Mutualistic microbes: engineering functional, multi-organism communities 

Project duration: July 2023 – June 2027 

The challenge

Outside of the laboratory, micro-organisms exist not in isolation but in multi-organism communities comprising hundreds of different species. All of them are living and working together, with varying specialisations and requirements. The networks of interaction between these microbes are complex and interdependent. This means that there are numerous organisms which will only grow as part of multi-organism communities. Therefore they can’t be isolated and characterised as individual species. 

A great deal of useful biology and chemistry occurs within the context of these microbial consortia. Harnessing these processes requires researchers to bring the advantages of communal culture from the environment into the laboratory. The challenge is to find ways to efficiently culture different organisms together while maintaining control of their behaviour and productivity at a scale that is viable for commercial applications. 

Our response

Using genetic modification and strain engineering, our researchers are building co-dependent microbial communities de novo. Initially, we are combining labelled strains of yeast that require specific feedstocks for growth with strains that produce complementary metabolites to support each other’s growth.

By creating strains carrying these designed, in-built co-dependencies and independencies, we will have multiple mechanisms through which we can control the population mix of co-cultured cells. Our research will provide insights into better ways to manipulate communities of micro-organisms and to create shared metabolic pathways to reduce productivity burdens on individual microbes. 

Impact

Dividing metabolic burdens associated with bioproduction can dramatically improve productivity and yields. It does this by allowing for specialist strains or species to do the jobs they are best suited for, rather than trying combine all steps in a single microbe.

By developing these systems from the ground up and using metabolic modelling to understand how they work we will harness this principle of division of metabolic burden to build efficient and productive systems for biomanufacturing.  

Over the course of this work, we will: 

• Develop insights into mechanisms for control and maintenance of productive microbial consortia.  

• Unlock utilisation of low-cost complex feedstocks for precision fermentation by using a mixture of interconnected specialist strains to handle each component of a mixture.  

• Work on the division of metabolic burden to enhance the productivity and carbon yield of complex biosynthetic pathways. 

Team

Dr Abubakar Madika, Dr Anjali Purohit, Dr Tom Loan, Dr Carol Hartley, Dr JP Molina