s grandeur and services, a life in which the species around me every day fill me with the sort of wonder the first microbiologist, Antony van Leeuwenhoek, felt. Leeuwenhoek woke up in his house each morning aware that most of life is benign or beneficial and that most of life, wherever you may be, remains to be studied. Leeuwenhoek lived at a time when the biodiversity around him was just beginning to be studied. So too do we.