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My Microbes, Therefore I Am: Fermentation, Health, and Human Identity

by Joanna Wright

Do I contradict myself?
Very well then I contradict myself,
(I am large, I contain multitudes.)
Walt Whitman, Song of Myself

My microbes, therefore I am.
Satish Kumar

I’ve recently developed an obsession with the diverse and time-tested food tradition of fermentation. Jars of kimchi and sauerkraut, kefir and kombucha, are regulars on my kitchen shelf, quietly teeming with life and effervescence. Little did I know, when I first chopped and salted cabbage, pounded it until my knuckles were pink, and left it to it’s own mysterious processes, that this simple act would take me on a journey through time and space, from the emergence of cellular life on earth 3.5 billion years ago, to the complex nature of human identity, to the inner workings of my own gut.

Allow me to introduce fermentation properly, personally, through one of my newer acquaintances: kefir. A fermented dairy drink known as “the champagne of the Caucasus Mountains” (Margulis and Sagan, 70), kefir is thought to have originated amongst nomadic shepherds, who inoculated cow, goat or sheep milk with kefir grains, over time selecting for the best starters and thereby propagating certain microbial individuals and eliminating others. Kefir grains form from a symbiotic community of bacteria and yeast (SCOBY) which share nutrients and coordinate reproduction. While some of the microbial members of this community have been identified, the synergistic effect of their relationships has so far defied replication in the laboratory. In the words of biologist Lynn Margulis, “Kefir can no more be made by the ‘right mix’ of chemicals or microbes than can oak trees or elephants.” (Margulis and Sagan, 74)

The grains look a bit like troll boogers. They form white, rubbery, pea- to walnut-size clusters which grow and reproduce quickly if fed and kept at the right temperature. I’ve learned that the fermentation happens more rapidly if the milk is stirred at least once a day, exposing more liquid to kefir grain surfaces, where metabolic activity is highest. The pace of the fermentation process has worked its way into the rhythm of my days; how long it ferments strongly influences its consistency, effervescence, and sourness, down to the hour.

It’s inevitable to begin regarding these strange little blobs as animate organisms. I admit to developing an affection for them. When I went away for Christmas, I left them in the fridge without milk to slow down their metabolism, and asked a friend to feed them every few days to keep them alive. She forgot, and I returned to find a sad, yellowing lump of grains. I assumed they were “dead”, their microbial composition irreversibly changed, no longer the coherent system that I had come to know and care for. But, just in case, I picked out a few whiter, plumper clusters beneath the exposed surface and transferred them to a jar of fresh milk. Within a few days, they had doubled in size, and the milk had soured and fizzed promisingly. I sipped it with caution, trusting my nose and tongue to know the difference between kefir and milk-gone-off. Joyously, the kefir grains had persisted, resilient little buggers. We’re back in business.

Next to “What is that?”, the most common questions I get while preparing kefir is, “Why should I drink it?” At first, I cobbled together a vague adaptation of the sales pitch for yogurt, saying something about “probiotics.” But what is fermentation, really? And what does it have to do with the human body?

It turns out, we humans are vast, complex collections of bacteria — host to ten times more microbes than human cells. The plural nature of self is an ancient poetic truth, now increasingly affirmed by scientific inquiry. “Do I contradict myself?” Walt Whitman asks in Song of Myself, “Very well then I contradict myself, (I am large, I contain multitudes.)” Not only do we “contain” approximately 100 trillion bacteria; emerging theory suggests we evolved in symbiotic relationship with them. Early life forms, single-celled bacteria, gradually incorporated each other to form more complex collectives, from which the processes fundamental to our existence — such as photosynthesis, respiration, metabolism, sensing, even movement — developed. Various ideas about how exactly this process happened bring forth many more questions than definitive answers. What is clear, however, is that the infinitely diverse, self-willed, highly networked and adaptive natures of bacteria are inextricably linked with our experience. Our story is their story. In this tale of symbiogenesis, “the merging of individuals into new collectives,” (Margulis and Sagan, 31) we are linked by what ecologist Stephan Harding calls a “continuous thread” running “from us right back to our earliest bacterial ancestors.” (159)

Like Michael Pollan, I’ve begun conceiving of myself “in the first-person plural”. This happened gradually, over many months of engaging in practices – fermentation among them – that bring me into direct contact with the more-than-human world. Increasingly, I find myself feeling less like an outside observer of nature and more like a participant. The membranes that define “me” are, at all scales, semi-permeable; my body is a community of bodies, all sensing and responding to their environments, taking in and transforming energy, and communicating. This concept of “self” Dorion Sagan and Lynn Margulis refer to as chimera. “Humans are one kind of self,” they write, “but we are composed of smaller selves, and we form parts of the more inclusive selves.” (Margulis and Sagan, 28)

Emerging research suggests that what goes on in our gut may have much more to do with our sense of self than was previously assumed. Food pyramids and diet fads are fed to us constantly, as if simply ingesting the proper ratios of protein and carbohydrates is the key to good health. But it’s much more complex than that. For instance, the vegetables we eat — viewed as a panacea to many Western diseases — tend to have much lower nutrient content than their botanical ancestors. Our physiological state while eating also has an effect; high levels of chronic stress and a sedentary lifestyle can cause systemic inflammation and interfere with organ function. Preparing a meal ourselves whets our appetite, priming the body for digestion; purchased meals rob us of the metabolically important experience of anticipation. And of course, not all carrots are created equal, as the organic food movement has highlighted. As Wendell Berry famously said, “Eating is an agricultural act,” linking us culturally and physiologically to the context in which our food is grown.

Eating is microbial act, as well. Just as a good gardener attends not merely to the health of individual plants, but to the health of the soil, we can eat in ways that support our microbial ecology. I’m not implying that it is possible to fully control the complexity that is a soil or an intestine — it isn’t. But by regarding health “as a collective property of the human-associated microbiota,” (Robinson et. al, 2010) perhaps we can begin to ask questions that humble us, and help us align our food choices with the diversity and resilience of the internal ecosystem upon which we depend.

Those questions have led me to fermentation. Fermentation refers to a process of anaerobic metabolism which, in the context of foods that we eat, essentially creates the conditions for bacteria and enzymes to pre-digest the food (and in doing so release by-products such as alcohol, lactic acid, or carbon dioxide, that change the quality of the substance in a way that pleases our palates). These bacteria have remarkable ways of self-organizing to inhibit the growth of other undesirable bacteria. For them, this keeps their environment hospitable and their communities intact. For us, this can extend the “shelf life” of our food, as well as make nutrients more available to our bodies — and diversify and refine our cuisines!

In a few years of experimenting, I have found fermentation to be a fun, easy, and empowering way to enrich my relationship with the food that I eat. Meanwhile, my microbiome is nourished by the live bacteria, particularly befidobacteria and Lactobacillus plantarum, which are believed to directly benefit the digestive tract, the immune system, and even the mind. In a society where food has become extremely sterile, we’ve lost a connection to it as something alive — and the perceptual and practical skills to properly nourish ourselves. Making kefir requires me to attend to a dynamic process on a daily basis, as do other fermented foods like sourdough or sauerkraut. Sauerkraut, for example, is perfectly edible for an extended period of time, but during that time, it’s quality can change significantly, going from being quite crunchy and mild to a bit softer, with a stronger, tangy flavor (at which point it’s wonderful served with raisins!). While learning to make sourdough bread, I sought advice from experienced sourdough baker when one of my attempted loaves did not rise. “Why?” I asked him. He gave me no straightforward answers, instead inquiring about the temperature, timing, salt content, and so on, thinking out loud about myriad factors that could have affected the sticky, sloppy dough still sitting limply in its tin.

Industrial-scale food processing and refrigeration have incubated a perception of food that is fixed, static, standardized, and impersonal. Fermentation as a home practice engages our capacity to observe and interact with the nuance of living processes.

To me, this practice is as much political as it is practical and philosophical. It is tool for cultivating a more participatory role in my own livelihood, in the community I grow, cook, and eat with, and, consequently, in the larger food system. As Sandor Katz writes, “Reclaiming our food and our participation in cultivation is a means of cultural revival, taking action to break out of the confining and infantilizing dependency of the role of the consumer (user), and taking back our dignity and power by becoming producers and creators.” (Xix) We’ve inherited a long legacy of culinary artistry and an even longer legacy of microbial innovation. What do we do with such an immense, refined gift? How do we give thanks, and keep that gift in motion? In his theory of the gift, Lewis Hyde describes gratitude as an active labor, a living-up-to the gift that has been given in order to pass it on in an authentic and generative way. What will we offer to the microbial ancestors still living in us and keeping us alive today — and to the microbiomes, food traditions, and identities of our children?

Want to explore fermentation further? Check out our forthcoming course Exploring the Microcosmos – New Paradigms from Microbial Communities with Sandor Katz, Eva Bakkeslett and Stephan Harding – 26 – 30 May 2014.


Berry, Wendell. “What are people for?”

Brown, Cynthia Stokes. 2007. Big History: From the Big Bang to the Present. New York: The New Press.

Farnworth, Edward R. “Kefir: A complex probiotic.” Food Science and Technology Bulletin: Functional Foods 2 (1) 1–17 DOI: 10.1616/1476-2137.13938. Published 4 April 2005. Accessed January 14, 2014.

“Food Failures: How to Spoil Your Food and Eat It, Too.” (2014) Science Friday, NPR. Accessed January 10. 2014.

Harding, Stephan. 2006. Animate Earth. Vermont: Chelsea Green.

Hyde, Lewis. The Gift: Imagination and the Erotic Life of Property.

Katz, Sandor Ellix. 2012. The Art of Fermentation: An In-Depth Exploration of Essential Concepts and Processes from around the World. Vermont: Chelsea Green.

Lozupone, Catherine A., Jesse I Stombaugh, Jeffrey I Gordon, Janet K. Jansson and Rob Knight. “Diversity, stability and resilience of the human gut microbiota.” 2012 Nature 489: September 13: Accessed Jan 17, 2014. doi:10.1038/nature11550

Margulis, Lynn and Dorion Sagan. 2007. Dazzle Gradually. Vermont, USA: Chelsea Green.

Pollan, Michael. “Some of My Best Friends Are Germs.” New York Times, May 15, 2013, accessed January 20, 2014.

Robinson, Courtney J., Brendan J.M. Bohannan, and Vincent B. Young. 2010. “From Structure to Function: the Ecology of Host-Associated Microbial Communities.” Microbial Mol Biol Rev. September; 74(3): 453-476. Accessed January 28, 2014.

Robinson, Jo. “Breeding the Nutrition Out of Our Food.” New York Times, May 25, 2013, accessed January 14, 2014.

Stein, Rob. “Gut Bacteria Might Guide the Workings of our Minds.” NPR. Nov. 18, 2013. Accessed January 3, 2014

Whitman, Walt. Song of Myself. Accessed online January 10, 2014. Poetry Foundation.

This article was oringally published in Joanna’s blog A Sensing of Place

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