A Hamburg–Lisbon startup is turning agricultural waste into protein powder using microbes, producing vegan dog treats today and working towards reshaping tomorrow’s food system.
MicroHarvest
MicroHarvest was founded in 2021 by Katelijne Bekers, Luísa Cruz, and Paulo Teixeira, and operates between Hamburg and Lisbon. The company specialises in microbial fermentation, a process that uses bacteria to convert by-products from the agricultural industry into protein-rich biomass.
At its Lisbon pilot plant, based in a former military food factory now known as the Unicorn Factory, large fermenters are filled with microbes and fed residual sugars from crops. Within 24 hours, those microbes multiply rapidly, creating a thick broth that is harvested, inactivated, and dried into a beige powder resembling flour. The result is a product with over 60 per cent protein content, alongside fibre, essential amino acids, iron, and vitamin B2.
MicroHarvest describes its approach as sustainable, scalable, and highly efficient. A life-cycle analysis suggests its process generates only 1.4 kg of CO₂ per kilogram of protein, two to three times less than most plant-based proteins and dramatically less than beef or dairy.
What Products Are Already on the Market?
While human consumption awaits regulatory approval, MicroHarvest has already moved into the pet-food sector. For example, in 2024, the company partnered with German brand VEGDOG to launch Pure Bites, a dog treat made with microbial protein, potato, and apple pomace. The snack was introduced at Interzoo Europe, one of the continent’s largest pet-food trade events, and is marketed as hypoallergenic, nutritious, and suitable for dogs with intolerances.
Dogs More Receptive To Microbial Protein Treats
Interestingly, palatability trials carried out by MicroHarvest found that dogs were more receptive to microbial protein treats than to poultry-based alternatives, with 85 per cent acceptance compared to 75 per cent. Also, a consumer survey across the UK and Germany showed similar openness, with around 78 per cent of dog owners saying they would consider buying pet food containing microbial protein.
This early focus on pet nutrition appears to make sense for the company as the animal feed and pet food sectors are less tightly regulated than human products, thereby enabling a faster route to market. They also represent a growing sector where sustainable, alternative protein sources are in high demand.
How the Technology Works
MicroHarvest’s process is based on microbial fermentation, a technique familiar from traditional foods such as yoghurt, kefir, and sauerkraut. The company cultivates specific bacterial strains in bioreactors, using agricultural by-products like molasses or other sugar streams as feedstock.
Once the microbes have multiplied, the biomass is separated, the cells are inactivated through heat treatment, and the material is dried into a stable protein powder. The entire cycle takes less than a day, compared with months for growing soy or years for raising livestock.
According to the company, the method reduces land use by up to 99 per cent and cuts carbon emissions by more than 70 per cent compared to beef. Also, because the process is carried out indoors, it can be established close to existing food or feed industries, bypassing the need for extensive farmland.
Why It Matters for Sustainability
The global demand for protein is expected to increase by around 50 per cent by 2050. Meeting that need through conventional farming would intensify deforestation, water use, and greenhouse gas emissions. Alternative proteins are seen as essential to bridging the gap without worsening environmental pressures.
A 2022 study in Nature suggested that replacing just 20 per cent of global beef consumption with microbial proteins could halve annual deforestation rates by mid-century. For companies like MicroHarvest, these figures highlight the potential of microbial protein to play a serious role in climate and food-security strategies.
MicroHarvest’s stated aim is to deliver protein that is not only sustainable but also versatile. Beyond dog treats, the company is developing applications in aquaculture feed, livestock diets, and eventually human food products such as shakes, protein bars, and dairy alternatives.
The Wider Landscape of Fermentation-Based Proteins
It’s worth noting here that MicroHarvest is certainly not alone in pursuing microbial solutions. The sector has attracted nearly $1 billion in global investment over the past year, with Europe claiming close to half of that. Examples of other companies in this space include:
– Finland’s Solar Foods, which has developed Solein, a protein made from microbes fed with hydrogen and carbon dioxide captured from the air. Its first commercial facility is under construction and it has received approval for human consumption in Singapore.
– Germany’s Formo, which is using precision fermentation to produce casein proteins for dairy-free cheese.
– Dutch company Vivici, which has raised over €30 million in 2025 to scale animal-free whey proteins made with microbes.
– UK-based Enough cultivates fungi to create mycoprotein, used in plant-based meat substitutes.
Also, large food companies such as Nestlé and Unilever are partnering with startups to explore microbial protein for mainstream products, seeing the potential for lower-impact ingredients that can appeal to sustainability-minded consumers.
Hurdles
Despite the momentum, microbial protein faces some serious hurdles. The first is, of course, regulation. MicroHarvest has already submitted a full dossier to the European Food Safety Authority seeking approval for human use. The process involves extensive safety and DNA screenings, and while the company is optimistic, approval timelines remain uncertain. Other alternative-protein startups have seen years of delay in Europe, forcing some to launch in more permissive markets such as Singapore.
Cost is another key concern. While microbial fermentation is highly efficient, building large-scale production plants requires significant capital investment. MicroHarvest has announced plans for a 15,000-tonne facility by 2027, more than 40 times its current output, but scaling to that level will test both its technology and its financial backing.
Consumer perception is a further challenge. For example, although microbes are commonplace in familiar foods, the idea of eating “bacteria powder” may not appeal to all shoppers. Industry observers note that how the products are framed, whether as “fermented protein” or as “next-generation ingredients”, could influence public acceptance.
The competitive landscape is also intensifying. For example, dozens of startups are experimenting with different microbes, feedstocks, and fermentation technologies. At the same time, insect protein, cultured meat, and plant-based innovations are all vying for space in the growing alternative-protein market.
What Does This Mean For Your Organisation?
The balance for MicroHarvest and its peers lies in proving they can deliver at scale while keeping costs competitive and building trust with regulators and consumers. If they succeed, microbial proteins could become more than a niche ingredient, offering a reliable and efficient source of nutrition at a time when global demand is set to rise sharply. For UK businesses in particular, this could mean opportunities in supply chain partnerships, retail adoption, and product innovation across both pet and human food markets. It also raises questions for existing agricultural producers, who may need to adapt to the emergence of new protein streams that use fewer resources and appeal to environmentally conscious buyers.
For policymakers and regulators, the challenge will be how quickly they can evaluate and approve these technologies without compromising safety. Investors, meanwhile, will be watching closely to see which companies can move from pilot plants to full commercial output. MicroHarvest’s ambition to open a 15,000-tonne facility in just two years will be one such test.
The future of food will not be decided by a single technology, but microbial protein now has a seat at the table. Whether it becomes a mainstay of diets or remains limited to specialist markets will depend on cost, regulation, and public acceptance. For now, the evidence suggests it has the potential to deliver real sustainability gains, and businesses across Europe and beyond are positioning themselves to find out just how far this promise can go.
