UK Institute of Microbiome Engineering

Lead Research Organisation: UNIVERSITY COLLEGE LONDON
Department Name: Cell and Developmental Biology

Abstract

he microbes that live within us influence our health and wellbeing. Research has shown changes in the microbiome are linked with inflammatory diseases, diabetes, obesity, cancer and mental health. They can also determine how effective treatments are and how well we recover from surgery. The microbiome has also become a multi-billion-dollar industry, with drug and diagnostic companies racing to capture the market for personalised medicine.
Despite these advances, our understanding of the interactions between the host and the microbiota remain primitive as we do not have the tools to interrogate these systems in a quantitative manner. Here we outline a proposal to build a world- leading multi-disciplinary and multi-centre UK Institute for Microbiome Engineering. This institute will leverage cutting-edge engineering approaches to biology - systems and synthetic biology - to influence and modify the microbiota in well determined ways. This investment will have a huge and significant impact for the NHS over the next 30 years, influencing hospital treatment, home healthcare, disease prevention, mental health and wellbeing.

Publications

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Barnes C (2023) An antimicrobial peptide expression platform for targeting pathogenic bacterial species

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Rutter JW (2022) Microbiome engineering: engineered live biotherapeutic products for treating human disease. in Frontiers in bioengineering and biotechnology

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Rutter JW (2024) A bacteriocin expression platform for targeting pathogenic bacterial species. in Nature communications

 
Description We have developed a new engineering biology platform for the delivery of antimicrobial peptides. This enables us to design new microbes (engineered live biotherapeutics) that can potentially target specific species of bacteria in the human body. We envisage that this platform can be used in the fight against antimicrobial resistance. It can also be used in combination with existing chemotherapeutic and immunotherapeutic drugs for cancer treatment.
Exploitation Route This platform is general and could be used to express bacteriocins to target any bacteria. This could be used by any academics/clinicians/companies interested in microbiome engineering.
Sectors Healthcare

Pharmaceuticals and Medical Biotechnology
 
Description As part of the responsible research and innovation (RRI) initiative, we launched a survey to assess current public attitudes towards microbiome engineering with a particular focus on healthcare applications. This work falls under the "Engage" component of the AREA (Anticipate, Reflect, Engage, Act) framework that EPSRC encourages researchers to follow (1). Our work could potentially have a therapeutic purpose for patients with colon cancer in the future, therefore success would be reliant on patients' acceptability towards engineered live bacterial therapeutic product (eLBP). This led us to design a survey to assess the attitudes towards microbiome engineering as a general principle and more specifically engineered live bacteria.
First Year Of Impact 2023
Sector Healthcare
Impact Types Societal
 
Description Syngulon 
Organisation Syngulon
Country Belgium 
Sector Private 
PI Contribution Working with Syngulon, we have expanded their area of interest from fermentation to helathcare.
Collaborator Contribution Partners brought knowledge on bacteriocins
Impact Development of our bacteriocin expressing platform. New targets in oncology
Start Year 2015
 
Title Engineered live biotherapeutic platform for the delivery of antimicrobial peptides 
Description We developed a new bacteriocin secretion platform that can be used to target pathogenic species. As a proof of concept we target two Enterococcus species as pathogens of interest, Enterococcus faecalis and Enterococcus faecium. We built on previous works in two main ways. We develop a modular platform based on the CIDAR MoClo assembly standard, which allows for flexibility in part interchange. Additionally we explore four different secretion signal peptides, to add another tunable parameter for eLBP delivery. We then used co-culture assays and Lotka-Volterra modeling to gain insights into the growth dynamics of these strains. Main source of funding was UKRI, EPSRC. 
Type Therapeutic Intervention - Cellular and gene therapies
Current Stage Of Development Initial development
Year Development Stage Completed 2023
Development Status Actively seeking support
Impact It is early stages but has formed the basis of further funding applications. 
 
Description RRI survey 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact As part of the responsible research and innovation (RRI) initiative, we launched a survey to assess current public attitudes towards microbiome engineering with a particular focus on healthcare applications. This work falls under the "Engage" component of the AREA (Anticipate, Reflect, Engage, Act) framework that EPSRC encourages researchers to follow (1). Our work could potentially have a therapeutic purpose for patients with colon cancer in the future, therefore success would be reliant on patients' acceptability towards engineered live bacterial therapeutic product (eLBP). This led us to design a survey to assess the attitudes towards microbiome engineering as a general principle and more specifically engineered live bacteria.
Year(s) Of Engagement Activity 2022,2023