By: The American Society for Microbiology
The flavors of fermented foods are heavily shaped by the fungi that grow on them, but the evolutionary origins of those fungi aren’t well understood. Experimental findings published this week in mBio offer microbiologists a new view on how those molds evolve from wild strains into the domesticated ones used in food production.
In the paper, microbiologists report that wild-type Penicillium molds can evolve quickly so that after a matter of weeks these strains closely resembled their domesticated cousin, Penicillium camemberti, the mold that gives camembert cheese its distinctive flavor. The study shows how a fungus can remodel its metabolism over a short amount of time; it also demonstrates a strategy for probing the evolution of other cultures used in food, said study leader and microbiologist Dr. Benjamin Wolfe, Ph.D., a member of the The Fermentation Association advisory board.
“In fermented foods, there’s a lot of potential for microbes to evolve and change over time,” said Wolfe.
Wolfe’s lab at Tufts University in Medford, Mass., focuses on microbial diversity in fermented foods, but he says the new experiments began with an accidental discovery. His lab had been growing and studying Penicillium commune, a bluish, wild-type fungus well-known for spoiling cheese and other foods. Wolfe likens its smell to a damp basement.
But over time, researchers noticed changes in some of the lab dishes containing the stinky mold. “Over a very short time, that funky, blue, musty-smelling fungus stopped making toxins,” Wolfe said. The cultures lost their bluish hue and turned white; they smelled like fresh grass and began to look more P. camemberti. “That suggested it could really change quickly in some environments,” he said.
To study that evolution in real-time, Wolfe and his collaborators collected fungal samples from a cheese cave in Vermont that had been colonized by wild strains of Penicillium molds. The researchers grew the molds in lab dishes containing cheese curds. In some dishes, the wild mold was grown alone; in others, it was grown alongside microbes that are known competitors in the fierce world of cheese colonization.
After one week, Wolfe said, the molds appeared blue-green and fuzzy—virtually unchanged—in all the experimental tests. But over time, in the dishes where the mold grew alone, its appearance changed. Within three or four weeks of serial passage, during which mold populations were transferred to new dishes containing cheese curds, 30-40 percent of the mold samples began to look more like P. camemberti. In some dishes, it grew whiter and smoother; in others, less fuzzy. (In the competitive test cases, the wild mold did not evolve as quickly or noticeably.)
In follow-up analyses, Wolfe and his team tried to identify genomic mutations that might explain the quick evolution but didn’t find any obvious culprits. “It’s not necessarily just genetic,” Wolfe said. “There’s something about growing in this cheese environment that likely flips an epigenetic switch. We don’t know what triggers it, and we don’t know how stable it is.”
Researchers suspect that the microbes used in most fermented foods—including cheese, but also beer, wine, sake, and others—were unintentionally domesticated, and that they evolved different flavors and textures in reaction to growing in a food environment. Wolfe says his lab’s study suggests that wild strains could be domesticated intentionally to produce new kinds of artisanal foods.
Starting with cheese, of course. “The fungi that are used to make American camembert are French,” said Wolfe, “but maybe we can go out and find wild strains, bring them into the lab, and domesticate them. We could have a diverse new approach to making cheese in the United States.”
The American Society for Microbiology is the largest single life science society, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.
ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.
Ever wonder why you crave umami, the savory food taste common in fermented foods? You were born with it.
“When you say taste, it’s actually just as much the nose because were actually using all the five senses when we say taste or taste experience,” says Ole Mouritsen, a professor of gastrophysics at Copenhagen University in Denmark. “Taste and particularly odor is very good to invoke memories, good memories and bad memories, because that’s the way its hardwired in the brain. These senders that store our memories are stored to the limbic center, and the processing center for taste and odor are in the same area. You can be brought back to your grandma’s kitchen in no time.”
The five basic tastes are: sweet, sour, salty, bitter and savory (umami).
He continues: “There are some basic tastes and odors that you prefer. We’re born to like sweet and umami, and we’re born to dislike bitterness and too much sourness. But our preferences change over time.”
Mouritsen and Adam James, founder of fermentation condiments company Rough Rice, spoke with Cooking with Science host Kevin Glidden on the topic of fermentation and taste. Glidden brings researchers and foodies together in an interactive interview for the Tasmanian Institute of Agriculture.
Glidden asked why Mouritsen and James think fermented foods played such a big part in other culture’s diets, but not in the Western diet.
James travelled on a Churchill Fellowship-backed fermentation world tour to study ancient and modern fermentation techniques. He pointed out that fermentation has never been part of Western culture.
“If you look at what my biggest influences are – Japan, Korea, China – they eat fermented foods pretty much with every meal, in the form of a pickle or a soy sauce,” James said. “But again, I think that’s something that’s just been part of their culture. Families would sit down and make kimchi together.”
Mouritsen agreed, adding: “If we want to learn about making old-fashioned pickles, we will not ask our mothers, we’ll ask our grandmothers, because the knowledge is lost.”
In the segment, James made a brown rice congee with Tasmanian abalone and fermented condiments. Congee – an Asian rice porridge – dates back 4,700 years, 1,000 years before shoes were invented. James’ cooked his congee using untraditional methods. Congee is usually made using a chicken stock or duck stock as a base, but James made his congee with shitake mushrooms, fresh tomatoes and kelp. Though no meat was used, the result was an umami-tasting flavor.
A new Kerry Health and Nutrition Institute white paper titled “Umami: The Taste that Perplexes” details why umami is a vital food flavor. Umami’s functions and biological mechanisms are not very well understood. “…Unfortunately the way many people have learned about umami is through the stigma of monosodium glutamate (MSG), the prototypical stimulus of umami taste,” writes author Nancy Rawson, the associate director of the Monell Chemical Senses Center.
The umami flavor, though, extends well beyond MSG. It can be found in every day food, like mushrooms, tomatoes and aged cheese. Umami is popular in Asian cultures, where fermented food is high in the glutamate compound. Fermented fish and fish sauce are a common cooking item in South East Asia cuisine, creating “a more balanced taste.” Miso and soy bean paste are used in North Asia, where they flavor food with “a natural and longer lingering taste and mouthfeel.”
Mouritsen said umami is one of the ultimate dining experiences. He adds: “It gives you appetite, when you stick it in your mouth, the saliva starts running. It’s a very good way of getting appetite. We have receptors in the stomach, in the intestinal system, that signals back to the brain that those umami-rich food, and it will eventually tell you to stop. It’s knowledge one could use to make more healthy eating patterns for people.”
The specialty chocolate market is growing, and research by the University of Copenhagen Department of Food Science found that fermentation conditions affect chocolate flavor. Different fermentation techniques changes the composition and activity of the microorganisms present on the cocoa beans. “Our research confirms this and we have also learned how to fine tune the cocoa by fine tuning the process itself, which means that you can get a higher quality out of your raw materials if you understand these processes,” says Dennis Sandris Nielsen, a professor in the food science departments at the University of Copenhagen. He adds: “…findings show that the treatment the cocoa receives after the harvest is at least as important for the quality and flavour as the genetics of the cocoa. Where the cocoa was grown also has some significance. By varying the conditions during fermentation, we can therefore also reasonably predict the final taste, which provides good opportunities for high-end producers in particular to develop chocolate with different flavours and scents.”
Read more (University of Copenhagen)
Summer Bock compares the gut microbiome to a forest. If a fire destroys the forest and forest restoration is attempted by just introducing a few animals, the forest would never rebuild.
“That’s what we’re missing with probiotic pills,” Bock says, adding that relying on a probiotic pill to fix the gut is like telling a few bacteria strains: “’You’re in charge of building our entire gut microbiome,’ you just can’t. if you’re just picking a few probiotics and saying ‘You’re the work horse, you’re going to do all of it,’ they can’t. You have to go think of this bigger picture ecosystem. When we use ferments, we’re bringing in some of the nutrition, the soil and even bringing in a greater variety of probiotics than what you find in most pills. …there’s a huge benefit of ferments that people are missing out on.”
A fermentationist, health coach and founder of Guts and Glory, Bock detailed how fermented foods can improve overall health at the Fairmentation Summit. She coined the word “gut rebuilding” and was the founder of the Fermentationist Certification Program.
Bock started fermenting after becoming incredibly sick. A trained herbalist, Bock began treating multiple food allergies, regular panic attacks and chronic exhaustion with herbs. This was long before terms like probiotics and gut microbiome were a regular part of diet discussions. But Bock was recommended by a naturopathic doctor to try taking probiotics, and “a lot of my symptoms started clearing up very quickly.”
Bock, though, is a purest, and wanted to know how she could ingest probiotics without taking a pill.
“What’s the whole food version of probiotics?” Bock said. “If I’m missing it and I’ve wiped it out with antibiotics, how did my ancestors get this into their body on a daily basis? That’s how I discovered fermented foods.”
So Bock started fermenting everything. During this experimentation process, Bock sold sauerkraut and kimchi from her fridge, launching her first sauerkraut company. She described sharing sauerkraut with her roommate’s friends, skeptics who would initially say “I don’t like it,” but would come back a week later and tell her “I have to come back and but it because I can’t stop thinking about that one bite.”
“This is an addictive healthy food, and I got fascinated by what is happening on your taste buds that makes your body go ‘I don’t like this right now,’ but your body recognizes that health benefit,” Bock said. “If there’s some communication happening through one little bite of food and that person can’t stop thinking about it and they want it, I’m still utterly fascinated by that today.”
Her favorite fermented food is kimchi “because it has all the benefits of lacto-fermented vegetables, it has all the great probiotics in it plus it has prebiotics, it has organic acids and the lactic acid which is a natural microbial.”
Studies during the avian flu outbreak found birds who ate kimchi were not contracting the bird flu. One microbiologist in South Korea found 11 of 13 chickens infected with avian flu who ate kimchi made a full recovery. All birds in the control group died.
“Fermented foods are really powerful, and I think that what’s fascinating about them for me is they differ from just probiotics. They contain probiotics, but they also have the prebiotics. They have the entire ecosystem,” she said. “We eat it because it’s delicious, but we also eat it because that food assists us in some way.”
Probiotic-rich ferments “acts as a fertilizer” for the gut microbiome, killing off pathogenic organisms. Microbes grow best at room temperature, a temperature the health department defines as a danger zone because it’s the best temperature for pathogenic, food-born illness to grow.
“What we’ve found is, when there’s that acidic environment, these pathogenic food-borne illnesses can’t exist there. They don’t grow,” she adds.
Multiple nutrients are produced through fermentation, like Vitamin B and Vitamin K. Only a few organisms produce these vitamins, Bock notes. They are critical vitamins because they’re not absorbed easily through food. Bok calls them the “star players” of the microbiome. People with an imbalanced microbiome are often lacking in vitamins B and K.
If not fermenting their own food at home, consumers need to practice due diligence when purchasing fermented food brands, Bock says. Kombucha, she shares as an example, is a great “gateway ferment” for most people, but how much sugar is in it? Is it fermented naturally or are lab strains of probiotics added?
“You have to ask yourself, what is the major probiotic we’re talking about,” in the food you’re eating, Bock said. “Is it a naturally-occurring probiotic or a…patented, genetically-modified probiotic?”
Americans have a “Supersize” mentality, Bock said. People shouldn’t be consuming bowls of fermented foods every day.
“Remember that fermented foods are generally a condiment, especially the ones with live organisms, like kimchi and sauerkraut, natto,” she said. “So if you treat it as such, you’re maintaining the respect for these organisms and for these foods,” she said. “Your body knows what it needs.”
As more people battle digestive problems, they’re turning to brands offering gut health solutions. Digestive health is the third most sought after health benefit in the latest International Food Information Council Food & Health Survey, behind weight loss and energy.
Though it’s a hot topic, it’s a space challenged with unsupported health claims and confusing ingredient additives. During a panel hosted by Food Navigator, four industry leaders shared insight into the growing gut health category.
“What we’ve learned is that many of our consumers come into our brand typically with serious, long term digestive health challenges. Bloating, regularity challenges, IBS,” said Mitchell Kruesi, senior brand manager for Goodbelly, which creates probiotic drinks and snacks. “They’ve tried supplements in the past, but weren’t super enthusiastic about them because often times taking a supplement felt medicinal to them. After that, they continue to seek out other probiotic options that are both effective, but also food-based so that it’s easy to fit in their routine.”
Plagued with health issues and fed-up with pills, consumers are desiring food brands that aid digestive health. Flavor, though, is key.
“That delicious taste…it sets up an everyday usage routine, which is critical with probiotics,” Kruesi said.
Probiotics is a confusing territory for consumers. Should probiotics be consumed in pills or as a strain added to food? How much should be taken?
Elaine Watson, Food Navigator editor, quoted GT Dave, founder of GT Kombucha: “In my mind, anything raw and fermented deserves to use the term ‘probiotic.” Watson asked the panelists if there’s a perception that all fermented foods contain probiotics because they contain live, active cultures – and should food advertising probiotics be verified by clinically proven studies?
“I think consumers are quite confused still around the whole topic, in all honestly. Live, active cultures are used to make fermented food beverages – but unlink probiotics, they’re typically not studied and shown to provide a health benefit,” said Angela Grist, Activia US marketing director. Really in order to be considered a probiotic, they would need to meet the criteria of survival and research-validated health benefits and also this point around strain specificity.”
Grist said probiotics need to survive the passage through the digestive track to the colon. Activia has five survival studies showing the benefits of probiotics.
Ben Goodwin, co-founder of Olipop, added he’s conducted genetic assays around the underlying culture banks of fermented food and beverages and “there have definitely been organisms in the culture banks which are deleterious for human health. So not everything that’s fermented is automatically good for human health, there’s all sorts of different biological modes that organisms can interact with each other and some become parasitic or become determinantal to your probiotic when consumed, so something to keep in mind.”
Note that the panel did not feature a raw, fermented food brand; the companies included on the panel all add probiotic strains to their food and drink product.
In a separate interview with The Fermentation Association, Maria Marco, professor in the Department of Food Science and Technology at the University of California, Davis, said there is a lot of confusion around probiotics, even among industry representatives. Marco, though, agrees with Grist and Goodwin. She says clinical studies on fermented foods are necessary.
“Although it might be possible to separate out the individual components of foods for known health benefits (e.g. vitamin C), the benefits of many foods are likely the result of multiple components that are not easily separated,” Marco said. “Yogurt consumption is a great example of a fermented food that, through longitudinal studies, was shown to be inversely associated with CVD risk.”
In one of Marco’s studies at UC Davis titled “Health benefits of fermented foods: microbiota and beyond,” Marco and her research associates concluded that fermented foods: are “phylogenetically related to probiotic strains,” “an important dietary source of live microorganisms,” and the microbes in fermented foods “may contribute to human health in a manner similar to probiotics.” The study adds: “Although only a limited number of clinical studies on fermented foods have been performed, there is evidence that these foods provide health benefits well-beyond the starting food materials.”
The panel said that the food industry is responsible for displaying integrity in their marketing on probiotic benefits.
“We believe it’s critical for leading brands in the space…to really educate consumers on, first, what probiotics are,” said Kruesi with Goodbelly. Consumers are seeking out probiotics for a specific health benefit, but most don’t know what strain they need to address their issue, he noted.
Probiotics are live microorganisms that aid the digestive system by balancing gut bacteria.
Currently, the demographic of consumers buying products geared toward gut health are millennial females in coastal cities. Both Activia and Olipop sell to more women than men (Activia customers are 60 percent female and 40 percent male; Olipop customers are 55 percent female and 45 percent male).
Goodwin said Olipop is hoping to tap into the rapidly declining soda market. Soda is a $65 billion industry, with 90 percent household penetration. But more consumers are turning to healthier options than unnatural, sugar-filled soda.
“We’ve tried to take on the extra responsibility as a brand of formulating something that’s spun forward, delicious and really approachable so that we can meet a real health need in a way that’s actually supported by research,” Goodwin said. “(Olipop) is not only low sugar, low calorie, it also has this digestive health function but obviously doesn’t taste like vinegar because it’s not a kombucha.”
Solving Digestive Stress
Products by Activia, Goodbelly, Olipop and Uplift Food (the fourth panel member) are “meant to be a mass solution for the lack of fiber prebiotics and nutritional diversity in the modern diet,” Goodwin said. Fiber contains prebiotics, which aid probiotics.
The USDA’s dietary guidelines recommend adult men require 34 grams of fiber, while adult women require 28 grams of fiber (depending on age). The reality, though, is that most Americans get about half the recommended fiber a day, only 15 grams. According to the National Institute of Diabetes and Digestive and Kidney Diseases, 60-70 million Americans are affected by digestive diseases.
Compare that to the diet of hunter-gatherers, who eat about 100-150 grams of fiber each day and maintain incredibly healthy guts or microbiome. The microbiome is the community of commensal microorganisms in our intestines, fed by fiber, probiotics and prebiotics.
“As it stands now, basically we’re putting in a starvation system for a lot of the microorganisms currently in your gut,” Goodwin said. “The average industrialized consumer has about 50 percent less diversity and abundance of beneficial microorganisms than the hunger-gatherers alive on the planet tonight.”
Future of Gut Health Products
Grist with Activia said probiotics need to be consumed in adequate, regular amounts to provide health benefits, or else probiotics will not consume the digestive track.
Kara Landau, dietitian and founder for Uplift Foods which makes prebiotic foods, added that each individual has a unique bacterial make-up, and providing diverse food to support the microbiome is critical.
Landau said the future of gut health probiotics will be selling a specific probiotic strain, one that a consumer can target for their desired health benefit. Prebiotics – “the fuel for the probiotics” – are also key, and a new part of the digestive health puzzle that brands need to communicate and simplify for consumers.
“Prebiotics are still very much in their infancy when it comes to consumer understanding,” Landau said. “Seeing them alongside probiotics enhances the clarity of their benefits.”
A “bread nerd” in California made a loaf of sourdough using yeast extracted from 4,000-year-old Egyptian artifact. Baker Seamus Blackley (creator of the Xbox) is a bread hobbyist who collects ancient yeast for delicious dough experiments. The New York Times feature on Blackley’s latest sourdough says: “Yeast is a living thing — a fungus. … Once they run out of food, yeast spores go dormant — rather than simply dying — and stay quietly viable for thousands of years until they are extracted.”
Read more (The New York Times)
Our gut microbial communities are being killed off by antibiotics, to the extent that “the most affluent children in the world have a variety of autoimmune diseases,” says Bruce German, a professor of food science and technology at the University of California Davis. In today’s advanced age of science, medicine and technology, rates of allergies, asthma and eczema are all increasing.
“By every criteria, humans should be enjoying the best health in human history,” says German, who has spent decades studying the infant gut microbiome. But instead, “most of us are suffering from a variety of chronic and degenerative conditions that are the result of inappropriate diets.”
German – also the director for the Foods for Health Institute and the co-founder of Evolve Biosystems – shared insights on the future of personalized diets at Natural Products Expo West. He said we shouldn’t be asking should diets be personalized, but why hasn’t it been done yet?
Antiobiotics & Unintended Consequences
He points to the unintended use of antibiotics. Though antibiotics have been hugely successful in eradicating nutrient-deficient diseases – like scurvy and goiters – we’ve now become too relent on vitamins.
“From a public health perspective, the strategy that made sure everyone got enough of essential nutrients just overdosed the population. Everyone gets more than they need. It’s been our public health strategy – and it’s worked,” German says. “But the consequences of that decision is that nutrients are more important than foods.”
Though infectious diseases no longer plague the human population, antibiotics have had unintended consequences.
“Antibiotics kill pathogens, but they also kill commensal organisms,” German says. “And our entire microbial community in and outside of us are now seeing the consequences that huge success of antibiotics.”
Adding to that disruption of the human microbial community: food product branding. German says that, by the end of the 19th Century, the No. 1 cause of infectious disease was contaminated food. Food had no value as an enterprise. Branded food products became important, “then we start to get the impression that foods are either food or bad. And, of course, that’s not true. It’s your diet that’s good or bad. An individual packaged food product has very little opportunity to make a significant dent in that. But the consequences of this wonderful economic brand model is we tend to overestimate the power of individual foods.”
Science today must address the consequences of the spectacular success of antibiotics, German says.
Health Answers in Human Milk
To improve human health, the faculty at UC Davis is taking an integrative approach to agriculture. They’re trying to answer the question “What should we eat in the 21st Century?” by bringing together various tool sets across campus, like biology, physics, business, chemistry and law.
“The problem is, for the past 70 years, we have not been investing in health,” German says.
Human milk, German believes, could provide answers to restoring damaged microbiomes. German has spent the past two decades studying lactation and its role in evolution. With the help of Carlito Lebrilla, chemistry professor at UC Davis, scientists found human milk contains a large proportion of oligosaccharides. Babies, though, are unable to digest oligosaccharides. These oligosaccharides, findings showes, exist to nourish bacteria.
That bifoda bacteria fuels the baby, protects the baby from pathogens, educates the immune system and provides nutritional components.
“Mothers are literally recruiting another lifeform to babysit their baby,” German said. “It’s as important to feed the bacteria in the baby as the baby. …
“The future is going to therefore be in microorganisms, using food as a delivery system. So it’s both bacteria for health and bacteria for delight,” German said.
Some of the great food success stories are a “combination of commodities plus organisms” German says, like chocolate, coffee, bread, beer and cheese. All are fermented foods.
Personalized Diets Core of Future Health Industry
A knowledge-based health industry is what personalized diets will look like, German said. He compared it to Google Maps, the massive, public, cloud-based database accessible by databases. Personalized diets could one day look the same, providing information on current health status, comparing it to an end goal and detailing foods that help achieve the end goal. The individual algorithms will highlight preference, highlighting needed nutrients based on an individual’s favorite food.
“In essence, we don’t think you have to personalize food. You have to personalize the diet,” German says.
Probiotics “Not Particularly Effective”
Could probiotics restore human’s microbiomes? German said studies find, though probiotics are safe, they’re not effective. Probiotics don’t colonize the intestines.
“You probably ingest more bacteria from oral cavity from saliva everyday than probiotics,” German says.
The creative genius behind Noma’s Fermentation Lab, David Zilber says one of the best parts of fermenting is “to get very nerdy and go really deep and taste the whole Patheon of flavors that the microbial world produces.”
Zilber, author of “The Noma Guide to Fermentation” with Noma founder René Redzepi, spoke to Science Friday about his extensive knowledge of the food science craft. When Zilber started at Noma in 2014, he had extensive experience working in high-end restaurants. He had made kimchi working in an Asian restaurant and cooked with amazing soy sauce imported from Japan, but he never gave a second thought as to where the ingredients came from. At Noma, Redzepi noticed Zilber “had a knack for science…I was usually the gut that had the far too detailed answer,” Zilber says laughing as he describes answering colleague’s food questions. Redzepi movied Zilber to the fermentation lab, a world-famous lab that has helped secure Noma’s Michelin ranking as the 2nd best restaurant in the world.
In the radio interview, Zilber details the fermenter’s roll as a scientist, gives advice on preventing mold and shares why he thinks everyone should have a koji started on their counter. Below are highlights from Zilber’s interview with Science Friday host, Ira Flatow.
What is fermentation?
Zilber: The most succinct way I can define fermentation, in Layman’s term, is it’s the transformation of one ingredient into another by way of a microbe. If you imagine you start out with cabbage, then you get lactic acid bacteria to grow in and alongside your cabbage, in two or three week’s time, you end up with sauerkraut. It’s not the same as it was going in. You’ve cultivated — cultured really — this microorganism in your container with your cabbage. And low and behold, this transformation has taken place.
The Noma book says there’s a fine line between rot and fermentation.
Zilber: The rest of the analogy is that, as a fermenter, there’s actually three people in play in the definition of fermentation: the ingredients, the vegetables or the food stuff, the microbes, but also the person whose acting on that situation and actually wiling the ferment into existence. As the fermenter, you’re kind of the bouncer outside of the nightclub. The guy with the velvet rope, the big muscly dude, and you’re deciding who gets into the club and makes a great evening where everyone is sipping champagne and beautiful people all around and all the drunkards and rowdy boys stay outside. So that velvet rope that you use as a fermenter, those are all sorts of control points. Whether that be salt or access to oxygen or temperature or PH and acidity levels, these are all things you have at your disposal as a fermenter to make sure you’re actually fermenting and not rotting. Rot’s a club where everyone gets in; fermentation is where the party is popping.
Take us through lactic acid bacteria and fermentation.
Zilber: Fermentation, it’s one of the simplest processes you could undertake. By adding a little bit of salt to let’s say were talking like sauerkraut. You have your cabbage, you shred it to rupture the cabbage cells, and it makes it easy for bacteria to get inside there. Now lactic bacteria are all around us. They live on your skin, they’re on the skins of fruits and vegetables, they’re basically ever present in our environment. And as you add salt to that shredded cabbage, you’re making sure that any malevolent microbes — things that might cause the mixture to rot — are kept at bay. Salt is a really great anti-microbial, but lactic acid bacteria have a little bit of resistant to it, they can tolerate salt up to a certain point. So, you kind of clear the playing field for lactic acid bacteria to do their thing. They start consuming the carbohydrates and sugar in that cabbage and in doing so they leave something else behind, and that something else is an exclusionary chemical. That’s lactic acid. It sours the mixture and then makes it even harder for different things to grow. And overtime, that fermentation process peters out, they consume as much sugar as they can, the PH drops because of all the lactic acid they’ve produced, you have sour cabbage literally translated from German sauerkraut.
What’s the difference between pickled and fermented?
Zilber: Anyway you break it down, a pickled product is fermented. Now there’s two routes to picking — you can either do a quick pickle, which is making vinegar and then boiling your vinegar with a bit of salt and sugar and spices and then pouring that over your vegetables, or you can sour your vegetables into a pickle. Now the difference is there’s two different acids at play in there. With a quick pickle, a vinegar pickle, you’re using acetic acid. But with a sour pickle, you’re using lactic acid. So, a vinegar pickle, you have to first make the vinegar, and that is the sugars of fruits first transformed into alcohol by yeast and then another fermentation process happens. You have acetic acid bacteria, another ever present bacteria that is floating on dust in the air that will settle on an open bottle of wine and eventually sour it into vinegar. That gets poured over your vegetables, whether that’s carrots or radishes or cucumbers, and the PH drops so much so that its effectively preserved.
Lactic acid fermentation, the sour pickle, that’s the process I just described with sauerkraut, you’re getting it all to happen at once, you’re getting that bacteria to grow in and around the vegetable you’re looking to ferment, and it sours the brine, it sours the plant matter itself, and in one shot you have a pickle you can keep in your fridge for months.
Does fermentation always produce alcohol as a byproduct?
Zilber: No, it does not. There are many different types of fermentation, and some types of fermentation have nothing to do with alcohol at all. Now a biochemist might say, technically, that’s wrong because the very strict, textbook definition of fermentation is the transformation of glucose into ethanol in an enzymatic pathway by yeast. But, in the real world, in the much broader sense, as I said there’s all sorts of different metabolites or byproducts that you end up with in fermentation. Sometimes its sugar or MSG, the actual flavor of umami. Sometimes its alcohol. Other times it’s acids. So there’s a whole plate of different end products in the world of fermentation. And the more you understand it, the more you can kind of paint with these flavors and really tweak the world of food to your will.
What are are your recommendations for someone getting into fermentation?
Zilber: For the novice, start with the things you like eating before you start making things you’ve never really had before, before you try and get into the first half into the process of making soy sauce, start with something you really like eating, if you love pickles on your hot dogs, make pickles for the first time. It’s really easy. It’s something you can do on your kitchen counter, you can watch it happen before your eyes. For a citizen scientist who wants to go a little deeper, I think it’s really fun to take like craft brewing and really try to understand the world of yeast, which there really are like tens of thousands of different varieties that all have these different flavor profiles.
And the coolest thing about fermenting at home, and really getting into it and getting really nerdy with it, is you almost get to taste places on earth in your own garage or in your own apartment. You can get yeasts from Belgium and taste a piece of history because these yeasts have been cultivated in the rafters of abbeys that Belgian monks are famed for making their beers in. So it is really cool to get very nerdy and go really deep and taste the whole Patheon of flavors that the microbial world produces. But that’s one of the funest parts about fermenting. Once you start making fermenter friends, people are just sharing culture and having a good time and you get to taste a little big or someplace else.
What are you excited about in fermentation?
There’s a lot of things that people in the world of fermentation know really well, that’s because all of these ferments that we consume on the regular — whether it’s chocolate or coffee or pickles or wine — these are all very traditional products that have been passed down through generations over hundreds of years, that’s why we still make them today. But in the same way that that makes fermentation amazing, I also think of the way pharmaceutical companies send out teams of scientists into the Amazon jungle to find a rare type of mushroom that might produce some type of miracle drug that will change the face of the pharmaceutical industry. I wish there was someone like that in the world of fermentation, looking for that rare microbe that would produce a flavor no one has ever tasted yet.
What exactly is kombucha?
Zilber: Kombucha is a sweet and sour microbial tonic, I guess you could call it. But folklore goes back to an ancient Korean physician that would travel around Asia, again I don’t even know when in history this would have taken place, but that this physician would brew this drink and kind of heal people with it. Kombucha is basically sweetened tea that is then fermented in a symbiotic way by yeast, which converts the sugar into alcohol, and then acetic acid bacteria that convert that alcohol immediately into acetic acid, the acid that you taste in vinegar, like white vinegar. Now if you drink kombucha and you buy it off the store shelf, sometimes it might taste really vinegary and that is probably because, in my opinion, it’s over fermented. The thing you have to understand about fermentation is fermentation is cooking, it’s just cooking that happens much more slowly. So just in the same way you can overcook a piece of chicken by roasting it in a pan for too long, you can also over ferment something like a kombucha and make it too sour by letting it ride out on your kitchen counter for three weeks instead of two. And sometimes if you taste a kombucha and you’re like “Oh, this it a little hard to get down,” try making it yourself with some of the guidelines in the book and you might find that’s its really, really pleasant to drink.
Are there live probiotics in kombucha?
Zilber: There can be. Kombucha can be pasteurized, just like you know milk can be pasteurized or canned goods can be pasteurized. You can heat it and kill everything in it and not really affect the taste that much. If they say that there are live cultures in it, it means that it was fermented and nothing was really done to it after it was put in a bottle. Now there’s a lot of conflicting information about kombucha out there. And I’ve read a lot of pretty hardcore studies that say, well, a lot of this is a bit bunk. But at the end of the day, I’d probably say that drinking kombucha is probably better for you than drinking a can of Coca-Cola.
How do you handle mold in homemade kombucha?
Zilber: That is something you are constantly trying to fight back, especially when you lacto-ferment in something like a crock. There are so many variables that go into making a successful ferment. How clean was your vessel before you put the food in there? How clean were your hands, your utensils? How much salt did you use? How old was the cabbage you were even trying to ferment in the first place? Every little detail is basically another variable in the equation that leads to a fermented product being amazing or terrible. It’s a little bit like chaos theory, it’s a little bit like a butterfly flapping its wings and Thailand and causing a tornado in Ohio. But with lots of practice, you’ll begin to understand that, if it was 30 degrees that day, maybe things were getting a little too active, maybe the fermentation was happening a little bit too quickly. Maybe I opened it a couple times more than I should of and it was open to the air instead of being covered. So there’s lots of variables. But I would say that, if you’re having a lot of trouble with mold, just up the salt percentage by a couple percent. It will make for a saltier sauerkraut, but it will actually help to keep those microbes at bay.
In the book, you say koji is indistinguishable from magic. What is koji?
Zilber: It’s the biggest microbe you’ve never heard of it. Koji is responsible for everything tasty that comes out of east Asia. From China to Korea to Vietnam to especially Japan, it is a mold, a helpful mold called aspergillus oryzae. It is responsible for turning the starches in rice and barley and all sorts of grains into sugar. And it’s turning the protein in those same grains into the flavor umami. It’s responsible for soy sauce, for sake, for rice wine vinegar, for miso and it can be used in all sorts of novel and inventive ways as well. But you never see it as a finished product because it usually is kind of the first step in that process. I liken it to the step of molting barley when you make beer or whiskey. That’s basically how ancient Asia’s civilization came about that process of turning grains into something sweet that you can then ferment with yeast. They found a mold instead of finding the process of molting, and it’s absolutely remarkable for the flavors it brings to the table themselves.
How do you get koji?
Zilber: There’s a line that I say when people ask “How do start growing koji.” All life comes from life, all life comes from cells. At the end of the day, everything living on earth today has been an unbroken chain of succession for three and a half billion years, and koji is no exception. If your kid wants a golden retriever puppy for Christmas, you have to find a golden retriever mom. And it’s the same for koji, you’re going to have find a koji breeder and actually get some spores from them. We buy ours from a laboratory in japan, and we have them shipped over to Copenhagen.
This morning, you probably had a cup of one of the most popular fermented beverages: coffee. The Growler magazine article “Science of Coffee: the changing chemistry of coffee beans from farm to cup” details how coffee makers have embraced fermentation in recent years “to take maximum advantage of beans’ unique potentials. … The fickle nature of fermentation’s microfauna plays a bigger role in coffee than even many coffee industry people understand.” One coffee company founder shared the story of buying a unique variety of Colombian coffee with incredible flavor. When he bought the brand a year later, the flavor wasn’t as good. The reason — the bean grower started making good money off the coffee, and upgraded the wood fermentation tank to a stainless steel tank. “That totally changed the coffee.”
Read more (The Growler)
Restrictive diets aren’t the secret to staying slim. The key is diversity says Tim Spector, professor and author of the book “The Diet Myth.” Eating foods high in fiber, fermented products and food loaded with micronutrient polyphenols are scientifically proven to improve weight and help the complex microbiome flourish.
“This is where we’ve lost track, we’ve tried to simplify it and we’ve tried to say that calories in equals calories out and that one-size-fits-all and that if everyone has these 2,000 calories a day, they’ll be perfect. And of course, that advice has led to the whole world getting fatter,” Spector says in an interview on webisode Health Hackers. “[People have been taught] erroneous advice that fat is bad for you therefore avoid all things with fat, even healthy things.”
The Health Hackers episode is titled “Why your diet may never work until you get to know your microbiome.” Journalist Gemma Evans interviews Spector in his London research lab. Spector is a professor of genetics at King’s College in London. He has published over 800 research articles, and Reuters ranked him as the top 1% of the worlds must published scientists.
Spector began researching the microbiome seven years ago, when he became sick and wanted to know which diet would help him heal. His early delve into the microbiome fascinated him.
“We hadn’t understood the gut microbiome, which is this whole new organ in our bodies that was previously ignored,” Spector says. “I really got into this whole field and diverted my group’s research interest into discovering more about that microbiome that we all have. We’re all so different in our microbes, and this difference is how we all respond differently to foods and it explains a lot of mysteries.”
Microbiome is a Living Community
Spector describes the microbiome as a living community of trillions of microbes that produce chemicals, vitamins and hormones. Ninety-nine percent of microbes are in the gut, most in the lower gut or colon. Human cells only make up 43% of the human body — the rest are microbe cells.
Healthy microbiomes are full of diverse species. They help avoid overeating or under eating because a healthy microbiome self regulates.
“The healthier your microbiome, the healthier your body is in general because it means that your immune system is being well balanced and not overresponding,” he says. “It’s giving you resistance against its infections; it’s not overreacting to give you allergies.”
Researchers like Spector study the microbes with fecal samples. He says you can tell more about a person and what they’re eating through their fecal matter. Many commercial companies today advertise accurate health measurements by measuring genes through DNA samples.
“As a geneticist, that’s rubbish,” Spector says. “Statistically, it might be true, but actually at a personally level, it’s virtually no use. Our microbes are so much different than our DNA makeup. We share any, for example, 20 to 30 percent of our microbes [between] any two people. And so, understand how that community is and what’s different should mean that I can tell whether someone is healthy or whether they’re more likely to get fat or diabetes, [by] looking at the general diversity [of their microbes]. And I can also try and now use this information when you’ve got thousands of people to predict what the best foods are for people.”
Healthy Eating Myth Busting
It’s fascinating insight into the future of predictive health. Spector’s book, “The Diet Myth,” detailed how the health industry has failed the general public for roughly the past 30 years. People were told to eat low-fat foods, count their calories and get lots of exercise. Spector calls that advice “very old-fashioned, very 20th Century.”
“We only really understood food around those primitive concepts in these very broad categories of fats and sugars and proteins and we’ve ignored one of the big ones, which is fiber,” Spector says.
Diets cannot revolve around the three blocks of fats, sugar and protein. What matters, Spector says, is the total amount of chemicals consumed and the effects on the body. Take, for example, a banana. A banana can’t be defined in one of the three categories because it’s made up of 600 chemicals. Once a banana is ingested and combines with gut microbes it converts to 6,000 chemicals.
Making the microbiome more complex: everyone will react differently to that same banana. The effects of the chemicals produced will present differently in each individual.
Diversifying Diets — and Microbes
“Virtually all diets, people end up restricting what they eat which actually has a long-term effect of reducing your microbes and therefore they’re less able to cope with modern living,” he adds.
Spector said you cannot generalize healthy eating guidelines with broad generalizations when it comes to the microbiome because everyone will react differently. Human genetics shape the gut microbiome.
“But if you had to have one rule, people on very restrictive diets don’t do well and people who have the more diverse diets…are healthier,” he says. This is because a diverse diet is full of different nutrients and, in turn, build a diverse group of microbes. Spector compares the microbiome to a garden – the nutrients consumed are like the fertilizer helping the plants or microbes grow.
As the head of the Department of Twin Research & Genetic Epidemiology at King’s College, Spector has studied the effect of microbes in twins. In one study, two mice with different weights were analyzed. The overweight mouse with less diverse microbes was given a fecal transplant from his twin, the skinnier mouse with a healthier microbiome. Once that healthier mouse was given the fecal transplant, the overweight mouse continued to lose weight, even when overfed.
“So those microbes are doing a really good job working overtime to convert metabolically to keep that stuff away from going into fat. They’re burning it up in ways we don’t really understand,” Spector says. “Your chances of having good microbes will increase the more you’ve got of them. So the people who have very limited number of microbes, who have very limited diets where they’re just on processed foods, have an increasingly smaller amount of nutrients in there and only a few microbe species like that restrictive species and they elbow the others out and then they can’t react in healthy ways:
Society has to stop demonizing junk food, Spector says, “we have to get away from the idea that these things are so deadly.” Eating a fast-food burger once a year could actually be good for the microbiome, Spector argues, because it will “wake up your system.”
Another study on mice found that mice who consumed lots of fiber (chickpeas, lentils), then were given a high-fat meal didn’t put on weight. Spector said it’s because they had a solid base, and then were given a high-fat meal once in moderation.
Spector is against the concept of clean eating (“There’s no such thing.”) and even processed food (“What’s processed food? It’s cheese. It’s milk. It depends where you draw the line.”). But he says ultra-processed food with harsh chemicals should be kept to an absolute minimum. Ultimately, no one should take a black and white view on food and limit what they eat.
What Should We Eat?
So what should we eat? Spector highlighted four food and drinks that help gut health: foods high in fiber, complex plants, fermented foods and polyphenols.
Fiber is important because it’s what microbes live off. Fiber is hard to digest early in the digestive track, so the nutrients reach the colon before being absorbed. Most ultra-processed foods are so full of sugar that they are absorbed extremely early in the digestive process. Microbes are destroyed by starving them of fiber — microbes can be wiped out if not fed fiber for long periods of time.
Complex plants, Spector advises, prioritizing vegetables first and fruit second. Fermented foods are full of the live bacteria critical for gut health. Spector suggests fermented foods like kefir, yogurt, kimchi, sauerkraut, kombucha, Japanese fermented soy and even quality fermented chocolate. Polyphenols are an energy source for microbes, and can be found in any food like blueberries, raspberries, blackberries, olive oil, dark chocolate, seeds, coffee and green tea.
As far as pill supplements, Spector points out that there’s no scientific evidence yet that probiotic supplements benefit healthy people.
“I’m generally in favor of using food – yogurt, kefir, cheese — rather than expensive supplements,” he says.