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The Origins of Probiotic Theory

Fermentation in the 17th century

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The abject fear with which modern society holds microbes stems from the twin legacy of two important scientists who lived a century-and-a-half ago. First, Louis Pasteur, whose research on the causes of spoilage in beer ultimately laid the foundation not only for our understanding of the role of living yeast in alcoholic fermentation but also for the advent of pasteurization, which almost single-handedly altered the modern food supply; and second, Joseph Lister, whose efforts to prevent bacterial infection in the operating theater underlie our terror of microbial pathogens that invade the human body, the development of antiseptics, and, later, the widespread use of antibiotics.

Counter to the radical scientific advances in biology of the 19th century, our appreciation for the benign role of bacteria in digestion is much older. Although modern praise for bacteria has often been anecdotal — as in the studies of Elie Metchnikoff, who around the turn of the century began to promote bacteria in yoghurt as the key to good health and longevity, and whose book, The Prolongation of Life, led directly to all 20th century research into what we now call probiotics — the scientific discourse on fermentation as an essential part of digestion and other metabolic functions is centuries older. That is, without actually understanding the role of bacteria in fermentation, scientists in the 17th century speculated about it and proposed fermentation as essential and sometimes the very definition of proper digestion and good health. Some even went as far as to call fermentation the key to all generation and corruption on earth.

Although we have only recently unlocked the DNA codes of the human gut biome and are only beginning to understand the role of bacteria (and fermented foods) in digestion and many other bodily functions, early modern scientists began this dialogue centuries earlier and without the fear of contagion that grips us and leads us to outright war against germs — what I would call a variety of speciesism. Nor did scientists of the past share our bizarre ambivalence as we wipe out legions of microbes with antibacterial soaps and antibiotics and then reintroduce some of these same species in yoghurt, probiotic foods, and dietary supplements.

17th-century scientists were not totally ignorant about bacteria, though; they had actually seen bacteria after the invention of the microscope by Leeuwenhoek and the work of Hooke in publishing images of the unseen world in his Micrographia of 1665. But what these organisms do and their connection to fermentation was not at all understood. There was also a theory of contagion formulated by Girolamo Fracastoro a century earlier (the man who gave us the name for the disease Syphilis, taken from his poem of that name) but his theory languished for 400 years. Nonetheless, though the connection between microscopic organisms and fermentation was never made, these scientists discussed fermentation as a living process, central to generation and decay and essential not only to digestion, but also to respiration, circulation of blood, brain function, and a host of other biological processes in ways that no one today seems to notice anticipated our own recent findings.

The major reason for this disjuncture is of course that few people concern themselves with outmoded scientific theories: the scientists themselves wrote in a language that is now obscure, often mystical, and usually in Latin. That is, the language of alchemy sounds so strange to us that we automatically dismiss it as either charlatanism or complete nonsense. To show that appreciation for fermentation within and without the human body has been a central concern of scientists for many centuries, we must unravel a bit of that spagyrical, iatrochemical, and iatromechanical mysticism.

In ancient times, Aristotle had a concrete idea of fermentation as being an essential part of generation. The way he saw it, all life arose out of the confluence of heat and moisture. While most animals reproduce sexually, there are many that simply arise when vital heat and radical moisture are enervated by what he called pneuma — which roughly translates as breath or spirit. It was translated into Latin as anima, which also means soul. Thus, creatures such as insects, worms, even frogs in pond muck are spontaneously generated through heat and moisture. Corruption, whereby living material is broken down, and fermentation, whereby matter bubbles and comes alive, as it were, Aristotle thought of as simply two sides of the same process. We now, of course, understand this as the action of bacteria, yeast, and mold on organic matter. Aristotle’s pneuma is essentially nothing other than bacteria.

But the ancients did not connect this process with digestion in the human body, whereby they understood not only digestion in the narrow sense of what goes on in the stomach breaking down food, but rather the entire process of transforming living matter into our own substance, into our blood, muscles, humors, and ultimately the “spirits” which circulate throughout the brain and constitute ideas, emotions, etc.

For the ancients, explained largely by Hippocrates and Galen of Pergamum, digestion, or more precisely concoction in the stomach was effected by heat. The stomach is like a pot heated by the liver in which food cooks, is broken down, and then the nutritious parts are passed to the liver and transformed into blood and thereafter the other three humors (phlegm, choler, and melancholy or black bile). This was not the only model of digestion in the ancient world: according to Erastistratus, the stomach actually grinds and crunches the food down into a smooth paste, and, at least to start, it is an entirely mechanical process, which he presumably surmised from the rumbling sounds stomachs make.

But the Galenic model of food cooking in the stomach prevailed for nearly 1500 years after his death, as did the whole system of humoral physiology. It was not until the mystic alchemist and lunatic known as Paracelsus (also known as the father of modern chemical pharmacy) proposed an alternate system of physiology based not on the four humors but on three chemicals: mercury, sulfur, and salt. Bodily processes, he insisted, were not dependent on the balance of humors, but rather on the transformative processes that occur through chemical reactions. These were not understood by Paracelsus as simple combinations of molecules into other ones (as we conceive it), but rather mystical and spiritual processes governed by supernatural forces. In fact, he believed that understanding the virtues of plants and minerals in healing was itself a mystical process of “overhearing” their properties and recognizing various signatures or signs that might be evident in color, shapes, or sounds. In other words, this was not modern chemistry in the least.

Paracelsus’ followers stripped his ideas of some of their more mystical features, but retained a key concept, also directly involved in fermentation and digestion: the archaeus. This was not exactly Aristotle’s pneuma, but rather a principle of life that connects the earthly to the astral planes in a kind of sympathetic magic, which explains why the medical powers of plants derive not within themselves, but through the energy they draw from the planets, through sympathy, resonating through this archaeus. It is what causes metals to transmute and gives life to plants. Jan Baptista van Helmont, Paracelsus’ most important follower, associated the archaeus specifically with chemical reactions in the body as well. It is the force that, among others, causes our stomach to break down matter into nutrients that our bodies can use.

Van Helmont further speculated that this process, which he called fermentation, was much like what happens to wine when it is refined from must to alcohol and when fermented foods become sour. The same process happens in the stomach as the archaeus generates acid that breaks down food. That is, this was an entirely new model of digestion, based on acid ferments. From the 1662 Oriatrike, after soundly criticizing Galen, he stated that, “[w]ithout controversie, it belongs to meats and drinks, together, and in like manner, to be dissolved into a Cream, plainly transparent in the hollow of the Stomach. I add, that that is done by vertue of the first Ferment, manifestly soure or sharp, and borrowed of the Spleen: for I have found as many suitable Ferments, as there are in us, digestions” (206). By digestions he means further and further refinement of foods in various parts of the body, starting in the stomach and ending in every part of the body, with blood in the heart and spirits in the brain.

These scientists were not merely theorizing here either: they made observations and ran experiments and actually knew that the stomach contains acid rather than heat or grinding mechanisms. It appears to me this theory is also in some way based on observations of bacterial action outside the body: the lowering of pH that occurs on lactobacillic fermentation, the refinement that occurs when yeast breaks down sugars into alcohol, and the corruption and decay that occurs when living matter rots, generates its own heat, and, in some cases gives, rise spontaneously to life forms, again flies and snails. The archaeus was, therefore, a kind of seed, he called it aura vitalis seminum, vitae directrix, or the force of the vital seed, director of life.

Van Helmont was also intensely interested in the aerial substances that are the biproducts of fermentation, and he actually coined the term gas in the modern sense. He was of course examining carbon dioxide that is given off as microbes digest plants, which he called gas sylvester, whether it came from burning wood or fermenting grapes or rotting vegetables.

These ideas were compounded into a comprehensive theory of acid digestion and actually an entire physiological system based on acids and alkalis in the body by Franciscus Sylvius de le Boë. Fermentation also played a central role in his ideas of metabolism, and he speculated that ferments require not only water and heat, but air, which of course carries bacteria and yeast. It is to Sylvius that historians attribute the origin of the chemical understanding of digestive enzymes. Digestion for Sylvius was nonetheless a species of fermentation. In his Praxeos Medicae of 1671 (vol 3, 27) he says that faulty digestion is the result of either too strong or too weak fermentation. In the latter, food is not resolved or broken down. It’s a concept entirely foreign to our own nutritional theory, which assumes that anything that goes into the body results in nutritional value in quantitative terms: calories, vitamins, etc. Earlier theories assumed that undigested food actually offered the body no nutrients. “A weakened fermentation of foods, when retained in the stomach a sufficient amount of time, raw or unchanged, though it churns up and down, is nonetheless diminished and still remains unchanged, whence results in none or very little nourishment.” On the other hand, when too quick, just as with bread dough that is over-fermented, it becomes sour, and is very bad for the body.

Another scientist of the late 17th century had many more intriguing and far-reaching theories on the topic of fermentation. This was Thomas Willis, remembered chiefly today for the arteries that supply blood to the brain which he identified in his anatomical studies, now known as the circle of Willis. Willis was also intensely interested in fermentation. In his, Philosophical discourse of Fermentation or the Intestine Motion of Particles in Every Body, Willis added to the chemical philosophy the theory of particles or corpuscles which collide and interact, something not unlike molecules interacting and changing structure. In the preface to the work, Willis admits that he intended merely to discuss the action of ferments and swelling in the Baker’s Oven and Brewer’s Furnace, but found instead that fermentation is central to everything in nature and is key to generation. “I found at length, those first begotten Particles, by whose Orgasm or Heat, those vulgar preparations do Ferment, to beget the causes of Motions, and Alterations, in Whatever things they are mix’d with besides.”

What he means is that fermentation is a process that explains changes in all of nature, both creation and decay. He was thinking how seeds generate into plants, how blood is formed and circulates within the human body, and, oddly, how precious metals are generated inside the earth. And, of course, how living matter decays and is broken down. We would categorize some of these today as reproduction rather than fermentation, but it was clear that he was searching for an overall theory that would explain all change in nature.

To understand this corpuscular philosophy, a brief mention must be made of Robert Boyle, his colleague, who at the time had been experimenting with water heated and enclosed in a chamber, which creates pressure. Boyle’s Law, as it is called, underlies Willis’s concern to unify the chemical idea of digestion/fermentation with a mechanical theory of colliding atoms. For Willis, there were a whole variety of substances in nature; those that are very stable are made chiefly of particles of similar shapes and size and therefore they don’t bounce around a lot or collide, but those with very different particles, such as the juices of vegetables and animals (because compounded of many different things), ram into each other, become agitated and effervescent, and thus generate heat and swell. Which is why when you seal up new ale, it will create pressure and sometimes cause the bottle to explode.

Interestingly, once these same substances are distilled — into pure alcohol in this case — the particles remaining are all of the same size and shape, and thus it is not only completely stable but incorruptible inside an enclosed container.

Willis also embraced concepts drawn from chemistry and had an elemental theory that included spirits, sulfur, salt, water, earth, etc. In discussing sulfur, he says that substances that contain a lot of it, when loosened, stir up those particles and they become very hot, as in a pile of dung or hay — he’s thinking of bacterial action in a kind of composting here — and they emit an odor of rottenness, which is the volatile particles flying off. On the other hand, those composed principally of salt (as an element, not table salt) as in human blood, milk, ripe fruit, sugar, vegetable matter – they start out sweet but in the process of fermentation become sour. Here he is definitely trying to understand lactobacillic fermentation as distinct from others.

The principal quibble with Willis’ theory is that he conflates growth and conception with fermentation, or considers it a species thereof. Unlike his contemporaries, he is right in thinking of fermentation as a living process, not merely a chemical reaction. For example, when discussing vegetables sprouting from seeds he says this:

You may take notice, that the times of year, for the Budding, Flowering, Ripening, and Decaying of Vegetables, are of great efficacy and virtue” not in the winter when the earth and air are cold, but when there is a confluence of heat and moisture that stimulates fermentation. “But in the Spring, when the bowels of the Earth begin to be a little warm by the vicinity of the sun, presently they are impregnated with a wonderful Feocundity and produce the effects of their seminality. Not only the superficies of the earth, but also Water and Air everywhere, grow big with spiritous particles, which as it were, raise up from the dead the little bodies of salt and sulfur, and bring them into motion: Therefore besides that plants bud, the Juice and Blood of living Creatures is quicker, and more apt to abound. … [T]he whole Bulk of Nature, as it were, inspired by lively fermentation, is abundantly fruitful of Motions and Generations. Yea these our Principals, at first separated and dispersed from one another, led as it were by an Appetite of Copulation, enter into mutual marriages, and being married together, almost by infinite Embraces, cause a most ample seeding and germination of the Herby state (10).

Willis also contends that the same process of fermentation occurs in the stomach, in this case acidic, which breaks down the particles of food, during which the chyle takes on a milky color. He describes what happens in a too-strong stomach when it becomes overly sour with belching as comparable to using too much yeast (derived from brewing) in bread dough, whence it becomes bitter, or too much leaven (meaning a natural ferment), and it becomes too sour.

His comments on substances which easily ferment are equally interesting. Solids, because they are stable and compact, are difficult to ferment, but liquids such as wine, beer, fruit juices, and herbs easily ferment, as do soft substances like bread dough. These also must be perfectly ripe, neither immature nor overly ripe. The former are too compact and the particles can’t collide properly, and the latter are too volatile, which is why they corrupt. Without knowing it, the ripeness here refers to available sugars for fermentation, and later he specifically discusses cider apples in this context, which also need a certain amount of acidity and bitterness to keep. Warm air facilitates fermentation, just as cold hinders it. Fermenting substances should also not be closed up too tightly in sealed vessels — beer and wine are thus begun in open vats, especially oak, which he contends promotes fermentation. Only once refined and the volatility spent should they be stored in a cool cellar and closed, but with vinegar exactly the opposite is the case: it is kept in a warm place near an oven or exposed to the sun, which is of course what acetobacter likes best.

Willis then explains exactly how bread, beer, and wine are made; why each is sometimes sweet, sometimes sour; and also why some corrupt. There is brief mention of fish pickled in salt brine as well as flummery, which is a fermented sour oatmeal dish. On the topic of pickles, he insists that they would take an entire book, “For it would be to describe under that rank the whole Art of Cooking and Diet.” Nonetheless he contends that through fermentation “so they greatly please the Palate, and by a more easier digestion go into nourishment” (22). This is as far as I know the first time someone contends that fermented foods not only taste better but are more nourishing. In the Galenic tradition, salted and fermented foods were always considered too crass or too likely to stir up sour melancholic humors.

Now what does all this mean in terms of dietary recommendations? Did physiologists and food writers actually recommend fermented products as aids to digestion or as probiotics that would promote health and longevity? If so, it would overturn basic Galenic physiology, which condemned most salted and fermented foods as too hard and difficult to digest, including pickled meats, fish, and old cheese, as well as fermented vegetables.

The answer might be in the Traité des aliments of Louis Lemery, written in 1702. His father, Nicholas, was a renowned chemist, exact contemporary of Willis, and also used the corpuscular theory. So it seems as if anyone were to hold this new attitude toward pickles it would be Lemery, the younger. Lemery does indeed use the concept of fermentation in his discussion of digestion. In discussing the role of saliva, he says, “certain acid salts which this liquor contains, also contribute to the fermentation of the aliments, the same as a little levain mixed with dough, contributes to make it ferment” (29).

Of specific food, Lemery’s comments are a curious mixture of Galenic, chemical, and mechanical theories. For example, on cucumbers he says that, although they are refreshing, they are also viscous and phlegmatic, difficult to digest, and should be mixed with onion, salt, and pepper to aid digestion. Those soaked in vinegar are also difficult to digest and should be eaten in moderation. On the other hand, he said that the extended conservation of cornichons “aids their digestion” (45).

His remarks on cheese are particularly interesting. Cheese is the solid curds separated from the whey by the action of an acid ferment. It is very nourishing taken in moderation, and “it is able to aid digestion taken in a small quantity because it adds its (own) ferment to the other aliments just as a sour levain ferments bread” (285). Or, as we would say, the bacteria in fermented cheese strengthen the bacteria of the gut biome.

In the early 18th century, there were violent academic battles waged between orthodox supporters of chemical digestion and those who believed in mechanical digestion. One of these, between Phillipe Hecquet and Nicolas Andry (the father of orthopedics), took place in the medical school of the University of Paris. Hecquet went so far as to claim that since digestion was entirely mechanical, food that are easily broken down are actually the most nutritious, so one need not fear eating vegetables or fish during Lent. He may be the first person to make a scientific argument in favor of vegetarianism. Andry ripped him apart point-by-point in a rejoinder.

These debates spilled over into dietary and physiologic treatises. So there were theorists who not only denied that fermentation served to break down food, but that it was also the cause of improper digestion, bloating, gas, and eventually other maladies. An example of this is in Gideon Harvey’s The Vanities of Philosophy and Physic, where he says “those who usually drink any Wines, not being diluted with Water, or commonly conclude their Dinners or Suppers with Banquets of Sweet-meats, Custards, Cheesecakes, Creams, and Gellies, do weaken, and in time destroy their Concoction, so as few of them are found to be long livers; because those before mentioned materials containing a fermentive Juice, by raising a Fermentation, do extremely interrupt and impede the dissolution of aliments in the stomach” (20). And he ultimately wonders how anyone can think of digestion as achieved by heat of the stomach or fermentation. In other words, the iatrochemical school was not the only theory around at the time.

Another factor was the proliferation of reports from travelers around the turn of the 18th century who mention various fermented foods eaten around the world and their salubrious effects. To mention just one: thickened sour milk. Ephraim Chamber’s Universal Dictionary states that there is a popular drink in Turkey which they call igur, which they drink diluted with water, which is found to cool and nourish much better than milk alone. Likewise, in 1691, a voyage of English merchants to Aleppo mentions “leben, a thick sour milk … a think in mighty esteem in these Hot Countries, being very useful to quench thirst: and Truly we had need of it here…” (156). Western physicians knew the ancients praised sour milk, oxygala, but in the east they encountered living traditions and were often interested in promoting them for health back in Europe. Coffee was a relatively new drink — promoted for health, which had just caught on in this period.

These examples do show that before the advent of modern nutritional science and the understanding of both digestion and bacteria, scientists were engaged in a fruitful dialogue about the role of living ferments in the stomach and other bodily functions and they may have accidentally stumbled on some truths that we are only now beginning to appreciate and understand regarding the probiotic function of bacteria in the human gut. •

Ken Albala is a professor of history and the director of food studies at the University of the Pacific.

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