Measuring and Monitoring Fermented Food Microbiomes
Analyzing the microbiome of a fermented food will help manage product quality and identify the microbes that make up the microscopic life. Though diagnostic techniques are still developing, they’re getting cheaper and faster.
“Why should we measure the microbial composition of fermented foods? If you can make a great batch of kimchi or make awesome sourdough bread, who cares what microbes are there,” says Ben Wolfe, PhD, associate professor at Tufts University. “But when things go bad, which they do sometimes when you’re making a fermented food, having that microbial knowledge is essential so you can figure out if a microbe is the cause.”
Wolfe and Maria Marco, PhD, professor at University of California, Davis, presented on Measuring and Monitoring Fermented Food Microbiomes during a TFA webinar. Both are members of the TFA Advisory Board. During the joint presentation, the two gave an overview on microbiome analysis techniques, such as culture-dependent and culture-independent approaches.
Measuring Microbial Composition
Wolfe says there are three reasons to measure the microbial composition of fermented foods: baseline knowledge, quality control and labelling details.
“Just telling you what is in that microbial black box that’s in your fermented food that can maybe be really useful for thinking about how you could potentially manipulate that system in the future,” he says.
What can you measure in a fermented food? First there’s structure, which can determine the number of species, abundance of microbes and the different types. And second is function, which can suggest how the food will taste, gauge how quickly it will acidify and help identify known quality issues.
Studying these microorganisms — unseen by the naked eye — is done most successfully through plating in petri dishes. This technique was developed in the late 1800s
“This allowed us to study microorganisms at a single cell level to grow them in the laboratory and to really begin to understand them in depth,” Marco says. “This culture-based method, it remains the gold standard in microbiology today.”
However, there’s been a “plating bias since the development of the petri dish,” she says. Science has focused on only a select few microbes, “giving us a very narrow view of microbial life.” Fewer than 1% of all microbes on earth are known.
The microbes in fermented foods and pathogens have been studied extensively.“Over these 150 years we have now a much better understanding of the processes needed to make fermented foods, not just which microbes are these but what is their metabolism and how does that metabolism change the food to give the specific sensory safety health properties of the final product,” she says
Marco and Wolfe both shared applications of these testing techniques from research at their respective universities.
Application: Olives
At UC Davis, Marco and her colleagues studied fermented olives. Using culture-based methods, they found that the microbial populations in the olives change over time. When the fruits are first submerged for fermentation, there’s a low number of lactic acid bacteria on them — but within 15 days, these microbes bloom to 10-100 million cells per gram.
Marco was called back to the same olive plant in 2008 because of a massive spoilage event. The olives smelled and tasted the same, but had lost their firmness.
Using a culture-independent method to further study what microbes were on the defective olives, she discovered a different microbiota than on normal ones, with more bacteria and yeast.
The culprit was a yeast.“Fermented food spoilage caused by yeast is difficult to prevent,” Marco says. “New approaches are needed.”
Application: Sourdough
At Tufts, Wolfe was one of the leaders on a team of scientists from four different universities that studied 500 sourdough starters with an aim to determine microbial diversity. Starters from four continents were examined in the first sourdough study encompassing a large geographic region.
The research team identified a large diversity among the starters, attributed to acetic acid bacteria. They also found geography doesn’t influence sourdough flavor.
“Everyone talks about how San Francisco sourdough is the best, which it is really great, but in our study we found no evidence that that’s driven by some special community of microbes in San Francisco,” Wolfe said. “You can find the exact same sourdough biodiversity based on our microbiome sequencing in San Francisco that you can find here in Boston or you could find in France or in any part of the world, really.”
Wolfe and Marco will return for another TFA webinar on July 14, Managing Microbiomes to Control Quality.
- Published in Science
Pandemic Bakes New Bread Business
Sourdough was the “breakout star of pandemic-era kitchens,” so it’s no surprise that sourdough hobbyists are turning their newly-found craft into a profession. There’s a new wave of bakers obtaining Cottage Food Operations licenses so they can sell their homemade bread. Max Kumangai (pictured), an unemployed Broadway actor, was one of many who started a bread-baking business during the pandemic.
“It’s a really exciting time,” says Mitch Stamm, executive director of the Bread Bakers Guild of America. “Many small bakeries — one-person bakeries, two-person bakeries — they are doing beautifully.” The Guild says recessions have historically fueled passion in cooking and baking. Home bakers are finding their new quarantine hobby is a passionate career move, allowing them to create delicious food and socialize with customers.
“For sure there was a feeling, ‘I hate my job, I hate my life, I’m going to wake up and follow my heart,’” says Penny Stankiewicz, a pastry and baking arts instructor at the Institute of Culinary Education. That school received 85% more applications in 2020 compared to 2019.
Read more (The New York Times)
- Published in Business
Building a Fermented Brand
Behind every fermented food or beverage is intriguing science that creates a pleasantly tangy taste. Customers want to know all about that chemical process, right?
No. Stop geeking out and appeal to the foodie instead.
“This is about the joy of eating, and so when you over-science me and you over-gut me, I forget the joy of eating. Remind yourself that your most important message is how pleasant, how tasty, how engaging, that’s the pleasure of eating, and then you can tell me how you make that pleasure,” says Sasha Strauss, managing director at Innovation Protocol (a marketing consulting & design agency). Strauss shared his brand strategy tips in the TFA webinar Building a Fermented Brand. He stressed fermented brands need to avoid getting stuck in the “scientific nuance of how you make your products. I’m not saying delete the science, just don’t make it the marquee.”
Alex Corsini, founder of frozen pizza company Alex’s Awesome Sourdough (and TFA Advisory Board member) agrees. Corsini, who moderated the webinar, says he began his brand with a heavy emphasis on the science of fermenting sourdough.
“Our customer didn’t really respond to that. And that’s something I see in fermentation all too often, is people aren’t selling the actual benefit. They want to understand the benefit, so that’s what you lead with,” Corsini advises.
If you’re selling kombucha, for example, share that it’s a feel-good product that will make you feel better than a soda, Corsini says. Don’t make your selling pitch the SCOBY’s technical specifications.
Teach, Don’t Sell
“I don’t understand fermentation. I don’t understand the health benefits. I don’t understand its cultural origins. I don’t understand what section to buy it in. I don’t understand what to eat it with or who to serve it too. Your first duty as a brand is to help me make sense of this, help me understand it,” Strauss says. “It’s not your job to be the sexiest, raciest, the most innovative, it’s your job to help me understand. And where understanding sits in the consumer’s mind is where buying behaviors originate. So the first and most important duty of your brand is to simply help me not feel alone, help me not feel confused, help me not feel overwhelmed.”
By educating the consumer, by inspiring them to learn about fermentation, “they will be indelibly connected to you,” Strauss continues. “They will prefer you. They won’t wonder if your price is a penny cheaper, they’ll prefer you because you’re who they learned from. We buy who we learn from.”
There’s not enough room on a label to detail all the health benefits or the scientific details of a product. But this information can go on a brand’s website, social media page or table-top display at a trade show or farmer’s market.
“I hope that your audience doesn’t hear from you just once,” Strauss says. They should find a video of your product on Instagram, find recipes on your website and see an ad in the local paper. Brands need to create multiple opportunities to engage, “don’t try to cram all of your value in a single channel.”
A New Economy
The COVID-19 pandemic has permanently changed the economy. Consumer lifestyles have changed, too, and these new behaviors create opportunities, especially for fermented products that are healthy and flavorful.
“Historically, if you were trying to build a consumer packaged goods brand, it was really about your resume, your long list of accomplishments , your heritage in farming, your understanding of the chemistry and that was what marked the person, the business, the brand,” Strauss says. “But actually now, it’s really about how you resonate, how I connect with you, how you inspire me, and that doesn’t require a long history, that requires a contemporary participation.”
“In a world where the audience is starting and ending their search digitally, each of the things that you share, post, write about, blog about, video dialogue about, those things are little breadcrumbs that will never go away,” Sasha says. “They’re little trails that lead to your brand, lead to your resources, lead to your understanding and this is powerful.”
Consumers rejected traditional brand loyalties this past year. They’re increasingly open to new brands, curious about new cultural flavors and want healthy food. Critically, Strauss points out, they want to purchase from socially responsible brands. “In a post-covid era, we want a brant to also do good,” he says.
Producers must make conscious choices about the farmers they use — how are they improving soil health? What is the environmental impact of their distribution line?
“Understand you have to make an impact, somehow do good for the world while building business,” Strauss says.
- Published in Business
Trends in Pandemic Eating
Consumers increasingly embraced adventurous and healthy food over the last twelve months, but “a big pandemic winner is fermented foods.”
An article from the Associated Press details how, now a year into isolation, people are cooking beyond comfort food. They’re “embracing foods long forgotten or rejected for taste, texture or smell.” Anne Alderete (pictured) details how she is finally enjoying natto (fermented soy beans) after rejecting it for years.
Read more (Associated Press)
- Published in Food & Flavor
The World of Fermented Foods
In the latest issue of Popular Science, a creative infographic illustrates “the wonderful world of fermented foods on one delicious chart.” It represents “a sampling of the treats our species brines, brews, cures, and cultures around the world,” and is particularly interesting as it shows mainstream media catching on to fermentation’s renaissance. Fermentation fit with the issue’s theme of transformation in the wake of the pandemic.
Read more (Popular Science)
- Published in Food & Flavor
Does Geography Matter for Sourdough Flavor?
Results of the first large-scale study of sourdough starters were released last week — and the conclusions are fascinating, challenging myths about sourdough. Scientists from four different universities studied 500 sourdough starters from four continents, with an aim to determine microbial diversity.
“We didn’t just look at which microbes were growing in each starter,” says Erin McKenney, co-author of the paper and an assistant professor of applied ecology at North Carolina State University. “We looked at what those microbes are doing, and how those microbes coexist with each other.”
The most striking finding: geography doesn’t matter.
Sourdough enthusiasts preach that location and climate will alter sourdough flavor. San Francisco has long held bragging rights for the most distinctive taste profile. But, of the 500 samples, there was little evidence of geographic patterns.
“This is the first map of what the microbial diversity of sourdoughs looks like at this scale, spanning multiple continents,” says Elizabeth Landis, co-lead author of the study and a PhD student at Tufts. “And we found that where the baker lives was not an important factor in the microbiology of sourdough starters.”
Alex Corsini, CEO and founder of sourdough pizza brand Alex’s Awesome Sourdough (and TFA advisory board member), says the research “demystifies the misconception that sourdough is only good in certain pockets of the world such as San Francisco.” Great sourdough, he says, is about the raw materials.
“It further shows why sourdough is ubiquitous all over the world — starters can thrive anywhere as nature provides the magic and bakers just need to be in a position to coax out a result without ruining the magic — the magic here being the microbial balance needed to ferment and levain baked goods,” Corsini says.
The research also found there is no one single variable responsible for sourdough variations, bucking conventional baking wisdom.
“What we found instead was that lots of variables had small effects that, when added together, could make a big difference,” says Angela Oliverio, co-lead author of the study and a former PhD student at the University of Colorado, Boulder. “We’re talking about things like how old the sourdough starter is, how often it’s fed, where people store it in their homes, and so on.”
As a commercial sourdough producer, Corsini values the “low and slow” process to master a sourdough batch, especially when making it consistently on a large scale. Alex’s Awesome Sourdough undergoes a 70-hour ferment using high-quality flour, filtered water and a decades-old starter.
“Although location makes little or no impact on the starters microbial ecosystem, regulating temperature and time is fundamental and adjustments need to be made based on the location you are in (hot climate, cold climate, humidity, etc.) to get a desired result,” Corsini says. “We make slight adjustments throughout the year to ensure a consistent texture and flavor in our dough.”
The study found variations in dough rise rates and aromas were due to acetic acid bacteria, “a mostly overlooked group of sourdough microbes.” The bacteria slowed the rise time and gave the sourdough a vinegary smell. Researchers were “surprised” that 29.4% of the samples contained acetic acid bacteria.
“The sourdough research literature has focused almost exclusively on yeast and lactic acid bacteria,” says Ben Wolfe, co-author of the study, associate professor of biology at Tufts University (and also a TFA advisory board member). “Even the most recent research in the field hadn’t mentioned acetic acid bacteria at all. We thought they might be there to some extent, since bakers often talk about acetic acid, but we were not expecting anything like the numbers we found.”
The 500 sourdough starters studied mostly came from home bakers in the U.S. and Europe. Researchers performed DNA sequencing for each sample, narrowing down to 40 starters as being representative of the diversity of the original array.
Those 40 were: assessed by sensory professionals for aroma profile, chemically analyzed to determine the organic compounds released by each and then measured for dough rise time.
“I think it’s also important to stress that this study is observational — so it can allow us to identify relationships, but doesn’t necessarily prove that specific microbes are responsible for creating specific characteristics,” says Wolfe. “A lot of follow-up work needs to be done to figure out, experimentally, the role that each of these microbial species and environmental variables plays in shaping sourdough characteristics.”
“And while bakers will find this interesting, we think the work is also of interest to microbiologists,” Landis adds. “Sourdough is an excellent model system for studying the interactions between microbes that shape the overall structure of the microbiome. By studying interactions between microbes in the sourdough microbiome that lead to cooperation and competition, we can better understand the interactions that occur between microbes more generally — and in more complex ecosystems.”
The research, “The Diversity and Function of Sourdough Starter Microbiomes,” was done with support from a National Science Foundation grant.
- Published in Food & Flavor, Science
The Science Behind Sourdough
Sourdough has become the darling of the pandemic pantry, as people experiment with a starter of microbes in their home kitchen. Scientists are just beginning to “discover that the microbes in a sourdough depend not just on the native microbial flora of the baker’s house and hands, but also on other factors like the choice of flour, the temperature of the kitchen, and when and how often the starter is fed,” according to an article in Scientific American. The magazine interviewed multiple microbiologists on the science behind a great sourdough loaf.
“When we study sourdough science, we learn that we know remarkably little for a technology that’s — what? — 12,000 years old,” says Anne Madden, a microbiologist at North Carolina State University.
Read more (Scientific American)
- Published in Food & Flavor
Stopping “Sourfaux” in the UK
Artisan bread bakers in the UK are banding together for Sourdough September, pushing for new government legislation to stop the rise of “sourfaux” bread. Laws in the UK allow retailers to sell unwrapped bread loaves without displaying an ingredient list.
Writes the Real Bread Campaign organizer Chris Young: “In the hands of skilled Real Bread bakers, this longer, slower fermentation, allows lactic acid bacteria in the starter to cause changes in the dough that result in bread with a glossy crust and crumb, and a greater complexity of flavour and aroma.”
The UK government promised in 2018 to protect consumers from buying products erroneously label led as “sourdough.” But no action has been made. More than 50 UK bread bakeries have launched their own labeling promise, signing The Sourdough Loaf Mark scheme last month, urging all bread makers to display a full ingredient list.
Read more (Food Navigator)
- Published in Food & Flavor
Sour Sells
American’s flavor choice of 2020: the funkier, the better. Fermentation reigns as sour becomes a selling point. A new article in Yahoo Life highlights fermented food and drink ancient roots and modern revival. A naturopathic doctor, kombucha brand leader, food influencer, wine shop owner and chef/owner of two Korean restaurants share their thoughts on why people love the “interesting and complicated” flavors of fermented food. Fermentation delivers on gut health benefits, is made with clean, unprocessed ingredients, preserves seasonal ingredients and “tells a story.”
The article continues: “They’re nuanced, many-layered. Kimchi and sourdough alike smack of acid and sour-sweet brine, even for those of us with less-than-refined palates. They taste like the process of aging. And while the wellness revolution would have us believe that fermented food’s uptick in popularity is merely a product of the fact that we’re eternally prepared to flirt with anything that just might make us feel better, the phenomenon cuts deeper than that. There’s something to be said for flavor that comes with a narrative — that tastes of its own timeline.”
Read more (Yahoo Life)
- Published in Food & Flavor
“Backslop Romance” — Inoculation, Not Contamination
By: Marina Jade Phillips, Trellis & Co.
The first two months of 2018 marked both my first trip to Mexico and my first bicycle tour. Living on two wheels did not slow my fermentation habit; I toted stainless steel jars of fermented vegetables in my panniers. I credit consuming lacto-bacteria with my lack of stomach troubles that can plague travelers in South America. Regularly introducing healthy bacteria into our digestive tract is a great way of inoculating our body with microbes that are on our team. The amount of attention probiotics have received in recent years is long overdue. Traditional cultures have known about the delicious and health-promoting qualities of fermented foods for hundreds of years, even before it was scientifically proven.
Backslop is Such Beautiful Word
Contamination and inoculation are two sides of the same food processing coin: the impact of a small quantity of the right or wrong material can be drastic. The former is the stuff of nightmares for food companies forced to recall tainted products, and suffering travelers perched atop or hunched over a toilet. The latter is how fermented flavors have been passed down through time, sometimes across generations, from one bottle, crock, or barrel to the next. Inoculation is so ubiquitous to the craft that traditional sausage makers gave it a name: backslop.
Backslop, unsavory as it may sound, simply refers to the practice of saving a bit of the last successful batch and incorporating it into the new one, ensuring a small number of the micro-organisms that populated the previous batch will go forth and multiply. There are several reasons why this technique is valuable to both professionals and home cooks. Foremost, the time required for complete fermentation decreases dramatically. A new jar of sliced cabbage or jug of fresh squeezed fruit juice is teeming with all kinds of bacteria and yeast, some of which will produce the desired results, and some of which will produce something inedible.
By introducing a healthy colony early in the process, desirable microbes get a head start and usually out compete less desirable ones in the race to inhabit a new environment. If those microbes have a particularly unique characteristic (champagne yeast produces more carbon dioxide than other wine yeasts, for instance), that character can be reproduced, sometimes leading to outstanding strains by which certain makers and regions become famous.
A 5-Year Love Affair
In more humble corners of the globe, far from French vineyards, I once had a relationship with a sourdough starter that lasted five years.
A sourdough culture becomes more complex with age, and as time went by she (yes, she—around her first birthday I named her Henrietta) developed her own unique flavor. One morning, I came into my kitchen and saw Henrietta’s container on the floor, licked almost all the way clean. A dog had gotten up on the counter, somehow removed the lid, and all but devoured my precious bread making ally. I scraped the dried crust of starter that remained from the edges of the bowl and rehydrated it with water.
Over the next few days I added a bit more flour and water at regular intervals, and in less than a week my robust friend was back in action. I could have sighed, cursed dogs under my breath, and made a new starter, but I was attached to Henrietta, and thrilled to revive her with such little material.
The beginning fermenter has a few options for ensuring success. Of course, there is always the option of simply hoping for the best. Usually, if the food to be fermented is fresh and healthy and the containers and hands in contact with it are clean, odds are in our favor that the microbes that make things sour and bubbly are going to win. However, a splash of the liquid floating around the top of high-quality yogurt (look for something with “active cultures”) will introduce a bit of the right bacteria and speed the process along. A small slosh of juice from a thoroughly fermented sauerkraut or brined vegetable jar will help get the next one going.
Those interested in experimenting with fermented dough will be delighted to know that a sourdough starter is incredibly easy to make: stir equal parts flour and water every day until it smells sour. Wild yeast lands on top of the mixture and is incorporated with every stirring.
Aid this process by dropping an unwashed and unsprayed berry (grapes work best) into the mixture for a couple of days (retrieve the berry before it starts breaking down). Yeast which covers the skins of all fruits will slough off and populate the latent starter. To keep this culture thriving, the sourdough baker saves a small amount of the starter and adds to it more flour and water. Starters exist that are rumored to be hundreds of years old, passed down in just this way.
Practice Safe Fermenting
Interestingly, foods that are not fermented are more prone to contamination from bacteria that can make us very ill, and in the worst cases, kill us. The culprits in large and small-scale food poisonings are often raw and unfermented vegetables. By fostering beneficial bacteria in a salty and acidic environment, we can safely enjoy raw vegetables with all their fiber and nutrient content without the risk of ingesting pathogens.
About Trellis & Co.: We started as a family business created by a bioengineer living on a homestead in one of the remotest areas in the Lower 48. When “running to the store” is a 4-hour drive, every purchase must be a robust and functional investment. Here at Trellis + Co. we design products worth investing in.
Our lifestyle inspired our line of garden-to-table kitchen tools. As gardeners, cooks, and canners, we develop creative solutions to our own kitchen conundrums and pass on that wisdom to you. Also, since we’re kind of obsessed with the planet, our products are designed to last a lifetime — keeping money in your pocket and garbage out of landfills.
- Published in Food & Flavor