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Microbes matter: Everything you need to know about fermentation

We could close down farms, and start producing food from microbes instead. Doing so will avoid animal suffering, and make space for rewilding nature. Here’s what our future could look like if we take food production to the next level.

By Christian-Frederic Kaiser and Martin Reich

(Photo: Freepik)

Nothing stirs the emotions like food. It connects us to our felt origin, culture and heritage, and is, simply, pure pleasure. If we consider where our crops, meat and fish come from, we are immediately enveloped in fuzzy, warm images of herds grazing on green grass, a lonely angler, or the calmness of the countryside.

But something revolutionary might be brewing just around the corner, something that could fundamentally change the connection between farm and fork, opening the door to a future that decouples the familiar connection between soil, land and food – using the power of microbes.

The story began millennia ago, when a tiny microbe started to turn grapes into wine, barley into beer, or to put it scientifically, fermented saccharose into ethanol. A true miracle that occurred over 9000 years ago, when our neolithic great-grandparents turned from hunter-gatherers to brewers, a shift that may have contributed to the dawn of a more settled, beer-enjoying, agricultural way of life. The culprit is a microscopic yeast named Saccharomyces cerevisiae, also known as baker’s yeast.

And our deep connection to microbes does not end there. Lactic bacteria turn our milk into yogurt, ripen our sausages, and pickle our vegetables. Other microbes grow on our cheese to create delicious delicacies like camembert or brie. In other regions of the world, microbes ferment soy to miso, cabbage to kimchi, fish to traditional sushi, and cassava to the spice tucupi.

All around the globe, fermentation is an integral part of making food delicious, healthier and of greater shelf-life. The microbial world is everywhere, reaching from the soil, through the plate and into our own bodies. Communities of microbes, fungi, bacteria and various others act together to perform extraordinary tasks like turning thin air (nitrogen) into protein, thereby providing nutrients for all the plants we consume. Their bodies are on second glance tiny chemical factories producing a palette of wonderful things like flavours, medicines and colours.

All around the globe, fermentation is an integral part of making food delicious, healthier and of greater shelf-life

Our relationship with these little critters has not been the same since 1917, when James Currie discovered that a fungus, actually a mould with the name Aspergillus niger, could turn sugar into citric acid. The start of the biotech revolution!

Citric aid? This may sounds somewhat boring, but citric acid is everywhere in foods, medicine, cosmetics – the list goes on. The name comes from its original source, citrus fruits, but actually only 3–5% of lemon juice is citric acid. Nowadays we produce 2,000,000 tonnes of citric acid worldwide, most of it originating from this mysterious fungi.

Why does this matter? In the same year, the worldwide lemon harvest reached 1,000,000 tonnes, which sounds like a lot, but with their citric acid content (5%) we’d require 54 times more lemons to meet global demand. We could say that a single mushroom has saved the Mediterranean from being turned into a desert of lemons!

Saving land space is one of the great achievements of microbial helpers, but it does not stop there. In washing powder, enzymes produced with microbes allow us to cut washing temperature, saving energy. Microbial rennet and insulin produced by bacteria and yeast helped us to move away from calves and pigs as the main source of these products, pushing us toward animal-free production.

Sustainability can be profitable if we turn to the chemical powerhouses of nature.

A single mushroom has saved the Mediterranean from being turned into a desert of lemons

Nowadays, agriculture stands at the crossroads, under unprecedented pressure from climate change, a growing population and limited available land, while at the same time contributing to pollution and the biodiversity crisis.

The main and most pronounced reason is land use. Half of our planet’s habitable land is used to house livestock (38.5%) and grow crops (11.5%), replacing and displacing natural habitats and ecosystems and endangering around two thirds of red-listed species. An area the size of both Americas has been utilised to grow livestock, and meat consumption worldwide is still projected to increase.

The task is clear: cut down land use as much as possible and rebuild biodiversity.

On the other hand, agriculture has achieved tremendous progress in the past century. We’re now able to provide food for more and more people on our planet while using less and less land. The decoupling of land use and yield has followed innovations in agrochemicals, technology and breeding.

Still, food security stands on thin ice, with around 13% of the world population in 2019 facing food insecurity. With unprecedented natural catastrophes like the global drought of 2021–2022 and massive flooding in Pakistan, and the resulting economic crises, we need agriculture to be both more resilient and to have a much lower environmental footprint. And microbes could be there to help.

We need agriculture to be both more resilient and to have a much lower environmental footprint. Microbes could be there to help

But where do we start? Where does food start?

Nearly everything we eat starts out as a plant, fungus or animal, some of which we use directly and others we need to process into ingredients like flour, milk and oils. Then comes the magic: we remix all these components into something amazing like pizza, crème brûlée, or a green matcha smoothie with a hint of papaya. Microscopically, food has two basic structural components: a scaffold, or tissue, and a selection of chemicals.

The idea of chemicals always makes us feel insecure, but these are what makes food so important and enjoyable. They add nutrition, flavour, colour and vitamins. Now we are eating the world and are looking for a solution, what if we restart here?

What if we could reboot the way we produce all these ingredients and change their origin?

What if the next great microbial success would not be boring citric acid but mozzarella?

This is where the ingenuity of microbes becomes relevant. The transformation of a substrate like sugar into a product like ethanol (e.g. beer) by microbes is termed fermentation. With great advances in microbiology, genetic techniques and biotechnology, the scope of fermentation has moved far beyond just wine and yogurt. These were products of decades or even hundreds of years of blind trial and error. Great products. But remember: time is running out.

After over a century of work by microbiologists worldwide, exploring, collecting and classifying the microscopic world, we now have access to the natural chemical diversity of microbes, while genetic techniques allow us to select specific genes from this palette and combine them into novel technology to produce milk protein, for example.

Thanks to genetic knowledge of the fermentation skills of microbes, and thanks to advanced tools to change them, we are now ready for a renaissance of fermentation.

What if we could reboot the way we produce ingredients and change their origin? What if the next great microbial success would not be boring citric acid but mozzarella?

Imagine it’s 2042, let's say early summer. After the first rays of sunlight wake you, the individualised newsfeed on your smart wall automatically turns on and, well, you can’t take the first news of the day about the ongoing consequences of climate change without a strong coffee. As you drink, you reflect on the fact that coffee used to actually be made from roasted beans. From real plants. That still exists today, but the vast majority of coffee is now made in fermenters, by microorganisms. Some ingenious guys at a startup back in the 2020s somehow managed to implant the genetic information for coffee flavour into bacteria, or something like that.

You go to the kitchen and drink a glass of milk that has never seen a cow, remembering that this idea first took off in the US while Europe worried about the legal issues. It consumes much less land than cow’s milk – science says so, it’s written on the package. Slowly the coffee takes effect and your thoughts perk up. While holding the milk package in your hand, you try to imagine how many cows there would have to be today to produce milk for all the world’s population. That would be a global pasture.

Okay, enough dawdling, your smart lens tells you it’s time to hurry. On the bike and off to work. You always have a protein drink with you, for between meals. Microorganisms produced it from just air and solar energy.

At lunchtime, you and some colleagues go to a restaurant that makes fantastic burgers. They have a new recipe using something called “heme” made from Kobe cattle. No wait, this heme gives the meat of Kobe cattle its flavour, but nowadays it comes from microbes. Oh, and the burgers are not made of ground beef like they used to be, of course. It’s all plants.

Later you treat yourself to some chocolate, and what can we say: the cocoa butter is also a product of precision fermentation. This has taken pressure off the remaining ecosystems near the equator, because today almost 9 billion people want to eat chocolate and there just isn't enough land for all the plants that would be needed to grow the cocoa beans.

After work, you don’t go to the gym today, but to a pub with some buddies. The landlady welcomes you and puts a bowl of protein-rich crackers made from mushroom mycelium on your table before taking your orders. Mushroom mycelium is one of the things that have become most widespread in recent years. You can make so much out of it, since they are producing it in fermenters in large quantities. Actually one of those facilities is close to your home, on the roof of a city house. And you’ve heard they can even repurpose the residual materials as feed. Crazy.

The pub owner brings your beer. You want me to tell you how the beer has changed? No, some things just stay the same as they always were.


Just replacing animals with microbes could disrupt the recycling of waste products like manure for fertilise

Sounds amazing? It does, but it all depends on the limits of our world. Many open questions surround precision fermentation and microbial agriculture.

First, agriculture has constantly adapted and transitioned to technologies, economic practices, geography and cultures, leading to an intertwined system that builds upon itself. Just replacing animals with microbes could disrupt the recycling of waste products like manure for fertiliser, for example. Extensive cattle herding can promote biodiversity.

If more and more food originates from bioreactors, what happens to farmers, especially in the Global South?

Who owns the licences and patents behind these technologies?

Will we accept or reject this technology?

What about safety?

It all comes down to managing this technology and its products in a sustainable way, keeping ecology, social aspects and economics in check, while not forgetting about politics and the public. Public opinion and regulation can be big hurdles for every new innovation, especially in biology.

For the products of precision fermentation, the science is very clear that there is huge sustainability potential. And of course, it is important that new products are safe, but is it fair to regulate new products more strictly than traditional food, as with the EU’s Novel Food Law? Or does this prevent us from untapping what science tells us is huge potential? And isn’t hindering new solutions that contribute to sustainability actually a threat to our future safety?

We face a big challenge to secure food for everyone while freeing up land for nature to recover. We need a backup if crops fail, droughts ravage, soil erodes and areas become less fertile. Microbial food production could make us more independent, as microbes don’t need proper soil, they don’t need as much land and they can produce all year long independent of the weather, moving us away from animal-dependency.

So let’s talk about how we can harness the power of microbes, and reboot the way we think of and produce food.

Christian-Frederic Kaiser is a microbiologist pursuing a PhD at the University of Düsseldorf exploring the interaction between plants and soil bacteria. Martin Reich is a biologist who works as a life science communicator on topics related to sustainability, bioeconomy and biotechnology. They are both co-founders of the Germany-based ÖkoProg, an ecoprogressive network and member of RePlanet.


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