Fermentation and Health Speaker Series: Presentations

Dr. Rob Dunn: What can microbes teach us about our human history?

Dr. Maya Hey: What are the social, rhetorical, and philosophical dimensions to studying ferments and (gut) microbiomes?

Alex Hozven: What can we learn from 25 years of fermentation practice?

Dr. Joshua Evans: What is the connection between fermentation, flavor innovation, and biodiversity?

Dr. Suzanne Devkota: What is the Role of Fermented Foods in Clinical Practice?

Recorded March 28, 2023, with Elisa Caffrey, David Zilber, and Dr. Justin Sonnenburg. Audio only link available here.

David Zilber: How Should We Think About Fermented Foods and Health?

Recorded January 24, 2023, with Elisa Caffrey, David Zilber, and Dr. Justin Sonnenburg. Audio only link available here.

Read more about the talk from The Fermentation Association.

Talk Q&A

Most fermented foods that we can buy are pasteurized or cooked and therefore without "live" organisms or sterilized. Are we still benefiting from the microorganisms or are we falling for selective marketing claims?

Elisa: As David mentioned, when consuming fermented foods we are ingesting nutrients from the food (like fiber from a sauerkraut or protein and fat from a yogurt), microbes involved in the fermentation process, and all the compounds (i.e. metabolites) they are producing during fermentation. Pasteurizing or cooking does kill off the microbes and slightly change the nutrient and metabolite profile, but for the most part remain intact. There is growing evidence from gut microbiome research that metabolites play a very important role in signaling to the host and other microbes. Whether metabolites produced during food fermentation have a beneficial effect on the host and host gut microbiome is an open area of research, but ealy evidence seems to point to metabolites being very important and you would still ingest these following pasteurization or cooking. How many metabolites are found in fermented foods and which are important remains to be explored. Also note that some foods are just pickled in salt and vinegar to mimick the taste of fermented foods–these do not contain the complex mix of metabolites (see below for more about this).)

Great talk, David. Always a pleasure. Fun stuff about GCF and other chemo-enzymatic ways of promoting/suppressing microbial metabolism in the mouth. What about mechanical ways of promoting/suppressing them (e.g. chewing)? Yeah, salivary amylase increases with more chewing. But I’m thinking more like blending foods (e.g., smoothies) or transformed textures prior to eating (e.g., cheese aged 3 days versus 3 years). Would love to hear more about that, if you’ve got thoughts to share.

DZ: Well, it all has an impact, that’s for sure. I feel like juicing is a great example a health trend that purports benefits that kind of fall apart when you think about it for more than a second–especially as it pertains to your microbes. Like, you take fruits and veggies (great!) but then blend them to hell, heat them up with friction in the process, introduce oxygen at super high levels to parts of their flesh that would normally never see it, strip it of its fiber, then concentrate the soluble parts of it (which is both good and bad). Like, great, if your juicing dark green leaves, you’ll get more iron than you’d ever realistically eat in one sitting, but also, if your juicing, I dunno, pineapple, you’ll get more sugar than you’d ever be able to eat in one sitting. So you end up with a huge spike in glucose with none of the flesh that would mediate your ability to take in that many calories. Fiber’s important. And when you consider that you end up robbing the bacteria in your hindgut of the things they feast on? And thats just juicing vs. eating. I feel like, with the aging food to change texture, you’re ending up with such drastic transformations in the products themselves, it almost becomes moot to talk about what effect might be had in the few second the food rests in the mouth. As it pertains to the microbes in the oral cavity, you would basically need a feeding tube to bypass them. Whether you’re drinking, chewing, slurping… they’re so small, and so numerous, that I feel as though they’ll get fed regardless. You don’t need physical pieces of food in your teeth to get cavities. Residues are enough to feed your oral microbiome.

How can I ensure the fermented foods I make at home don’t get contaminated?

Elisa: It will be very hard to prevent all contamination, but starting with a clean area and washing your tools with soap and warm water is usually enough. Contamination is not always preventable, but if something smells or looks off, you can always wash everything and try again! Starter cultures or backslopping from a successful ferment can help as well.

Is there a difference in how the lactofermented vegetables and pickled vegetables (containing vinegar) influence your body?

Elisa: We don’t know much yet about how fermented food or picked foods impact the body, but I know this is an active area of research in a few labs. In fermentation, you get the fiber, microbes, and a complex mix of their metabolites, while in pickling you get fiber and some of the metabolites (like acetic and lactic acid) if they have been added as ingredients. We know both these metabolites are important immune signals, but they have only been looked at when they are produced by the host or the gut microbiome. Whether ingested lactic and acetic acid have the same immune effects needs to be explored.

How are you thinking differently about what you eat and cook now that you're cooking as a father?

DZ: Well, to be honest, I think how I fed myself changed more after quitting noma than since Io’s been born. I do make my kid’s food however, and that’s really enjoyable. But its also so simple! Bake an apple, blend it. Boil some broccoli, blend it. Slice a fruit, watch him struggle to suck on it… I do think that’s made me more conscious of food’s freshness. When I see cans of baby food in store, the jars and sippy packets of purees that can line shelves for months without expiring, and especially now that I get to see an intimate side of food industry, I know very well just how drastic nutrient drop off is from the moment something’s plucked out of the ground, til the time its opened up out of a can. A squash picked off a vine, a squash shipped across the atlantic, a squash cooked and served immediately, a squash cooked and frozen immediately, and a squash pasteurized and sold 3 months after canning are NOT all the same squash.

Thank you for an amazing presentation. Do you know how much the acid in our stomach kills the microbes?

Elisa: While hydrochloric acid is very effective at killing off microbes, we know that dietary microbes can make it to the gut (as we find them alive in plenty of stool sample), so it is likely a combination of the abundance of microbes you consume when eating fermented foods and that they potentially are ‘protected’ by food particles to avoid the harsh stomach environment.

Ilya Metchnikoff at the beginning of the 20th century was maybe amongst the first ones to realize the continuum of us and fermentations of milk into yoghurt. Do you think it is legitimate to say that fermentation is a potential selection process of which of the environmental microbes are beneficial to us?
DZ: Ya, Metchnikoff was going to make it into my talk, but uhhh, I spent too much time talking about teeth haha. I absolutely think that’s what it is, but more broadly, I think that what you just described is the main mechanism for symbiosis. Over the course of evolutionary time, species will butt up against all other species in their environment, like molecules of gas in a box, some of those encounters will the positive, and some negative, that's evolution. But when a positive interaction is positive ENOUGH, over some threshold, it becomes sticky. First behaviourally, then, if its persistent enough, genetically, as the species co-evolve to be even better fit to each other, improving both members fitness in the process.

Are there any allergy risks when eating fermented food and how can we prevent if any?

Elisa: Fermented foods can contain higher levels of histamines, which can be an issue for some. Fermented animal products (dairy, meat) are likely to contain more, so if histamine allergy or intolerance is an issue, best to avoid. Whether fermented foods play a role in allergy suppression (aside from histamine) is currently being studied, so more to come in the next few years!

Are there foods you'd avoid eating at the same time (or near the same time) because of it inhibiting good gut activity?
DZ: Honestly, for most people, I don’t think so? Most people don’t eat more than 250 different ingredients in their whole life. And there’s a lot of overlap in that list. If you’re shopping from within it, you can’t mess things up THAT badly. I can’t think of any two ingredients you could eat in the same meal that would explode your system, aside from things that are poisonous on their own. I mean, I’ve seen first hand problems with people on very W.E.I.R.D. diets go full ham in a day on foraged and raw foods, and completely throw their guts for loop, thinking its food poisoning, while dining partners sat next to them with more adventurous palates and varied diets didn’t feel a thing. I’ll revert to my analogy to exercise. If you NEVER go to the gym, don’t think you can one day wake up and decide you’ll start training at the level of an olympic weight lifter. You’ll end up in the hospital. The communities of microbes inside you experience population level dynamics the same as snowshoe hares and lynx do in the wild-they just do it on much shorter timescales. So be aware of that when consuming wildly new foods, or shifting the big ways in which you eat (going on a raw diet, all meat diet, fasting etc…)

How can one drink Yak milk multiple dozen times a day?
DZ: As yak butter tea! Its a warm drink they’ll have a small cup of again and again. If there are people who can go out for dozens of cigarettes a day, traditional Tibetan can sip on their fermented drink just as much.

Additionally a number of fermentations see an interplay of yeasts and bacteria, how much of these interactions have you experienced at Noma.
DZ: Well, unless you’re working in hyper sterile conditions, when you REALLY look, you’ll find they’re often living together. In any standard wild fermented pickle, even with the addition of salt, you might be priming the environment for lactic acid bacteria, but the yeasts are still there, only their growth is suppressed. “Blow out” from heterofermentative yeast is an age old problem in cucumber pickle making (I remember reading a fascinating technical paper on the topic from like, 1972) because, try as you might, they really are everywhere. Same goes in the opposite direction. It’s very hard to make alcohols without ANY activity from bacteria. And sometimes, (like with malolactic fermentation in wine) its absolutely desired. Koji, even when you have a pure culture, always ends up growing along side a handful of commensal bacteria and yeasts, and don’t even get me started on soy sauce, that’s a absolute FREE for all. Even at super high salt levels! I wasn’t joking when I quoted Bass Becking. Everything really IS everywhere. (That’s not entirely true, but you’ll think it true when you ferment).


Thanks a lot! I have a question related to the pasteurization and all the beneficial metabolites present in fermented foods. Can't we assume fermentation temperature destroys or denature these?

Elisa: Metabolites are fairly small, so won’t denature the same way proteins do, and tend to be fairly stable. However, thermal degradation can have an effect on the structure of some metabolites. One paper that compared select metabolites at 60C, 100C and 250C found no changes at 60C, some at 100C, with the most changes happening at 250C. But time could affect metabolite concentrations as well. Microbes can both consume and produce metabolites, so at any point pre-pasteurization a metabolite that is produced during the fermentation process might be consumed by another microbe. Until we know which metabolites are in there and which might be important, it will be hard to say. But you are likely still ingesting metabolites when eating pasteurized or cooked fermented food than you would by not consuming that fermented food.

Do you see fermentation commercially as eventually being regulated in the U.S.? Like there will be restrictions around what can be put on a label?

Elisa: This is a great question for Alex Hozven & Kevin Farley from Cultured Pickle Shop in Berkeley who have worked in the fermented food production space for almost 20 years. They talk is April 18th, 2023!

Could you talk about HACCP and fermentation?

Elisa: Another great question Alex Hozven & Kevin Farley! They will be much more insightful.

Thank you! Are we aware of a "minimum amount" (realizing there are many variables) or level of variety (different types) of fermented foods for health benefits?

Elisa: We don’t have a great understanding yet of what a “minimum amount” would be, but we might have a starting point. The paper from the Sonnenburg and Gardner groups at Stanford in 2021 started participants on 1-2 servings per day and then increased to 5-6 servings a day in order to prevent any potential gut distress brought on by a sudden change in diet. Participants worked closely with Dalia Perelman, a nutritionist in Christopher Gardner’s lab, to make sure they consumed food that were actually fermented, but could eat any they had access to, including kimchi, sauerkraut, yogurt, and kefir.

What have you've read that has most influenced your thinking on this topic that seemingly have nothing to do with fermentation and food?
DZ: Even though it’s not THAT far away, most anything by Lynn Marguils has been greatly influential on my thinking. She only ever talks about fermentation a handful of times in her books, but that doesn’t matter. Fermentation is but a slice of the living world. A potent one! But still just a fraction. And what’s true in fermentation is also true in the Amazon rainforest, the pelagic zone of the pacific, and sewer system of NYC. That’s maybe the best part about viewing food as ecology, its cyclical lessons rhyme all over nature.

I’ve been wrestling with the amount of fermented foods to eat in a week. Too much seems to be disruptive to digestion. But we want some amount each week. Have you sought this kind of balance, and if so, what have you found?

Elisa: Starting slow and testing your reaction to different fermented foods is the best way to go. Your body (and gut microbes) need time to acclimatize to the new diet, so starting with just one serving day (or less) and then increasing seems to work. As a personal anecdote, I went most of my life avoiding most fermented foods because they caused digestive issues. Last April, I was fortunate to attend Sandor Katz’s fermentation retreat, where all we ate for the 5 days was fermented foods. The food was amazing, but my gut felt absolutely terrible. But, after those 5 days, I found myself able to process fermented foods just fine, and now am able to include them in my daily diet. I am definitely not recommending my approach, but it is possible to get there!

David's thoughts on Noma closing?