Yogurt Alters Gut Microbiome

It’s widely appreciated that consuming high-quality yogurt can aid a healthy diet. Now new research shows eating yogurt changes the composition of the human gut microbiome.

In a new human study published in BMC Microbiology, researchers studied the microbiome of European twins. Results found those regularly eating yogurt had less visceral fat mass, reduced insulin levels and an increase of bacterial species in the gut. Strains S. thermophilus, B. animalis subsp. lactis., S. thermophilus and B. animalis subsp. lactis were all present in yogurt eaters.
The study also found the yogurt bacteria are “transient members of the gut microbiome and do not durably engraft within the gut lumen.”

Read more (BMC Microbiology)

Thyme and oregano possess an anti-cancer compound that suppresses tumor development, but adding more to your tomato sauce isn’t enough to gain significant benefit. The key to unlocking the power of these plants is in amplifying the amount of the compound created or synthesizing the compound for drug development.

And exciting for the field of fermentation: extracting those beneficial compounds from the plant is done through fermentation. 

“The fermentation process is so important to food and beverage, pharmaceutical and biofuels production that Purdue now offers a fermentation science major,” reads a press release from Purdue University. 

Researchers at Purdue took the first step in using the compound in pharmaceuticals by mapping its biosynthetic pathway, a sort of molecular recipe of the ingredients and steps needed. 

“These plants contain important compounds, but the amount is very low and extraction won’t be enough,” said Natalia Dudareva, distinguished professor of biochemistry in Purdue’s College of Agriculture and director of Purdue’s Center for Plant Biology, who co-led the project. “By understanding how these compounds are formed, we open a path to engineering plants with higher levels of them or to synthesizing the compounds in microorganisms for medical use. “It is an amazing time for plant science right now. We have tools that are faster, cheaper and provide much more insight. It is like looking inside the cell; it is almost unbelievable.”

Thymol, carvacrol and thymohydroquinone are flavor compounds in thyme, oregano and other plants in the Lamiaceae family. They have antibacterial, anti-inflammatory, antioxidant and other properties beneficial to human health. Thymohydroquinone has been shown to have anti-cancer properties and is particularly of interest, said Dudareva..

In collaboration with scientists from Martin Luther University Halle-Wittenberg in Germany and Michigan State University, the Purdue team uncovered the entire biosynthetic pathway to thymohydroquinone, including the formation of its precursors thymol and carvacrol, and the short-lived intermediate compounds along the way.

The findings alter previous views of the formation of this class of compounds, called phenolic or aromatic monoterpenes, for which only a few biosynthetic pathways have been discovered in other plants, she said. The study results were published in the Proceedings of the National Academy of Sciences. 

“These findings provide new targets for engineering high-value compounds in plants and other organisms,” said Pan Liao, co-first author of the paper and a postdoctoral researcher in Dudareva’s lab. “Not only do many plants contain medicinal properties, but the compounds within them are used as food additives and for perfumes, cosmetics and other products.”

Now that this pathway is known, plant scientists could develop cultivars that produce more of the beneficial compounds, or it could be incorporated — using fermentation — into microorganisms like yeast for production. 

A $5 million grant from the National Science Foundation supported the research. Using RNA sequencing and correlation analysis, the team screened more than 80,000 genes from plant tissue samples and identified the genes needed for thymohydroquinone production. Based on what was known about the compound structure and through metabolite profiling and biochemical testing, the team identified the biosynthetic pathway.

“The intermediate formed in the pathway was not what had been predicted,” Liao said. “We found that the aromatic backbone of both thymol and carvacrol is formed from γ-terpinene by a P450 monooxygenase in combination with a dehydrogenase via two unstable intermediates, but not p-cymene, as was proposed.”

More pathways are now being discovered, thanks to the availability of RNA sequencing to perform high-throughput gene expression analysis, according to Dudareva.

“We, as scientists, are always comparing pathways in different systems and plants,” Dudareva said. “We are always in pursuit of new possibilities. The more we learn, the more we are able to recognize the similarities and differences that could be key to the next breakthrough.”

Microbes on our bodies outnumber our human cells. Can we improve our health using microbes?

“(Humans) are minuscule compared to the genetic content of our microbiomes,” says Maria Marco, PhD, professor of food science at the University of California, Davis (and a TFA Advisory Board Member). “We now have a much better handle that microbes are good for us.” 

Marco was a featured speaker at an Institute for the Advancement of Food and Nutrition Sciences (IAFNS) webinar, “What’s What?! Probiotics, Postbiotics, Prebiotics, Synbiotics and Fermented Foods.” Also speaking was Karen Scott, PhD, professor at University of Aberdeen, Scotland, and co-director of the university’s Centre for Bacteria in Health and Disease.

While probiotic-containing foods and supplements have been around for decades – or, in the case of fermented foods, tens of thousands of years – they have become more common recently . But “as the terms relevant to this space proliferate, so does confusion,” states IAFNS. 

Using definitions created by the International Scientific Association for Postbiotics and Prebiotics (ISAPP), Marco and Scott presented the attributes of fermented foods, probiotics, prebiotics, synbiotics and postbiotics.  

The majority of microbes in the human body are in the digestive tract, Marco notes: “We have frankly very few ways we can direct them towards what we need for sustaining our health and well being.” Humans can’t control age or genetics and have little impact over environmental factors. 

What we can control, though, are the kinds of foods, beverages and supplements we consume.

Fermented Foods

It’s estimated that one third of the human diet globally is made up of fermented foods. But this is a diverse category that shares one common element: “Fermented foods are made by microbes,” Marco adds. “You can’t have a fermented food without a microbe.”

This distinction separates true fermented foods from those that look fermented but don’t have microbes involved. Quick pickles or cucumbers soaked in a vinegar brine, for example, are not fermented. And there are fermented foods that originally contained live microbes,  but where those microbes are killed during production — in sourdough bread, shelf-stable pickles and veggies, sausage, soy sauce, vinegar, wine, most beers, coffee and chocolate. Fermented foods that contain live, viable microbes include yogurt, kefir, most cheeses, natto, tempeh, kimchi, dry fermented sausages, most kombuchas and some beers. 

“There’s confusion among scientists and the public about what is a fermented food,” Marco says.

Fermented foods provide health benefits by transforming food ingredients, synthesizing nutrients and providing live microbes.There is some evidence  they aid digestive health (kefir, sourdough), improve mood and behavior (wine, beer, coffee), reduce inflammatory bowel syndrome (sauerkraut, sourdough), aid weight loss and fight obesity (yogurt, kimchi), and enhance immunity (kimchi, yogurt), bone health (yogurt, kefir, natto) and the cardiovascular system (yogurt, cheese, coffee, wine, beer, vinegar). But there are only a few studies on humans  that have examined these topics. More studies of fermented foods are needed to document and prove these benefits.

Probiotics 

Probiotics, on the other hand, have clinical evidence documenting their health benefits. “We know probiotics improve human health,” Marco says. 

The concept of probiotics dates back to the early 20th century, but the word “probiotic” has now become a household term. Most scientific studies involving probiotics look at their benefit to the digestive tract, but new research is examining their impact on the respiratory system and in aiding vaginal health.

Probiotics are different from fermented foods because they are defined at the strain level and their genomic sequence is known, Marco adds. Probiotics should be alive at the time of consumption in order to provide a health benefit.

Postbiotics

Postbiotics are dead microorganisms. It is a relatively new term — also referred to as parabiotics, non-viable probiotics, heat-killed probiotics and tyndallized probiotics — and there’s emerging research around the health benefits of consuming these inanimate cells. 

“I think we’ll be seeing a lot more attention to this concept as we begin to understand how probiotics work and gut microbiomes work and the specific compounds needed to modulate our health,” according to Marco.

Prebiotics

Prebiotics are, according to ISAPP, “A substrate selectively utilized by host microorganisms conferring a health benefit on the host.”

“It basically means a food source for microorganisms that live in or on a source,” Scott says. “But any candidate for a prebiotic must confer a health benefit.”

Prebiotics are not processed in the small intestine. They reach the large intestine undigested, where they serve as nutrients for beneficial microorganisms in our gut microbiome.

Synbiotics

Synbiotics are mixtures of probiotics and prebiotics and stimulate a host’s resident bacteria. They are composed of live microorganisms and substrates that demonstrate a health benefit when combined.

Scott notes that, in human trials with probiotics, none of the currently recognized probiotic species (like lactobacilli and bifidobacteria) appear in fecal samples existing probiotics.

“There must be something missing in what we’re doing in this field,” she says. “We need new probiotics. I’m not saying existing probiotics don’t work or we shouldn’t use them. But I think that now that we have the potential to develop new probiotics, they might be even better than what we have now.”

She sees great potential in this new class of -biotics. 

Both Scott and Marco encouraged nutritionists to work with clients on first  improving their diets before adding supplements. The -biotics stimulate what’s in the gut, so a diverse diet is the best starting point.

“Human civilization simply would not have been possible without fermented foods and beverages…we’re here today because fermented foods have been popular for humans for at least 10,000 years,” says Bob Hutkins, professor of food science at the University of Nebraska (and a recent addition to TFA’s Advisory Board). 

Hutkins was the opening keynote speaker at FERMENTATION 2021, The Fermentation Association’s first international conference. His presentation explored the history, definition and health benefits of fermented foods.  

Cultured History

The topic of fermentation extends to evolution, archaeology, science and even the larger food industry. 

“The discipline of microbiology began with fermentation, all the early microbiologists studied fermentation,” Hutkins says. 

Louis Pasteur patented his eponymous  process, developed to improve the quality of wine at Napoleon III’s request. The microbes studied back then — lactococcus, lactobacillus and saccharomyces — remain the most studied strains.

“What interested those early microbiologists — namely how to improve food and beverage fermentation, how to improve their productivity, their nutrition — are the very same things that interest 21st century fermentation scientists,” Hutkins says. 

Hutkins is the author of one of the books considered gospel in the industry, “Microbiology and Technology of Fermented Foods.” He says that fermented foods defined the food industry. In its early days, it was small-scale, traditional food production that “we call a craft industry now.” At the time, food safety wasn’t recognized as a microbiological problem.

Today’s modern food industry manufactures on a large-scale in high throughput factories withmany automated  processes. Food safety is a priority and highly regulated. And, thanks to developments in gene sequencing, many fermented products are made with starter cultures selected for their individual traits. 

“But I would say that there’s been kind of a merging between these traditional and modern approaches to manufacturing fermented foods, where we’re all concerned about time sensitivity, excluding contaminants, making sure that we have consistent quality, safety is a vital concern and extensive culture knowledge,” Hutkins says.

Defining & Demystifying

Fermentation — “the original shelf-life foods” — is experiencing a major moment. “Fermented foods in 2021 check all the topics” of popular food genres: artisanal, local, organic, natural, healthy, flavorful, sustainable, entrepreneurial, innovative, hip and holistic. “They continue to be one of the most popular food categories,” Hutkins continues.

Interest in fermentation is reaching beyond scientists, to nutritionists and clinicians. But Hutkins says he’s still surprised to learn how many professionals don’t understand fermentation. To address  the confusion, a panel of interdisciplinary scientists created a global definition of fermented foods in March 2021

“Fermentation was defined with these kind of geeky terms that I don’t know that they mean very much to anybody,” he says. 

The textbook biochemical definition of fermentation that a microbiologist learns in Biochemistry 101 doesn’t work for a nutritionist or clinician focusing on fermentation’s health benefits. The panel, which spent a year coming to a consensus, wanted a definition that would simply illustrate “raw food being converted by microbes into a fermented food.” The new definition, published in the the journal Nature and released in conjunction with the International Scientific Association for Probiotics and Prebiotics (ISAPP), reads: “Foods made through desired microbial growth and enzymatic conversions of food components.” 

Fermentation in 2022

Hutkins predicts 2022 will see more studies addressing whether there are clinical health benefits from eating fermented foods. The groundbreaking study on fermented foods at Stanford was important. It found that a diet high in fermented foods increases microbiome diversity, lowers inflammation, and improves immune response. But research like this is  expensive, so randomized control trials are few.

Fermented foods could also make their way into dietary guidelines.

“Fermented foods, including those that contain live microbes, should be included as part of a healthy diet,” Hutkins says.

Fermented foods have had an impact on human evolution, and they continue to affect social dynamics, according to a new collection of 16 studies in the journal Current Anthropology. This research explores how “microbes are the unseen and often overlooked figures that have profoundly shaped human culture and influenced the course of human history.”

The journal’s special edition, Cultures of Fermentation, features work from multiple disciplines: microbiology, cultural anthropology, archaeology and biological anthropology. Researchers were based all over the globe.

“Humans have a deep and complex relationship with microbes, but until recently this history has remained largely inaccessible and mostly ignored within anthropology,” reads the introduction, Cultures of Fermentation: Living with Microbes. “Fermentation is at the core of food traditions around the world, and the study of fermentation crosscuts the social and natural sciences.”

The impetus for the articles was a 2019 symposium organized by the non-profit Wenner-Gren Foundation. This organization aims to bring together scholars to debate and discuss topics in anthropology.

“Fermentation is at the core of food traditions around the world, and the study of fermentation crosscuts the social and natural sciences,” the introduction continues. The aim of the symposium and corresponding research was to “foster interdisciplinary conversations integral to understanding human-microbial cultures. By bridging the fields of archaeology, cultural anthropology, biological anthropology, microbiology, and ecology, this symposium will cultivate an anthropology of fermentation.”

Here is a listing the included studies:

  • Predigestion as an Evolutionary Impetus for Human Use of Fermented Food (Katherine R. Amato,Elizabeth K. Mallott, Paula D’Almeida Maia, and Maria Luisa Savo Sardaro). Using research on nonhuman primates, researchers conclude that “fermentation played a central role in enabling our earliest ancestors to survive in the forested grasslands in Africa where key anatomical features of our species emerged. Fermentation occurs spontaneously in nature. Most nonhuman primates cannot metabolize fermented products, but humans evolved the capacity to use them as fuel. …By breaking down tough and toxic plant species, fermentation helped humans meet the caloric requirements associated with their growing brains and shrinking guts. These anatomical changes both stemmed from and fueled the emergence of collective forms of know-how — microbial and human cultures fed on one another, in this view of the human past.”
  • Toward a Global Ecology of Fermented Foods (Robert R. Dunn, John Wilson, Lauren M. Nichols, and Michael C. Gavin). This ecological view of fermentation maps the “emergence and divergence of the world’s many varieties of fermented foods.” 
  • Cultured Milk: Fermented Dairy Foods along the Southwest Asian–European Neolithic Trajectory (Eva Rosenstock, Julia Ebert, and Alisa Scheibner). Using archaeological evidence of fermentation, researchers track the “emergence of lactase persistence in sites where dairying made an early appearance. It appears that people ate cheese and yoghurt well before they drank milk: only a small subsection of the human population retains the enzymes needed to digest lactose into adulthood.”

FERMENTATION 2021 Wrap-Up

Nearly 300 individuals from around the world participated in The Fermentation Association’s first conference, FERMENTATION 2021. The virtual event included 35 educational keynotes, presentations, and panel discussions from more than 60 speakers over three days. Topics ranged from the science of fermentation to the art of fermenting to create flavor, from how fermented products are selling at retail to what’s next in the world of fermentation.

“I’ve been in this field for 40 years and, in all honesty, this is one of the biggest honors I’ve received, to be the speaker for this opening meeting of this really cool organization,” said Bob Hutkins, professor of food science at the University of Nebraska. Hutkins presented the conference’s opening keynote, Definition & History of Fermented Foods.

Over five years ago, John Gray, TFA’s founder, envisioned a trade show for producers of fermented foods and beverages, to make those artisanal items a more prominent part of the retail space. John connected with Neal Vitale, TFA Executive Director, and the organization was born out of their collective vision. TFA has grown, with a robust website, biweekly newsletter,a series of webinars and, now, an international conference. TFA has an Advisory Board that includes food and beverage producers, academics and researchers, and food and flavor educators and authors. TFA has formed working relationships with a number of other like-minded trade associations and organizations, and established a Buyers Council to create an active dialogue with food and beverage distributors, brokers and retailers.

“I have to tell you what a thrill it is to have you all here to witness and to participate in the beginning of a dream coming true,” added Gray in his welcoming remarks. Gray is the chairman and CEO of Katalina Holding Co., a food incubator and parent company of Bubbies Pickles.

FERMENTATION 2021 content paralleled TFA’s primary missions: first, help consumers better understand fermentation and its potential health benefits; second, work to improve health and safety regulations as they pertain to fermented products and third, connect the science and health research communities with producers, supporting scientific research and for a better understanding of the “state of the art.” 

What made FERMENTATION 2021 unique is that it was the first event to bring together everyone involved in the world of fermentation — producers, retailers, chefs, scientists, authors, suppliers and regulators. The conference was not a how-to fermentation education event, as TFA feels there are numerous, effective resources for the person looking to, for example, make kimchi or learn about using koji. 

“”We were delighted with how well FERMENTATION 2021 met — in fact, exceeded — our goals,” said Vitale. “While we were disappointed that the continuing impact of COVID-19 kept us from meeting in person, we were gratified by how all the participants responded, interacted, and engaged during our three jam-packed days. And, with recording of all our sessions now available online for our registrants, we expect that energy and excitement to continue.”, 

“Fermentation is experiencing a major surge of interest in restaurants and kitchens around the globe,” says Amelia Nielson-Stowell, TFA Editor. “Our conference was a major milestone for the industry and we are already in the planning stages for FERMENTATION 2022 next summer. And, assuming we will be able to meet in person once again, we plan to host a tasting and sampling event for consumers alongside our conference.” 

Primeval Poop Profiles

Studies of ancient poop found “humans as long as 2,700 years ago in the Iron Age were already using sophisticated techniques in flavoring the fermented foods.” They especially loved pairing pale ale with blue cheese.

A paper published in Current Biology detailed how researchers used paleo fecal samples  found in salt mines in Austria to analyze the food ancient people were consuming. Their stool dehydrated in the salt, creating an ideal, preserved sample.

Researchers from the Institute for Mummy Studies, the University of Trento and the Vienna Museum of Natural History also found industrialization transformed the Western diet. Humans used to have healthier, more biodiverse gut microbiomes “because they were eating unprocessed foods.”
Frank Maixner, one of the paper’s lead authors, believes combining archaeology and microbiology could “illuminate the greater puzzle of human history.”

Read more (Popular Science)

Researchers have discovered a milk alternative: fermenting pea and rice with probiotic strains. This dairy-free mixture is  highly digestible and has the same animal protein as  found in milk, casein. 

Fermentation was critical to the results. Plant-based proteins are poorly digested because they are often insoluble in water, explains Professor Monique Lacroix of Institut National de la Recherche Scientifique (INRS). Animal proteins, in contrast, “usually take the form of elongated fibers that are easily processed by digestive enzymes.” But lactic acid bacteria in the fermented pea and rice drink predigested the proteins, improving digestibility.

“Fermentation allowed for the production of peptides (protein fragments) resulting from the breakdown of proteins during fermentation, facilitating their absorption during digestion,” notes an article on the research in Nutrition Insight.

INRS partnered with probiotics company Bio-K+ on the research. Their findings were published in the Journal of Food Science.

Read more (Nutrition Insight)

Natto significantly lowers levels of both glucose and insulin, according to research by Japan’s National Agriculture and Food Research Organization. Natto, a traditional food in Japan, is a fermented soybean dish valued for its high-nutrient content. It’s characterized by sticky strands that stretch from the dish when stirred and, the research showed, stickier natto is healthier.

Natto’s stringy texture is produced by y-polyglutamic acid (y-PGA), and stickier natto has higher levels of y-PGA. When nondiabetic men and women were fed a series of meals of both high-and low-y-PGA natto, high y-PGA natto “significantly” lowered glucose and insulin levels in the test subjects.

Study results were published in the scientific journal Nutrients. Researchers next hope to “study the long-term health impacts of a diet that includes high γ-PGA natto.”

Read more (Chemical & Engineering News)

Tea connoisseurs have long believed that black tea’s flavor comes from the chemicals created during oxidation, but a new study reveals microbes at play. Black’s tea’s rich flavor is partly due to fermentation, the same microbial process used to create fermented teas like kombucha, jun and pu’erh.

What does this mean for tea producers? By adjusting the microbes on the tea leaves, fermentation could amplify the flavor in the final brewed cup of tea.

“The finding that bacterial and fungal communities also drive tea processing suggests the microbiome of the leaves can be manipulated to create greater quantities of tasty compounds due to fermentation,” says Dan Bolton, founder, editor and publisher of Tea Journey.

In research published in the Journal of Agricultural and Food Chemistry, a team of scientists from Anhui Agricultural University in China studied how sterilization of tea leaves affected tea flavor. They began by sampling the microbes on leaves from the Dongzhi tea plantation in Anhui province. Half the leaves were sterilized in mild bleach for five minutes — the other half were left untouched. All the leaves were then processed traditionally: withered, rolled, oxidized in the sun and dried.  

Their conclusions found black tea produced through microbial fermentation from the unsterilized sample was full of catechins and L-theanine. Catechins are flavonoids and a naturally-occurring antioxidant; L-theanine is an amino acid (also found in  mushrooms) known to ease stress and insomnia. Both compounds  help make tea flavorful. The sterilized leaves produced tea that didn’t have the same amount of compounds, and so wasn’t as flavorful.

“The sterilization process dramatically decreased the content of total catechins and theanine in black tea, indicating that microbes on the surface of tea leaf may be involved in maintaining the formation of these important metabolites during black tea processing,” says Ali Inayat Mallano, PhD, professor at the university.

Interestingly, sterilization had no effect on green tea. Both samples of green tea, sterilized and unsterilized, had the same levels of caffeine and theanine.

[To explore premium dark teas, TFA recently organized a webinar Beyond Kombucha: Pu’erh, Jun and Dark Tea with Bolton and tea experts Jeff Fuchs (author, Himalayan explorer and co-founder of Jalam Teas) and Brendan McGill (chef and James Beard nominee who owns Hitchcock Restaurant Group in Seattle and Junbug Kombucha).