The magical microbiome

January 20, 2023 - 6 minutes
Photo/Shutterstock

By Brittany Niccum and Han Wei

Now that we are past the holiday season and time when we might have over-indulged on rich foods, many of us are seeing how we can help our bodies bounce back. Science can help.

Every environment – organic or inorganic – has a myriad of microorganisms living on the surface and inside. Called the microbiome, the bacteria in this unique mix have made a significant contribution to the food we eat. In many of the foods we enjoy, fermentation in the biome begins the process of breaking down chemicals that release the amazing flavors in chocolate, cheese, kimchee, beer, sauerkraut, miso, and sourdough bread, just to name a few. 

Thanks to science, we can begin to understand and harness the magic of the microbiome to improve food production, and our bodies’ response.

It is hard to go a single day without eating fermented foods because they’re part of the diet in nearly every country, holding an important place in regional and cultural identity. 

Depending on the customs of a country, region, or town, nearly the same process is used to create cheese whether from cow, goat, or sheep’s milk. It begins with separating the solid curd from the liquid whey to transform the curd; but the microbiome inside and outside of any cheese is what contributes to the unique flavor of the final product.

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From cave to table

Anyone who’s enjoyed Cheddar or Parmesan made in different parts of the world knows that no two varieties taste the same. Once those cheeses are formed into wheels, some cheesemakers put the cheese into caves to age. And that’s when the unique microbiome in that cave gets to work. Each wheel is colonized by the same community of microorganisms. So when that same cheese is made over and over again – in some cases for a thousand or more years – it always tastes the same.

That’s because those particular bacteria and other microbes like to grow together in that particular environment. They cover the cheese, feeding off it as they protect each other from outside invading species. The rind of the cheese is easier to see on soft cheeses such as Brie, but the outside of every kind of cheese has a layer of microbes that ultimately create the outer coating.

What can be learned from studying the small microbiomes of cheeses with specific bacteria and fungi is how slight differences will impact how they perform. While these combinations are all different and behave differently, it’s important for each unique combination to make up its own community to survive and thrive.

Yet some cheeses, unlike the production of other fermented foods, include an ingredient that isn’t sustainable for meeting the demands of growing human populations – the enzyme rennet.

Engineering bacteria

Rennet is found in the stomach of calves and is extracted after their death. This particular material is only created by certain animals in their stomachs to digest food. However, thanks to the science of genetic sequencing, it’s now possible to engineer bacteria to produce rennet. 

The same fermentation process used to make insulin and other genetically engineered enzymes produces the rennet enzyme, suitable for large-scale commercial cheese production, although rennet is not found in all cheeses on the market today.

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This approach is better for the environment because it dramatically reduces the burdens created by livestock. It lessens the requirement of land and water.

Studying microbiomes also creates an opportunity to improve the long-term quality of our food supply by studying and maintaining the health of the gut microbiome of animals. The first step is to know what’s there, and a lot of bacteria grow only in the intestines. We can’t watch the bacteria interact in their environments and therefore can’t answer the next important question – what are the bacteria doing?

Sequencing has helped us figure out the makeup of the microbiome of different animals and plants, and, in some environments, sequencing has helped scientists identify changes that happen if you alter the mix of microbes present at the beginning of the creation of the microbiome or the conditions of the environment. This same approach can be used to develop new kinds of cheese or troubleshoot why a batch of yogurt didn’t ferment properly.

Expanding the magic

Figuring out the challenges and complexities in a fermented food isn’t always easy for small-scale production or when working in your kitchen.

As we study the microbiome of a fermented food, we now have the possibility to genetically modify the microbiome. This can present several advantages – including speeding up the process or avoiding a potentially large-scale process mistake.

We have all the tools to identify a microbiome and understand what it looks like. It’s just a matter of adapting which microbes are there and what they’re doing in our fermented food of choice to make it better.

We have good evidence showing that specific bacterial species do specific things, but only in certain environments. But we don’t have enough data yet. For example, there is a particular bacterium that has been associated with improving gut health and reducing anxiety in mice

Studying pet microbiomes

Some work has been done to correlate that to pets. Dogs and cats have gut microbiomes similar to humans. That makes sense because we share the same external environment. But studying their microbiomes in conjunction with ours is important because we can learn about things that change their health that could have an impact on humans as well.

Many fermented foods are eaten without people ever knowing it is fermented, and some are sought out for their ability to reduce excess bloating and other gastrointestinal discomfort. Kombucha and yogurt are examples. Carbohydrates can be broken down in the fermentation process, lessening the digestion workload on our small intestines. This may also explain why eating sauerkraut on New Year’s Day is a popular tradition for some people after a night of celebrating.

While some may say there’s a bit of magic in the making of cheese and fermented foods, science is greatly aiding the understanding and analysis of the process. As more diet trends come and go – and to help those with certain intestinal issues – we could see a growth of diets rich in fermented foods. This could lead us to one day finding ourselves with more fermented foods in production as we can now better understand and copy the fermentation process, and then accelerate it through automation.

Brittany Niccum is a product manager at IDT and most recently at Beckman Coulter Life Sciences.

Han Wei is a market development scientist at Beckman Coulter Life Sciences with a focus on building collaborative relationships with external partners.

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