Fermenting — in Space?

Microbes that coexist on plants influence a crop’s size, shape, color, flavor and yield. What would these microbes do in microgravity? The International Space Station (ISS) is testing to find these results. 

Flight engineer Shannon Walker (pictured) shows sample bags collected for the Grape Juice Fermentation in Microgravity Aboard ISS study. Astronauts will observe the fermentation process, measuring microbial differences. Back on earth, a matching, control sample is being observed in an environmental control chamber that mimics the ISS ambient temperature. The space and earth samples then will be analyzed for changes. Both flight and ground control samples are analyzed post-investigation for genetic change.

Read more (NASA)

A new study on kefir found that the individual dominant species of Lactobacillus bacteria in kefir grains cannot survive in milk on their own. The bacteria need one another to create the fermented dairy drink, “feeding on each other’s metabolites in the kefir culture.”

The research, conducted by EMBL (Europe’s laboratory for life and sciences) and Cambridge University’s Patil group and published in Nature Microbiology, illustrates a dynamic of microbes that had eluded scientists. Though scientists knew microorganisms live in communities and depend on each other to survive, “mechanistic knowledge of this phenomenon has been quite limited,” according to a press release on the research.

“Cooperation allows them to do something they couldn’t do alone,” says Kiran Patil, group leader and author of the paper. “It is particularly fascinating how L. kefiranofaciens, which dominates the kefir community, uses kefir grains to bind together all other microbes that it needs to survive — much like the ruling ring of the Lord of the Rings. One grain to bind them all.”

To make kefir, it takes a team. A team of microbes.

The group studied 15 samples of kefir, one of the world’s oldest fermented food products. Below are highlights from a press release on the published results. 

A Model of Microbial Interaction

Kefir first  became popular centuries ago in Eastern Europe, Israel, and areas in and around Russia. It is composed of ‘grains’ that look like small pieces of cauliflower and have fermented in milk to produce a probiotic drink composed of bacteria and yeasts.

People were storing milk in sheepskins and noticed these grains that emerged kept their milk from spoiling, so they could store it longer,” says Sonja Blasche, a postdoc in the Patil group and an author of the paper. Because milk spoils fairly easily, finding a way to store it longer was of huge value.”

To make kefir, you need kefir grains, which must come from another batch of kefir. They cannot be made artificially. The grains are added to milk, to ferment and grow. Approximately 24 to 48 hours later (or, in the case of this research, 90 hours later), the kefir grains have consumed the available nutrients. The grains have grown in size and number, and are removed and added to fresh milk — to begin the process anew.

For scientists,  kefir is more than just a healthy beverage: it’s an easy-to-culture model microbial community for studying metabolic interactions. And while kefir is quite similar to yogurt in many ways – both are fermented or cultured dairy products full of ‘probiotics’ – kefir’s microbial community is far larger, including not just bacterial cultures but also yeast.

A “Goldilocks Zone”

While scientists know that microorganisms often live in communities and depend on their fellow community members for survival, mechanistic knowledge of this phenomenon has been quite limited. Laboratory models historically have been limited to two or three microbial species, so kefir offers – as Patil describes – a ‘Goldilocks zone’ of complexity that is not too small (around 40 species), yet not too unwieldy to study in detail.

Blasche started this research by gathering kefir samples from several sources. Though most  were obtained in Germany, they may have  originated elsewhere, grown from kefir grains  passed down through the years..

“Our first step was to look at how the samples grow. Kefir microbial communities have many member species with individual growth patterns that adapt to their current environment. This means fast- and slow-growing species and some that alter their speed according to nutrient availability, Blasche  says. This is not unique to the kefir community. However, the kefir community had a lot of lead time for coevolution to bring it to perfection, as they have stuck together for a long time already.”

Cooperation is key

Finding out the extent and nature of  cooperation among kefir microbes was far from straightforward. Researchers combined a variety of state-of-the-art methods, such as metabolomics (studying metabolites’ chemical processes), transcriptomics (studying the genome-produced RNA transcripts) and mathematical modelling. These processes  revealed not only key molecular interaction agents like amino acids, but also the contrasting species dynamics between  grains and  milk.

“The kefir grain acts as a base camp for the kefir community, from which community members colonise the milk in a complex yet organised and cooperative manner,” Patil says. “We see this phenomenon in kefir, and then we see it’s not limited to kefir. If you look at the whole world of microbiomes, cooperation is also a key to their structure and function.”

In fact, in another paper from Patil’s group (in collaboration with EMBL’s Bork group) in Nature Ecology and Evolution, scientists combined data from thousands of microbial communities across the globe – from in soil to in the human gut – to understand similar cooperative relationships. In this second paper, the researchers used advanced metabolic modelling to show that the co-occurring groups of bacteria, groups that are frequently found together in different habitats, are either highly competitive or highly cooperative. This stark polarization hadn’t been observed before, and sheds light on evolutionary processes that shape microbial ecosystems. While both competitive and cooperative communities are prevalent, the cooperators seem to be more successful in terms of higher abundance and occupying diverse habitats — stronger together!

After Dr. Bob Hutkins finished a presentation on fermented foods during a respected nutrition conference, the first audience question was from someone with a PhD in nutrition: “What are fermented foods?”

“I thought ‘Doesn’t everyone know what fermentation is?’ I realized, we do need a definition. Those of us that work in this field know what we’re talking about when we say fermented foods, but even people trained in foods do not understand this concept,” says Hutkins, a professor of food science at the University of Nebraska-Lincoln. He presented The New Definition of Fermented Foods during a webinar with TFA

Hutkins was part of a 13-member interdisciplinary panel of scientists that released a consensus definition on fermented foods. Their research, published this month in Nature Reviews Gastroenterology & Hepatology, defines fermented foods as: “foods made through desired microbial growth and enzymatic conversions of food components.”

“We needed a definition that conveyed this simple message of a raw food turning into a fermented food via microorganisms,” Hutkins says. “It brings some clarity to many of these issues that, frankly, people are confused about.”

David Ehreth, president and founder of Alexander Valley Gourmet, parent company of Sonoma Brinery (and a TFA Advisory Board member), agreed that an expert definition was necessary.

“As a producer, and having started this effort to put live culture products on the standard grocery shelf, I started doing it as a result of unique flavors that I could achieve through fermentation that weren’t present in acidified products,” Ehreth says. “Since many of us put this on our labels, we should be paying close attention to what these folks are doing, since they are the scientific backbone of our industry.”

Hutkins calls fermented foods “the original shelf-stable foods.” They’ve been used by humankind for over thousands of years, but have mushroomed in popularity in the last 15. Fermented foods check many boxes for hot food trends: artisanal, local, organic, natural, healthy, flavorful, sustainable, innovative, hip, funky, chic, cool and Instagram-worthy.

Nutrition, Hutkins hypothesizes, is a big driver of the public’s interest in fermentation. He noted that Today’s Dietitian has voted fermented foods a top superfood for the past four years. 

Evidence to make bold claims about the health benefits of fermentation, though, is lacking. Hutkins says there is observational and epidemiological evidence. But randomized, human clinical trials — “the highest evidence one can rely on” — are few and small-scale for fermented foods. 

Hutkins shared some research results. One study found that Korean elders who regularly consume kimchi harbor lactic acid bacteria (LAB) in their GI tract, providing compelling evidence that LAB survives digestion and reaches the gut. Another study of cultured dairy products, cheese, fermented vegetables, Asian fermented products and fermented drinks found that most contain over 10 million LAB per gram. 

Still, the lack of credible studies is “a barrier we have to get past,” Hutkins says. There are confirmed health benefits with yogurt and kefir, but this research was funded by the dairy industry, a large trade group with significant resources. 

“I think there’s enough evidence — most of it through these associated studies — to warrant this statement: fermented foods, including those that contain live microorganisms, should be included as part of a healthy diet.”

Probiotics and fermented foods are not equivalent, says Mary Ellen Sanders, PhD and executive science officer of the International Scientific Association of Probiotics & Prebiotics (ISAPP). She advises fermented food producers that don’t meet the criteria of a probiotic to use descriptors such as “live active cultures” or “fermented food with live microbes” on their labels rather than “probiotic.”

“There are quite a few differences between probiotics and many fermented foods. You cannot assume a fermented food is a probiotic food even if it has live cultures present,” says Sanders. She highlighted her 30 years worth of insight into the field during a TFA webinar, Are Fermented Foods Probiotics? 

Some fermented foods do meet these criteria, such as some yogurts and cultured milks that are well-studied. But many traditional fermented foods do not. 

Using multiple peer-reviewed scientific studies and conclusion from expert panels in the fields of probiotics and fermented foods, Sanders shared the ways in which fermented foods and probiotics differ:

  1. Health benefits

By definition, a probiotic must have a documented health benefit. Many fermented foods have not been tested for a health benefit. 

“If you are interested in recommending health benefits from a fermented food in an evidence-based manner, many traditional fermented foods fall short. They don’t have the controlled randomized trials that will provide a causal link between the food and the health benefit,” she says. “A food may be nutritious, but probiotic benefits must stem from the live microbe, not the nutritional composition of the food. Otherwise you just have a nutritious food that happens to have live microorganisms in it. You don’t have a probiotic food.”

  1. Quality studies

In her presentation, Sanders shared  multiple randomized clinical trials on human subjects with supported health evidence for probiotics. But there are few randomized, controlled studies on fermented foods. Most are cohort studies, which inherently have a higher risk of bias and cannot provide a causal link between consuming fermented foods and a health benefit. 

“A strong hypothesis is not the same as proof,” Sanders says. “Evidence for probiotics must meet a higher standard than small associative studies, many of which are tracking biomarkers and not health endpoints.” 

She noted, though, there are some studies on fermented milk and yogurt that show a conferred health benefit.

  1. Strain designation

Though many fermented foods do have live microbes, a probiotic is required to be identified to the strain level. The genus and species should also be properly named according to current nomenclature. Many fermented foods contain undefined microbial composition. Without that strain designation, one can’t tie the scientific evidence on that strain to the probiotic product.

  1. Microbe quantity

Another key differentiator is that probiotics must be delivered at a known quantity that matches the amount that results in a health benefit. Probiotics are typically quantified in colony forming units (or CFUs). 

“A probiotic has a known effective dose. But fermented foods often contain unknown levels of microbes, especially at time of consumption,” Sanders says.

What Can Brands Do?

If food brands keep using the word probiotics as a catch-all to describe a fermented product, the term will lose its utility. Using “probiotics” on food with unsubstantiated proof of probiotics is a misuse of the term.

“When I see a fermented food that says probiotics on it, I very often think what they’re trying to communicate on that label [is that it] contains live microbes,” Sanders says, “because I’m doubting, at least some of the products I see, that they have any evidence of a health benefit. And so they’re just looking for a catchy, single word that will communicate to people that this has live microbes in it. ‘Live active cultures’ is something that resonates with people as well. So why not use that?”

Sanders encourages fermented brands to standardize the terms “live active cultures,” “live microbes,” “live microorganisms” or “fermented food with live microbes.” For products pasteurized after fermentation, there’s a term for them too: “Made with live cultures.”

Controlled human studies on fermented foods can be challenging, Sanders admits. Such studies can be difficult to properly blind, since placebos for foods are hard to design. The fermentation process affects the product taste so that study subjects may know what they are consuming. But the health benefits of fermented foods could be studied, though. She also advises producers to focus on the nutritional value of their food. 

“That’s one thing that really has me excited about this concept of core benefits,” says Maria Marco, PhD, professor  of food science and technology at University of California, Davis (and a member of TFA’s Advisory Board) and moderator of the webinar. “I think it kind of opens the doors to the possibility of fermented fruits and vegetables where there’s certain organisms, microorganisms that we’d expect to be there but again we need to know really if those microorganisms are needed to make those foods healthy.”

Scientists have found a sustainable solution for dealing with both food waste and soil health. They’ve discovered fermented food waste boosts bacteria that increases crop growth, makes plants more resistant to pathogens and reduces carbon emissions from farming. 

“Beneficial microbes increased dramatically when we added fermented food waste to plant growing systems,” said Deborah Pagliaccia, the microbiologist who led the research at University of California Riverside (UCR). “When there are enough of these good bacteria, they produce antimicrobial compounds and metabolites that help plants grow better and faster.”

The UCR research team used two types of fermented byproducts: beer mash (byproduct of beer production) and food waste discarded by grocery stores; neither tested positive for salmonella or any other pathogenic bacteria.

Read more (Science Daily)

Pandemic Spurs Fermented Beverages

The coronavirus continues to drive sales of fermented drinks. Lifeway’s kefir, Farmhouse Culture’s kraut juice, Probitat’s fermented planted-based smoothies, Flying Ember’s hard kombucha and Buoy Hydration’s fermented drinks all report increased sales as consumers take a bigger interest in the immune-enhancing benefits of fermented beverages.

“As demand ramps up for immune-enhancing products, manufacturers have an opportunity to innovate with immune-supporting ingredients and flavors,” says Becca Henrickson, marketing managed of Wixon, a flavor and seasoning company. “When flavoring beverages with immune support ingredients, selecting flavors that increase or complement a product’s health perception is optimal.”

Read more (Food Business News)

Kombucha and cosmetics are driving growth in the probiotic and prebiotic markets by making products that use non-classic strains of bacteria.

The e-commerce market for probiotic supplements was estimated at $973 million across 20 countries in 2020. America accounts for almost half of those sales. Ewa Hudson, director of insights for Lumina Intelligence, shared this info at the Probiota Americas 2020 Conference. (Lumina and Probiota Americas are parts of William Reed Business Media, the parent company for FoodNavigator.com.) The session, New Horizons for Prebiotics & Probiotics, included Lumina’s insight into non-classic bacteria strains and a panel discussion with leaders in the probiotics field.

In 2020, 32% of all probiotics in America — and 41% of the best-selling ones — contained non-classic species. Hudson said this species classification is a messy space, especially from a consumer’s perspective, because there are so many species. Kombucha includes the most  non-classic probiotic species — of those products with probiotics, 93% include non-classic bacteria .

Most products with probiotics include one of the four common bacteria species: lactobacilli, bifidobacterium, bacillus and saccharomyces. Lumina excluded these four from their research to focus on the growth of the non-classic probiotic strains. These include: streptococcus thermophilus, kombucha culture, lactococcus lactis, bifida ferment lysate, enterococcus faecium, streptococcus salivarius, clostridium butyricum and streptococcus faecalis. 

Though probiotics are often used in supplements, more fermented food and beverage manufacturers are using probiotic strains in their products, especially in the growing alternative protein market.

Synbiotics are also becoming more widely used; the study found synbiotics were the most prevalent formulate in probiotics. Synbiotics are a combination of both prebiotics and postbiotics. A synbiotic ensures that probiotics will have a food source in the gut.

(Probiotics are live microorganisms, friendly bacteria that provide health benefits. Probiotics can be found in fermented food and taken as supplements. Prebiotics are dietary fibers that feed the probiotics. Postbiotics are an emerging concept in the “biotics” space — postbiotics are the waste byproduct of probiotics.)

“With probiotics, we are really only starting to scratch the surface with the development of synbiotics,” says Jens Walter, PhD, professor of ecology, food and the microbiome at APC Microbiome Ireland. 

The new generation of probiotics will depend on strains that are “efficacious in the gut,” Walter noted.

“If you look into the probiotic market, most of the lactobacillus species — and also species like bifidobacterium lactis — are not inherent organisms of the human gut. We’re using a lot of organisms that I would argue have an ecological disadvantage in the gut,” Walter says. “If you’re talking about next generation probiotics, I think what will become is we are looking for the key players in the gut, specifically key players that are underrepresented or linked to certain benefits, and then we are trying to put them back in the ecosystem.”

It’s challenging to find a prebiotic or postbiotic that is precise, he continues.

“Every human has a distinct microbiome. So it’s likely a synbiotic designed for one human may not be as functional in another human,” Walter says. “The opportunities here are tremendous.”

Daniel Ramon Vidal, vice president of research and development and health and wellness at the American food processing company Archer-Daniels-Midland (ADM), also spoke. He noted that the human body is made up of trillions of microbial cells, but we know little about these microbial worlds.

“There is an enormous amount of possibilities to isolate new strains that are living in our body,” Daniels says. “We need as much science as possible, that’s my message”

The panel agreed that postbiotics has become one of the next great concepts that scientists, manufacturers and gastroenterologists have latched onto. But consumers are not as familiar with postbiotics as they are with probiotics and prebiotics , notes Justin Green, PhD, director of scientific affairs for EpiCor, a postbiotic ingredient produced by Cargill. 

“This causes more confusion, so I think that’s going to be another interesting aspect of postbiotics — both the identity of what postbiotics are and how it confers its benefits and (how that will be) communicated to the consumer,” Green says.

Over several decades, the genus Lactobacillus became unmanageable, encompassing 262 species. Rudimentary research tools lumped any newly-discovered bacteria  into the genus, making the taxonomy “very screwed up.” 

“The lactobacillus taxonomy became a stack of dirty dishes — everyone knew somebody should do it, anyone could have done it, but nobody did it,” says Michael Gänzle, PhD, professor and Canada Research Chair in Food Microbiology and Probiotics at the University of Alberta. He spoke at a TFA webinar The New Taxonomy of Lactobacillus. “It has become very obvious that the genus is too diverse to group all or the organisms into a single genus. …We need taxonomy to actually describe which group of organisms they mean because if you say lactobacillus in the old sense, we mean a group of organisms that is so diverse that using the same genus name doesn’t make too much sense.”

The lactobacillus genus is large, regulated in many countries and economically important. Gänzle is one of 15 scientists involved  in a year-long project using sophisticated DNA tools to analyze the new taxonomy. Findings’ published in the April issue of the Journal of Systematic and Evolutionary Microbiology, spread the species over 26 genera, including 23 new (novel) ones. 

“The new taxonomy of lactobacilli means taxonomists have to navigate 23 new names, but maybe I can convince you that renaming the taxonomy is also the best thing since the invention of sliced bread because it does facilitate the communication on all things which relate to lactobacilli,” Gänzle says. He referred to the completed taxonomy as the “lactobacillus monster” because it covers 77 pages. 

Despite its heft, he’s proud of the completed project, which  reclassifies the genus into relevant groups. “It makes it easier to identify cultures of food applications,” Gänzle says. The group of authors also developed an online tool that makes it easy to look up old names and new names, and provides reference to (genome) sequence data at lactobacillus.ualberta.ca or lactobacillus.uantwerpen.be

Ben Wolfe, PhD, Associate Professor at Tufts University, moderated the webinar. Wolfe studies the ecology and evolution of microbiomes in his lab (and is a TFA Advisory Board member).“It’s really great to see this community coming around this very important problem,” Wolfe says. “This really helps clarify a lot of things for us. 

For the average artisanal fermented food producer, not much will change with the new taxonomy. Producers of traditionally fermented foods don’t put the organisms in their food or drink on their labels — it’s the companies selling starter cultures. 

“For someone who doesn’t buy and sell cultures, this doesn’t change,” Gänzle adds. “There will be a transition period until everyone is familiar with the names and putting them on the label. Most, if not all, can still be abbreviated with L.”

There are thousands of molecules in the food we eat, but most have yet to be identified. This is especially true in the world of fermentation. 

“Lactic acid is not the only byproduct of lactic acid fermentation,” says Suzanne Johanningsmeier, a research food technologist with USDA-ARS. During a TFA webinar, Johanningsmeier presented  her research into health-promoting pickled vegetables. “There could be hundreds or thousands of byproducts of this lactic fermentation. As an analytical chemist and someone who is very interested in the composition of foods, I find that fascinating and exciting and a world to explore.”

Johanningsmeier, a leading expert on the chemical and sensory properties of fermented food and veggies, notes that fermentation is a trending food technique. Consumers today want food that is plant-based, enhances gut health, introduces new flavors, made with simple labels and returns to tradition. 

“All these things have aligned and intersected for a fermented foods megatrend. It’s exciting to see so much momentum in the Americas rolling for fermented foods,” she says. “All of these trends are based on the belief that these are health promoting foods for consumption.”

The USDA-ARS office in North Carolina State University is staffed by five research scientists, and there are an additional 2,000 more affiliated scientists across the country. Their mission is to deliver scientific solutions to national and global agricultural challenges. 

“My long-term goal is to develop science-based technologies that enable the sustainable preservation of fruits and vegetables for production of high-quality, health-promoting consumer products,” Johanningsmeier says.

The most recent USDA-ARS study explored the potential health benefits of fermented cucumbers. Cucumbers are one of the top five vegetables preserved in the U.S. but the only one that’s not canned or frozen. The USDA-ARS found that fermented and pickled cucumbers include many beneficial by-products, including proline, bioactive peptides and GABA (Gamma-Aminobutyric acid, which works as a neurotransmitter in the brain). 

“Food processing has a negative connotation. But, actually, fermentation is processing and, as you can see, processing can be good. Processing can add things and certainly make food available to people year round,” Johanningsmeier says. “I think the idea here is how do we preserve [food] so we retain or enhance those inherent, health-promoting properties? The abilities we have now to more comprehensively look at composition are going to help us understand that in the future.”

Maria Marco, professor of food science and technology at University of California, Davis (and TFA Advisory Board member), moderated the discussion. Marco praised Johanningsmeier’s use of analytical techniques to implement fermentation technologies.

“These are exciting compounds, and we know that they have neuroreactive properties or antihypertensive properties,” Marco says. 

A new study shows kefir affects the microbiota-gut-brain axis. Researchers at APC Microbiome Ireland SFI Research Centre at University College Cork and Teagasc published their results in the journal Microbiome. They found that feeding mice kefir reduced stress-induced hormone signaling, reward-seeking and repetitive behavior. Interestingly, different types of kefir affected mice behavior and changed the abundance of gut bacteria. The researchers concluded that kefir should be studied as a dairy intervention to improve the mood and behavior in humans.

Read more (APC)