† Designated as an Exemplary Final Project for 2017-18 Microbe Farmers: How Fermentation Artisans are Bringing Peace to the War on Microbes Max P. Sinsheimer Faculty Advisor: Misha Angrist Social Science Research Institute March 2018 This project was submitted in partial fulfillment of the requirements for the degree of Master of Arts in the Graduate Liberal Studies Program in the Graduate School of Duke University. Copyright by Max P. Sinsheimer 2018 Abstract In the nineteenth century the French scientist Louis Pasteur proved that the proliferation of certain microorganisms in a host body causes most diseases. His “germ theory” catalyzed twentieth century antimicrobial attitudes, which in the gastronomic realm meant reducing or eliminating microbial activity in food products. Fermentation artisans object that this ongoing “War on Microbes” devalues culturally important food traditions, and misses exciting discoveries that have transformed our understanding of the microverse. Microbes are no longer simply the enemy of food safety – they are the solution to better food. As one cheesemaker put it, “We say that we milk cows, but what we are really doing is farming the microbes.” This paper presents case studies of science-minded artisans helping Americans move beyond the Antimicrobial Age. Chapter One contextualizes the War on Microbes; whereas fermentation is arguably our oldest food technology, the relatively recent discovery of a microbiological basis for fermentation moved production practices away from the home or farm and into the factory. Chapter Two introduces artisans and their laboratory collaborators, and describes the genomic analytical tools they are using to sequence individual microorganism DNA and RNA (such as for brewing yeast), or to map an entire microbiome (such as for raw milk used in cheesemaking). Chapter Three focuses on wild craft beers, and suggests that lab-domesticated “wild” yeasts are an apt metaphor for the American environmental imagination. Chapter Four profiles a biotech company producing a specialty coffee to illustrate how fermentation is bleeding into biotechnology. Chapter Five visits a creamery in upstate Vermont, where the microbiology of the whole cheesemaking system is essential to an ecological conception of American terroir. The paper concludes with a meditation on the nature of disgust, and a final nudge in the direction of microbial delight. i Table of Contents ABSTRACT .............................................................................................................................................................. I LIST OF ILLUSTRATIONS ........................................................................................................................................ III ACKNOWLEDGEMENTS......................................................................................................................................... IV ANCIENT FERMENTATION ................................................................................................................................... 6 MODERN ARTISANSHIP ...................................................................................................................................... 9 CHAPTER ONE: DISCOVERING, AND DECLARING WAR ON MICROBES ..................................................................13 DECLARING WAR ON THE MICROBE...................................................................................................................16 PASTEUR’S GASTRONOMIC LEGACY ..................................................................................................................20 CHAPTER TWO: CELLULAR GASTRONOMY ............................................................................................................28 MAKING WASP BEER ........................................................................................................................................29 MEASURING THE MICROBIOME ..........................................................................................................................33 TESTING FERMENTATIVE FABLES ......................................................................................................................37 CHAPTER THREE: TAMING WILD YEASTS ..............................................................................................................44 WHAT “WILD-FERMENTED” MEANS ..................................................................................................................46 MICROBES, THE FINAL FRONTIER ......................................................................................................................59 CHAPTER FOUR: FERMENTATION AS BIOTECHNOLOGY ........................................................................................69 CULTURED COFFEE ...........................................................................................................................................71 WHEN IN DOUBT, CALL IT A PROBIOTIC .............................................................................................................74 ARTISANSHIP AND TECHNOLOGY .......................................................................................................................79 CHAPTER FIVE: AMERICAN TERROIR .....................................................................................................................82 DEFINING TERROIR ...........................................................................................................................................90 OBLITERATING TERROIR ...................................................................................................................................97 CONCLUSION: DISGUST, AND DELIGHT ............................................................................................................... 102 BIBLIOGRAPHY ................................................................................................................................................... 106 ii List of Illustrations FIGURE 1: “MICROBIAL SUNRISE.” ASPERGILLUS FLAVUS (FUNGUS) AND A YEAST COLONY FROM A SOIL DILUTION PLATE. CREDIT: TRACY SCOTT DEBENPORT ........................................................................................................ 12 FIGURE 2: THE MOLD SPORENDONEMA CASEI, WHICH COMMONLY COLONIZES THE SURFACES OF NATURAL RIND CHEESES. CREDIT: BEN WOLFE .......................................................................................................................... 12 FIGURE 3: LEEUWENHOEK’S "ANIMALCULES" – IN THIS CASE, RED BLOOD CELLS AND ONE WHITE BLOOD CELL, TOP RIGHT. CREDIT: BRIAN J. FORD ....................................................................................................................... 14 FIGURE 4: AN EARLY TWENTIETH CENTURY SCHEMATIC OF THE BALLANTINE AND SONS BREWERY, SHOWING A CARBON DIOXIDE CAPTURE STEP. ...................................................................................................................... 24 FIGURE 5: JOHN SHEPPARD POURS A TASTER OF SOUR MINEOLA ALE, AN UNRELEASED BEER BREWED WITH LACHANCEA YEAST AND MINEOLA ORANGE PEELS. ..................................................................................................... 32 FIGURE 6: DR. MANUEL KLEINER IN HIS OFFICE AT NCSU. HE GETS GRIEF FROM COLLEAGUES ABOUT THE DUKE-BLUE WALLS. ............................................................................................................................................ 43 FIGURE 7: SHEPPARD IN FRONT OF THE YEAST PROPAGATOR THAT HE BUILT AT NC STATE'S BREWERY. ......................... 54 FIGURE 8: A CURRENT VIEW OF THE TREE OF LIFE, ENCOMPASSING THE TOTAL DIVERSITY REPRESENTED BY SEQUENCED GENOMES. FROM "A NEW VIEW OF THE TREE OF LIFE," NATURE 2016. ......................................................... 65 FIGURE 9: THE ASIAN PALM CIVET, A SMALL MAMMAL WHOSE DIGESTIVE PROCESSES FERMENT COFFEE CHERRIES, SOMETIMES UNDER FORCED CONDITIONS. CREDIT: EVGENY TCHEBOTAREV .................................................... 71 FIGURE 10: CULTURED COFFEE (LIGHT BROWN) VS. MY USUAL FRENCH ROAST (DARK BROWN)................................... 72 FIGURE 11: A 5-OZ BOTTLE OF CULTURED COFFEE COSTS ABOUT DOUBLE A 2-LB BAG OF SAFEWAY'S FRENCH ROAST. ..... 72 FIGURE 12: THE CULTURED COFFEE LABEL REVEALS A FOCUS ON HEALTH CLAIMS. .................................................... 75 FIGURE 13: JASPER HILL FARM WHEN I VISITED IN FEBRUARY. MATEO’S HOUSE IS ATTACHED TO THE BARN, WITH A CREAMERY IN THE BASEMENT WHERE THEY MAKE BAYLEY HAZEN. ................................................................ 82 FIGURE 14: MATEO AND AN INTERN NAMED VICENTE IN VAULT THREE, WHERE BAYLEY HAZEN WHEELS ARE MATURED. ... 85 FIGURE 16: INCUBATORS ON THE LEFT, AND A STANDARD FUME HOOD ON THE RIGHT. .............................................. 89 FIGURE 15: THE TWO-ROOM LAB AT JASPER HILL FARM PACKS A LOT OF EQUIPMENT INTO A SMALL SPACE. .................. 89 FIGURE 17: "HARBISON HALVES," AN OIL PAINTING BY MIKE GENO HANGING IN MY KITCHEN. ................................. 102 iii Acknowledgements Thank you first to my advisor, Misha Angrist, whose course on science journalism sparked an interest that absolutely nothing in my undergraduate work predicted. This project unfurled over many phone calls after I moved to D.C., and fermented beverages when I visited Durham, and I am grateful as much for his friendship as for his good guidance. Thank you to the entire Graduate Liberal Studies team,