Sociocultural themes in the experience of fermenting
Our goal in collecting qualitative anthropological data was to relate the stories and the practice that fermentation revivalists carry with them to the microbiology we would detect later. From this perspective, every family recipe and kitchen improvisation is a step toward shaping microbial biodiversity in our foods and in our own bodies. Every cheese cave, wine valley, and cabbage patch likely has its own collection of microbes, to say nothing of our kitchens and stirring spoons. After transcribing interviews and uploading field notes into QDAMiner, we identified a number of inductive and deductive themes that we will explore below.
The workshop was a masterclass in learning to cultivate biodiversity through smell, taste, and texture, well suited to the anthropological methods of participant-observation and open-ended interviewing. Beginning with a sweeping introduction on the history of fermented foods Katz oscillated between microbiological discussions of specific strains, proteins, and fermented foods, and observations rooted in sensory perceptions and general guidelines. Although we discussed how Lactobacillus species tolerate salty and acidic environments in ways that other bacteria do not, Katz quickly lightened the mood as we nervously asked if we were preparing the food correctly. “When I make a brine, I like to taste like the sea,” he offered, inviting us to taste, rather than measure our way to a successful microbial ecology. The following day he continued to first situate us within scientific concepts, such as a chemical description of anaerobic respiration, before emphasizing “but today we’re going to learn and get more of the experience – what it smells like, what it feels like.” These shifts between the scientific nomenclature and phenomenological ways of knowing centered the group’s expectations somewhere between culinary and biochemical expertise.
The workshop created an educational space apart from microbiopolitical food safety regulation, catering to an educated group of fermenters eager to similarly claim expertise within a range of sensory, scientific, and culinary bodies of knowledge. Unsurprisingly, as Katz’s bookshelf featured anthropological work including Paxson’s (25) The life of cheese, Katz and workshop participants rejected the Pasteurian logic of food regulation in favor of actively shaping a microbial landscape that was influenced by a larger socioecological landscape. During the first day, several participants asked how best to avoid harmful bacteria or contamination, questions motivated by living within the larger US and Canadian regulatory system that polices bacteria. Explicitly influenced by Paxson, Katz deconstructed these assumptions, explaining “there’s not a registry of good and bad bacteria…we ultimately don’t know enough about microorganisms to make these moral judgements.” Rather, he described fermentation as a means for shaping a particular community through different pushes and pulls of acidity, vegetable matter, and salinity. “Of all the communities of microorganisms, the question is which will develop?” he continued. Conceived as such, the practice of fermentation is thus a practice of creating different landscapes, what Katz called “manipulating environmental conditions” to make a fermented food amenable to acidic, salty, hot, or ammonium-rich bacterial communities.
Workshop participants seized on this heuristic of shaping environments as they reflected on their experiences with fermentation during interviews and participant observation. Maya, a trained cook and fermentation entrepreneur, spoke specifically about interacting with microbial environments. “I don’t really do anything,” she explained, contrasting her experience as a high-end chef to her new work as a fermented food seller decentered from the creation of her products. “I mean, I’m not making the vegetables ferment. I’m just creating an environment where that will happen. You know, I’ve learned along the way certain things to make sure that I have a better result, but I’m not actually fermenting things…I set it all up and I step out of the way.” No longer a cook as such, Maya describes her work in terms of being an environmental steward. Carl, a Midwestern IT professional, similarly referenced letting the fermented environment work to cultivate unique, strong flavors at the microbial level that are otherwise absent in the larger food system. “We can introduce a lot of umami flavors, it seems like…that’s part of the funk that develops,” he explained. This search for distinctive tastes differs from the nationalist discourses around fermentation described above in that Carl is not recreating family or place-based recipes so much as chasing the byproducts of this microbial ecology. “In all these ferments there’s the souring that happens through the production of lactic acid. Some people can taste the difference between lactic acid and acetic acid, and I can, and I prefer the lactic acid.” Carl, who distinguishes between the vinegary taste of acetic acid and the sharper “funk” of lactic acid, takes pride in the ways that he has learned to shape the distinctive variations in his food. Although he references protein structures and glutamate compounds in our discussion, Carl’s definition of a successful ferment leans more on sensory experiences of taste and touch to guide the ferments that he creates.
While all the fermenters referenced microbes in our interviews, most described fermentation as part of a larger set of environmental practices including gardening, foraging, or simply walking in forested spaces. Maya, who grew up eating fermented food, began making fermented products after learning to have “a conversation with plants. And that was so exciting for me to, like, meet the neighborhood go around and spend a lot of time on the trails…and then as a chef you get knowledge of plants and you’re like ‘Okay – how do I eat you?’ Or, what medicine are you. What’s your power, what’s your personality?” Similarly, Karen, in the early stages of starting a fermentation business, explained “I started looking at how I could value the marginal, like the weeds in my garden. Instead of ripping them out. And so we started playing around with dandelion, and nasturtium, and calendula marigold, and infusing those into our krauts…So we thought between the wild fermentation and the wild edibles, lets market ourselves as this business that helps you re-wild yourself and get back in touch with nature.” Every member of the workshop took pride in gardening or growing foods as a way to resist homogenizations of flavor or in the experience of eating. Maya’s idea of meeting the neighborhood and Karen’s hope that fermentation could help her family and her customers “re-wild” themselves speaks to the larger ways in which fermentation is helping this community embrace a place-based knowledge and praxis. All but two fermenters mentioned that fermentation has entered their lives along with small-scale vegetable cultivation and foraging, particularly growing cabbage that can be used for sauerkraut or kimchi.
Workshop participants described how these small changes to the landscapes where they live influenced their fermentation, while Katz reminded us they are part of the story of heritage fermentation as well. A few hours into the workshop, Katz drew our attention to the ecological constraints within a larger landscape that would influence the possibilities for a microbial landscape. “You know the famous Belgian open fermented beers,” he told us. “Where that happens is in a valley that was once dominated by cherry orchards. So if you have a concentration of a certain kind of agriculture in the geographical area that would certainly have implications for the density of microbes in the air, the distribution of what kind of microbes you find in the air…and then I think that that's definitely an aspect of terroir that people are talking about more and more.” Where some commercial food suppliers leverage local microbes as a scientific marker of terroir (26,58), the participants in this workshop saw microbial terroir as a means to an end featuring creativity, flavor, and distinction in an alternative food system. “The first time I made kraut I remember moving my body,” explained one participant, “squeezing the fruits, the vegetables, it’s like a work out in a really nice way…the physical component of it is just really important to me to feel more connected to the food.” Terroir as such is a means to an end, not a marker of high-end cuisine or geographic distinction in a market but a result of a locally situated authenticity. As Paxson and Helmreich (31) argue, microbes in this context provide a way to think through larger sociopolitical relationships between people, place, and the food system. In particular, fermentation as a skill rediscovered or reaffirmed in spaces like these workshops help to support a body of knowledge and practice where participants feel greater control and agency over the foods they eat and the spaces where they live. Kelsey, who came to fermentation after seeking to rebuild her gut microbiota, sees the creative possibilities of learning to ferment as a means to build ecological knowledge. “It’s amazing that we’re in this period of time when people can reach adulthood with such a limited skillset, or zero skillset,” she laments. Her enthusiasm for fermentation has led her to both new foods and new medicines as she explores non-pharmaceutical and plant-based medical traditions.
Similarly, several participants credited fermentation with providing a new kind of creative outlet through which they could both experiment and actively reject a homogenous food system. “With the work that I do, it is kind of nice cooking. I mean, because even an act as simple as just slicing up cabbage can feel, like: well here’s what I’ve done,” said Matt, a pastor from Pennsylvania. “There’s just some immediate satisfaction when others can join you and then you can gather around a table. It’s really nice.” Warren, a professor at a liberal arts college who had joined him for the drive to Tennessee, described this process as riffing. “Initially I’ll look at a recipe and follow it, but I’m always riffing on it…what I'm feeling spontaneously in the moment.” While providing him with a creative outlet, the improvisatory nature of fermentation also helped him embrace more diverse food options. “The whole “Walmartization and McDonaldization of society, especially in the West that we live in. It’s creeping in everywhere, right? I mean the homogeneity, it’s just dumb and it takes away the beauty of a difference, right?” During a later interview, another fermenter was more direct: “I feel a little bit constitutionally unable to exactly follow a recipe.” We laughed, but there may be something about encouraging bacteria to grow on your food that attracts people hostile to the industrial food system.
Warren was not alone in these sentiments. Several other participants and Katz himself contrasted the diversity of flavors and knowledges of local and fermented foods with a larger homogenization in a global food system. Long a signifier of cooperative and anti-establishment politics in American Left and Green circles (39), the workshop space featured counter-culture books, zines, and artwork lamenting corporate control in industrialized agriculture. Like Warren and Kelsey, Katz placed the practice of fermentation within a larger critique of a Pasteurian state that welcomed industrialized agriculture and criminalized local and microbially variable food production. “I feel like, here we are among this population of de-skilled, infantilized people, and you know food is just food – it’s this transaction at the supermarket. And depending on how much money you have in your wallet you have more choices, but I just feel like food is so much deeper than that.” It is beyond the scope of this paper to review the scholarly literature on the ways in which food is and is not a capitalist commodity (73–76), but ethnobiologists and agrarian studies scholars recognize the transformative effects of practice on knowledge and identity (77,78). Fermenters were keenly aware of the need for knowledge-sharing spaces like this workshop to structure the transfer of knowledge and microbial cultures. While all in attendance had at least some of Katz’s books early in their experience, most mentioned informal networks that allowed them to swap recipes, find community, and, importantly, share microbially rich cultures that could be used as starters for fermented foods like yogurt, sourdough bread, or kombucha. As living gifts, these fermented starters share qualities with seeds or plant starts studied by ethnobiologists (34,79), sustaining not just a food product but also a social relationship.
In addition to distinctive carriers of place, flavor, and skill, several fermenters used the workshop to embrace the healing potential of a balanced microbial ecosystem. Four told stories in which fermented foods were central to their experiences of living with chronic illnesses, including cancer, HIV, and severe gastrointestinal distress. Warren, a cancer survivor, explained that he first encountered fermented foods by looking through peer-reviewed literature on probiotics, particularly kombucha. “Yeah when the cancer thing happened, I'm the type of person where I’m kinda all in. Alright, okay, let’s fight this right?” Later, he continued, “I probably drink 7-14 ounces at least per day.” Fermenters who looked to these foods for health did so within a larger dietary context of promoting some kind of healthy gut flora in their own bodies. Although many had read medical reports on the microbiome, none articulated specific probiotic or prebiotic genera that they hoped to introduce into their bodies. Rather, they came to imagine some microbes as allies in their fight to stay healthy and others as impediments. “I know we can’t put it into good and bad like that, but you can turn a dis-biotic situation into a balanced situation,” argued Kelsey. “I probably took antibiotics, the five day Z packs [azithromycin], twice a year every year,” she continued. Kelsey blames this childhood exposure to antibiotics for chronic bowel problems, a condition that led her first to read Weston Price’s (80) early work on comparative nutrition and later to literature on fermentation and the microbiome. Like Warren, she pursues fermentation not necessarily because it provides a specific healthy bacterial genera but because she wants to create a healthier environment within herself where her gut flora can flourish. “So you arrived to adulthood and you have these problems but it's not mysterious…it's like going to battle, you kill first and then you have to regenerate. And I did that with bone broth and with fermented foods.” Both Kelsey and Warren used military language to describe how specific fermented foods provided microbial allies for their bodily ecosystems, noting their frustration with conventional medical approaches that favored chemotherapy and antibiotics respectively. More generally, fermenters named benefits including clearer skin, regular bowel movements, stronger immunity to seasonal illnesses, and improved energy throughout the day. “There’s literally a quickening, you feel yourself coming alive from the inside out. And then you start to seek those foods out,” explained Maya. Coming alive, which Warren also described, is a function of how fermenters imagine themselves to be reshaping their bodies through the live microbial cultures of their fermented foods.
Both implicitly and explicitly, the creative and engaged changes that fermenters experienced as they learned to make fermented foods then manifest in how fermenters imagine themselves to cultivate the microbial communities within themselves and their foods. Over the course of our interviews and participation in the workshop, the fermenters discussed questions of health, place, and creative labor on scales ranging from fermenting crocks to farms. In agrarian studies and ethnobiology scholarship (1,13,81), landscapes are assumed to be in dialectic relationship with the cultures that manage them. There are no farms without farmers, and local cultural knowledge or norms relating to that natural resource management goes on to create new habitats for human and non-human life. However, the innumerable dietary and lived confounds in the human body, as well as the difficulty in studying how fermented foods impact the gut microbiome in the places where they live and eat mean that we cannot assume that the same dynamics work the same way in our fermented foods. To test what sorts of microbial ecologies fermenters created when they made these foods, as well as how those ecologies interacted with human bodies, we conducted a series of microbiological and genomic analyses.
Food and gut microbial analysis: Results
In total we identified 6,923 ASVs from the 82 samples that passed quality control. The 40 food samples contained 1,595 ASVs, and we identified 6,067 ASVs in 42 fecal samples. Of the 6,923 ASVs, 605 were shared between the food and fecal datasets. Both food and fecal samples were dominated by a small number of phyla. The fecal samples were dominated by Bacteroidota, Firmicutes, with lesser contributions of Proteobacteria, Actinobacteria, and low abundance phyla (figure 1a). The food samples contained predominantly members of the Firmicutes and Proteobacteria (figure 1b). At the generic level, most food samples were represented predominantly by a small number of high abundance genera, predominantly lactic acid bacteria and Gammaproteobacteria (Lactobacillus, Lactococcus, Leuconostoc, Pseudomonas, Weisella, Yersinia, Bacillus, Acinetobacter, and Pantoea) (figure 2). In total, we identified 226 different variants of lactic acid bacteria in our food samples, 90 of which belong to the genus Lactobacillus. In contrast, the microbial communities of the fecal samples generally were less dominated by high abundance genera, with Bacteroides, Faecalibacterium, Parasuterella, Phascolarctobacterium, Prevotella, and Catenibacterium being the most common taxa (figure 2).
Beta diversity ordinations indicated a clear and significant separation (PERMANOVA: R2 = 0.204; p < 0.0001) in the food and fecal microbial communities (Figure 3, top left) along the first dimension. Food samples clustered into distinct communities (PERMANOVA: R2 = 0.325; p < 0.0001) corresponding with the five food categories listed in table 1 (Figure 3, top right). The final tempeh sample (24 hours fermentation) and the two yogurt samples plot as outliers from the other members of their corresponding food categories. Bacterial communities within the fecal samples (Figure 3: bottom) clustered tightly by individual (PERMANOVA: R2 = 0.805; p < 0.0001). The chronological order of the fecal samples was not significantly associated with fecal beta diversity (p = 0.197). Along the first dimension there was a clear separation between one individual, Fermenter 6, and the other members of the workshop, and in general, beta diversity was evenly spread along the second dimension. This separation may be explained by a difference in relative fermentation experience or medications taken between Fermenter 6 and the others.
From the 605 ASVs shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants (Table 2). Seven of 25 ASVs were from the genus Lactobacillus, followed by 2 each of Bacillus, Lactococcus, Leuconostoc, and single representatives of 12 other genera. In three cases, we were able to identify these ASVs to the species species level (Bacillus cereus, Lactobacillus paracasei, and Lactobacillus curvatus).
Table 2: ASVs identifiable to the genus level that are suspected to have transmitted from fermented foods to the gut microbiomes of fermentation workshop participants.
Food and gut microbial analysis: Discussion
Bacterial diversity and variation
As expected, the microbial abundance and diversity found in the fecal and food samples indicate distinct communities. We identified far more bacteria in the fecal samples and stark differences in community structure. Whereas the food samples were often dominated by a small number of taxa, the fecal microbial communities were more diverse. Among the fecal samples we observed a clear pattern of clustering by individual, which indicates that while the broader gut microbial communities of the participants fluctuated throughout the workshop, diet alone was not a dominant determinant of composition over this time period. In contrast, the fermented food samples largely clustered according to their broader food category (e.g grain, salted vegetable, etc.), although the amount of time that a food fermented had a strong influence on the microbial communities As expected, the fermentation process had a substantial effect on the microbial communities of many foods in relatively short periods of time. Additionally, we did observe some evidence to indicate that bacteria originating in the food samples were transmitted to the guts of the workshop participants.
To paraphrase a point that Katz made early in the workshop, fermentation is the transformative action of microorganisms and desirable changes are subjective and culturally determined. Throughout the fermentation process we observed substantial changes in microbial communities that coincided with increased fermentation time. In some cases, there was a stark transition from a highly diverse to a nearly uniform community. After 24 hours, once the tempeh had become completely covered in white mold, the bacterial community was almost entirely composed of the genus Bacillus. In similar fashion, the early stage kimchi microbial community reflected a high number of low abundance genera, but after a full day of fermentation, it came to be dominated by lactic acid bacteria, predominantly Weissella and Lactobacillus. In other cases, some microbes persisted throughout fermentation in spite of large scale turnover. The early and middle stage sweet potato fly was dominated by Gammaproteobacteria (Pseudomonas, Yersinia, and Panotoea), but after ~36 hours of fermentation, they were overtaken by lactic acid bacteria. The kefir chevre bacterial community began as very similar to that of the goat milk (predominantly Yersinia and Pseudomonas). However, as fermentation continued, Pseudomonas was largely replaced by lactic acid bacteria (Lactococcus and Leuconostoc), while the Yersinia persisted. Curiously, Lactobacillus and Acetobacter were the predominant bacteria genera in the kefir grain, but these genera do not appear to have transferred to the kefir in large numbers. In contrast, the yogurt we produced originated from the same goat milk as the kefir chevre, but the microbial community was almost entirely Lactobacillus at the start and finish of fermentation. This is likely a result of the milk being heat treated prior to its inoculation with the yogurt culture killing most of the microbes that originated in the goat milk.
We also observed some evidence that subtle changes in preparation can bring about major differences in microbial communities. For example, we used the same koji starter to inoculate both cooked rice and barley, and while both had similar bacterial communities by the end of fermentation, subsequent culinary processes had strikingly different effects. We added cooked mashed garbanzo beans to the barley koji to begin the transformation into miso. The early stage miso saw an increase in the abundance of Pseudomonas, but the bacterial community was not largely altered otherwise. In contrast, the addition of salt, soy sauce, and wild fermented rice to produce shio koji, shoyu koji, and sake, respectively resulted in substantial increases of different lactic acid bacteria. We also observed subtle variation in our pao cai samples. We sample two batches of Katz’s pao cai, a mix of vegetables with Sichuan spices, salt and sugar, that had been fermenting for 1 week (pao cai 1) and 6 months (pao cai 2). Pao cai 3, made during the workshop, was a mixture of the two pre-existing brines with the addition of fresh vegetables. The bacterial genera in the older two pao cai were largely the same, but differed in relative abundances; this could reflect differences in age or the seasonings used. In contrast, pao cai 3 lacked the high abundance of Enterobacteraceae ASV found in the other samples and had a strong presence of an additional lactic acid bacteria, Pediococcus. Each of the three pao cai were eaten by workshop participants and differed slightly in flavor and texture. Given the continued replenishment of vegetables and seasonings, this finding suggests that pao cai could be a particularly variable source of probiotic microbes.
Pathogens probiotics, and microbial transmission
In many cases, the predominant microbial genera that we identified in the fermented food samples were lactic acid fermenting bacteria, such as Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weisella. This was the case for bean-based ferments, salted vegetables, yogurt, some of the grain-based ferments (salt-rise bread, injera, and buckwheat batter). This result is consistent with the widespread appreciation of the role of such microbes in fermentation, and their probiotic effects (48,82,83). In some cases, we also observed other probiotic bacteria. For example, Clostridium butyricum was present in several ferments, most notably in salt-rise bread, where it reached 10% relative abundance. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes.
In contrast to the lactic acid ferments, others including the later koji-based ferments, tempeh, goat milk, kefir chevre, and sweet potato fly, had large contributions from other genera that are commonly associated with food spoilage and food-borne pathogenicity (e.g. Acinetobacter, Bacillus, Yersinia, and Pseudomonas) (84–88). In the most extreme example of a pathogenic member of these genera Y. pestis--which we thankfully did not observe in any of the samples we collected and consumed at the workshop -- is the microbe responsible for plague (89); however, other species can have more benign effects. Strains of Yersinia have been reported in traditional and dairy products in Iran (87), and both genera have been linked to a “fruity off flavour” in milk (88). Species of Acinetobacter, including A. baumannii, which we observed at highest abundance in some of the later stage koji-based ferments, have been associated with a large number of maladies and often occur in clinical settings with poor sanitation (85). In some cases, e.g. tempeh and salt-rise bread, the cooking process likely rendered most bacterial strains inert. In others, such as miso, continued fermentation will likely result in substantial changes in the microbial community. Nonetheless, many of these “pathogenic” microbes are likely benign strains of genera and families often used as indicators of non-sterile sanitation practices.
A limitation of our study is that we only sought to identify bacterial taxa. Furthermore, the 16S metabarcoding approach we used can rarely identify bacteria beyond the genus or species level. Determining precisely which bacterial (and fungal) strains are present in these fermented foods--and potentially their functional and health consequences--would be aided greatly by metagenomic assembly and metabolic approaches. Ferments like koji and tempeh are dominated by fungi (typically Aspergillusoryzae and Rhizopus spp., respectively), which could interact with bacteria we observed. To similar effect, after longer periods of fermentation, the sake and sweet potato fly will develop alcohol, which will introduce a new selective environment. Nonetheless, it is worth noting that inoculated fungal ferments can have rich bacterial communities that result from wild fermentation. Additionally, our study only sampled a small number of food items. Broader scale replication within these food items as well as expansion to other production environments would greatly improve our ability to understand the variation within fermented foods and the consequences of their consumption.