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Case study: Discovering new enzymes to upcycle food waste

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How the MGnify microbiome-protein database is helping researchers identify cocktails of enzymes to upcycle animal bones and other by-products

Credit: Karen Arnott/EMBL-EBI


  • To support a growing global population, the food industry needs to rethink production processes while simultaneously reducing waste. 
  • With the right biotechnological solutions, animal by-products, such as bones and skin, could be upcycled into protein powder for animal and human consumption. 
  • Researchers are using the vast protein space in EMBL-EBI’s MGnify microbiome data resource to identify new enzymes that can help extract animal proteins from bones in a robust and sustainable manner. 

Challenge – more protein, less waste

The United Nations predicts that the global population will peak before the end of the century at just over 10.4 billion people. To feed this growing population, countries need to devise new approaches for sustainable food production. 

One significant issue in animal production is the large amount of by-products, such as bones and skin. For instance, about 45% of a salmon’s total weight currently goes to waste because many people only use the fillet meat. Researchers have been exploring ways to use more of an animal’s body mass in food production, and consequently reduce waste and increase yields. 

One way forward is to extract animal proteins from animal by-products or plus-products, such as bones and skin, and use them in protein powders. Bones are particularly robust, however, making it a challenge to degrade and extract protein from them. To overcome this difficulty, researchers need a powerful agent, such as an enzyme cocktail.

What are enzymes?

Enzymes are biological catalysts. They drive chemical reactions without the need for lab-made chemicals that sometimes pollute the environment. Enzymes can be used to improve industrial processes.

Proof of concept

Scientists at NORCE, an independent research institute in Norway, found a solution at the bottom of the ocean. They studied worms and microbes that live on the seafloor and ‘eat’ the bones of dead whales, extracting nutrients. These bacteria contain specific enzymes with bone-degrading properties.

This is an ingenious ability, but it does come with some limitations. For example, many enzymes are sensitive to heat, which means they risk losing their properties above a certain temperature.

Having identified bone-degrading enzymes that live in marine environments, NORCE researchers are now trying to find out if they could use these enzymes in industrial processes, considering the following requirements:

  1. large-scale production 
  2. expedited bone degradation (in nature, the process takes months)
  3. determining the optimal temperature for activity
  4. ensuring scalability and sustainability

“There is a great need to discover both better and new enzymes for the industry. And find the right combinations, just like in a cocktail. This new study provides us with a good starting point where we see that the enzyme cocktail has a greater effect than single enzymes when it comes to bone degradation,” said Antonio Garcia-Moyano, Senior Researcher at NORCE.

Using MGnify to identify bone-degrading enzymes 

Now that researchers know what bone-degrading enzymes look like, they can use this knowledge to identify related enzymes with even more promising properties. To this end, researchers are taking advantage of the treasure trove of microbiome data housed in the MGnify database, which is managed by EMBL’s European Bioinformatics Institute (EMBL-EBI). 

A publicly accessible resource, MGnify enables researchers to share, analyse, discover, and compare microbiome and protein sequence data in a comprehensive manner. It’s a unique hub of large microbiome datasets from a range of environments, including the world’s oceans. 

“MGnify will help us to identify the right enzyme or cocktail of enzymes with the traits required for a specific bioprocess.”

– Antonio Garcia-Moyano, Senior Researcher at NORCE

Scaling up

Once a suitable cocktail of enzymes is identified, the development process moves to the next step, where researchers work with a company that produces enzymes for a range of applications. One such company is the UK-based Biocatalysts Ltd, which manufactures enzymes on an industrial scale. 

Biocatalysts Ltd, part of the BRAIN Biotech Group, develops, among other things, enzyme formulations for food processing in areas such as dairy, baking, brewing, and more.

“Bioinformatics is very important to identify new proteins of industrial interest and the advent of artificial intelligence tools have helped refine the development, scale-up, and manufacturing of specialty enzymes for different industrial applications,” said Lilly Amore, Head of Technology Development at Biocatalysts Ltd. 

Through a previous collaboration with the MGnify team at EMBL-EBI, Biocatalysts Ltd developed MetXtra™, a metagenomics database that includes open datasets from MGnify as well as proprietary sequences. MetXtra™ has been a valuable upstream tool at Biocatalysts Ltd to identify new enzymes and offer customised solutions in different market sectors. 

“Bioinformatics is very important to identify new proteins of industrial interest.”

– Lilly Amore, Head of Technology Development at Biocatalysts Ltd.

Developments of Biocatalysts Ltd and BRAIN Biotech AG have expanded the potential of MetXtra™ and the sequence-driven discovery approach even further. By fusing the MetXtra™ data and BRAIN Biotech’s proprietary metagenomics library SeqPool, the BRAIN Biotech group offers one of the most powerful databases for the discovery of new enzymes of industrial interest. The high diversity of this in-house database provides access to more than 99.8% novel sequences expanding the publicly-known sequence space. This database is integrated with advanced bioinformatics and AI workflows for sequence- and structure-driven enzyme identification. More widely, pipelines like MetXtra™ and SeqPool can be used to search the vastness of protein sequence and structure space to identify suitable enzyme combinations to enable bone degradation in an industrial setting.

An interdisciplinary effort

This work of identifying suitable enzymes for bone degradation is part of the wider BlueRemediomics project coordinated by Rob Finn at EMBL-EBI. Blue Remediomics aims to systematically catalogue marine microbe datasets to facilitate the development of industrial processes that reduce waste, increase the reuse of natural and man-made products and by-products, and improve aquaculture processes. The project closely aligns with EMBL’s Microbial Ecosystems and Planetary Biology themes.  

Bone degradation is just one of many exciting applications explored by BlueRemediomics, which assembles experts from different disciplines. With the help of Christine Orengo from University College London (UCL), the team is leveraging artificial intelligence to search huge volumes of data to find the most suitable enzyme candidates.

The blue economy requires a huge range of expertise and skills, spanning microbiologists, molecular biologists, data scientists, bioinformaticians, biotech specialists, food manufacturers, and more. Translating a concept from the research lab to the market is a complex and lengthy process, but it can have significant benefits. 

Cross-disciplinary projects like BlueRemediomics represent an ideal platform to unite experts from diverse fields and explore the feasibility of new biotechnologies with potential applications in different industries. 

The final products

Other companies can use such mass-produced enzymes to process animal bones into create protein powder that can be upcycled into products for human or animal consumption.

NORCE scientists are in discussion with Norilia, a Norwegian company working on creating new products from meat and poultry industry by-products. The company’s mission is to ensure that the whole animal is used and waste is minimised. 

big data, bioinformatics, embl-ebi, finn, metagenomics, mgnify, microbe, microbial ecosystems, planetary biology, sustainability


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