Microbes and Food Safety: Microbial survival in established and evolving food systems
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
To understand the mechanisms allowing important organisms to survive within communities in the food chain.
Planned Impact
unavailable
Publications
Abi Assaf J
(2024)
Common food preservatives impose distinct selective pressures on Salmonella Typhimurium planktonic and biofilm populations.
in Food microbiology
Acton L
(2024)
Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica.
in Journal of virology
Adriaenssens EM
(2025)
ICTV Virus Taxonomy Profile: Duplodnaviria 2025.
in The Journal of general virology
Bloomfield SJ
(2024)
Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection.
in BMC microbiology
Bolduc B
(2025)
Machine learning enables scalable and systematic hierarchical virus taxonomy.
in Nature biotechnology
Cook R
(2024)
Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages.
in ISME communications
| Description | Evidence for UK AMR review |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | END2AMR |
| Amount | € 31,500,000 (EUR) |
| Funding ID | 101253465 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 12/2025 |
| End | 12/2029 |
| Description | Engineering Biology Hub for environmental processing and recovery of metals; from contaminated land to industrial biotechnology in a circular economy |
| Amount | £14,881,069 (GBP) |
| Funding ID | BB/Y008456/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 02/2028 |
| Description | Engineering biology for critical metal recovery from industrial wastestreams |
| Amount | £1,838,843 (GBP) |
| Funding ID | BB/Y008448/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 01/2026 |
| Description | Exploiting the TraDIS-Xpress platform to identify unexplored and essential intracellular targets for MDR invasive Salmonella |
| Amount | £207,100 (GBP) |
| Funding ID | TC320 |
| Organisation | Tres Cantos Open Lab Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2025 |
| End | 04/2027 |
| Description | Multi-Agency Regulatory Groundwork for Engineered Phage Regulatory Sandbox |
| Amount | £921,246 (GBP) |
| Organisation | Department for Science, Innovation and Technology |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2025 |
| End | 10/2027 |
| Title | Introduction to Flux Balance Analysis (FBA) |
| Description | Flux balance analysis (FBA) is a mathematical approach to finding an optimal net flow of mass through a metabolic network that follows a set of instructions defined by the user. This protocol covers the mathematical principles behind FBA and provides coding examples that can be followed using Python3. A basic understanding of the following aspects of linear algebra is advantageous: vectors, matrices, transposition, matrix multiplication, and matrix decomposition. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Available on protocols.io, this has been viewed over 500 times between September 2024 and February 2025. |
| URL | https://www.protocols.io/view/introduction-to-flux-balance-analysis-fba-rm7vzjm7rlx1/v1 |
| Title | Mixed community biofilm model |
| Description | Generation and validation of a mixed community biofilm model incorporating stable levels of multiple relevant organisms from the food chain. Allowing evolution of specific pathogens to be studied in community context |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Allows impact of bystander organisms and interactions between multiple species to be modelled to follow evolution in a more realistic context |
| Title | Model for studying foodborne pathogen colonisation of fresh produce |
| Description | This model is widely used to characterise colonisation of fresh produce by foodborne pathogens and to study competitive interactions on fresh produce. |
| Type Of Material | Model of mechanisms or symptoms - non-mammalian in vivo |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Ability to characterise complex microbial interactions on fresh produce in the lab environment, Vehicle for further microbiome related studies |
| Title | Shewanella TraDIS library |
| Description | An ultra dense Transposon mutant library containing a cocktail of promoters has been created in Shewanella onediensis |
| Type Of Material | Biological samples |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The library is being used by multiple collaborators for different projects including those at Manchester, Durham and the University of East Anglia |
| Description | Collaboration with Concert Bio |
| Organisation | Concert Bio |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Ongoing collaboration on engineering microbial interventions to prevent foodborne pathogen contamination of fresh produce. Through this collaboration we further developed our understanding on how foodborne pathogens colonise fresh produce, identified microbial agents that can prevent this colonisation and we are currently engineering enriched communities with biocontrol activity to apply them to vertical-farming-mimicking systems. This collaboration started with building skills, expertise, capabilities based on the ISP work, which then led to uplift funding including 2 proof of concept grants, one from the Food Safety Research network (total project cost: £60,000) and a recent active one from the National Biofilm Innovation Centre (total project cost:£95,000). |
| Collaborator Contribution | Insights into the vertical farming industry sector, planned sequencing and metagenomic analysis of communities with the potential to control human pathogens on fresh produce. |
| Impact | Scientific advances in the following areas: characterisation of commensal bacteria with biocontrol activity against foodborne pathogens, characterisation of expanded activity of identified agents against multiple human disease agents, characterisation of the mechanisms required for biocontrol activity in different food-chain relevant environments. |
| Start Year | 2023 |
| Description | Collaboration with Huvepharma |
| Organisation | Huvepharma |
| Country | Bulgaria |
| Sector | Private |
| PI Contribution | Attracted funding for a CASE studentship to work with Huvepharma. My research group is providing expertise in molecular biology, pathogen genomics, gut metagenomics and phage biology to work with Huvepharma to develop technologies and materials to develop potential products for the use as antimicrobials and probiotics in livestock feed. |
| Collaborator Contribution | Huvepharma provide expertise in developing products and their commercialisation for use in the feed industry. |
| Impact | Successfully attracted funding for a studentship to develop antimicrobials |
| Start Year | 2023 |
| Description | GSK |
| Organisation | GlaxoSmithKline (GSK) |
| Country | Global |
| Sector | Private |
| PI Contribution | We are partners in an EU funded project 'END2AMR' which aims to develop novel antimicrobials. We will apply our transposon mutagenesis methods to help understand mechanisms of action and resistance to novel compounds |
| Collaborator Contribution | There are a range of 15 collaborating partners including GSK who provide half the value of the grant and access to their pre clinical compound libraries for novel drug development |
| Impact | None to date - project kick off was Jan 2026 so early |
| Start Year | 2025 |
| Description | GSK global health |
| Organisation | GlaxoSmithKline (GSK) |
| Department | GSK Oncology |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Deploying our transposon mutagenesis expertise in a new project to study Salmonella responses to novel antimicrobials |
| Collaborator Contribution | Contribution of a intramacrophage screen and lead compounds for analysis |
| Impact | Award of a TCOLF grant |
| Start Year | 2024 |
| Description | MRC MMB DTP studentship |
| Organisation | UK Health Security Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Training of a PhD student in high molecular weight DNA extraction and long read sequencing, working on a strain collection of interest to UKHSA. |
| Collaborator Contribution | Provision of public health expertise and a route to impact in regards to outbreak detection. |
| Impact | Poster presented at Microbiology Society Conference 2023. |
| Start Year | 2022 |
| Description | MTA with Public Health England |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Long read sequencing and metabolic analysis of Salmonella isolates provided by PHE. |
| Collaborator Contribution | Provision of Salmonella isolates, associated metadata and short read sequence data. |
| Impact | Joint publications, some used as evidence base for improving clinical guidelines |
| Start Year | 2021 |
| Title | BACTERIOPHAGE COMPOSITIONS |
| Description | A method of identifying and/or isolating one or more bacteriophages that display lytic activity against at least one target bacterial genus, species, or strain. The method includes the creation of a transposon mutant library using at least one bacterial strain from said genus or species and identifying the genes involved in resistance and/or susceptibility by exposing said library to at least one or more bacteriophages. |
| IP Reference | WO2025008620 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2025 |
| Licensed | No |
| Title | QuaTraDIS |
| Description | The QuaTradis pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. QuaTradis provides functionality to: detect TraDIS tags in a BAM file add the tags to the reads filter reads in a FastQ file containing a user defined tag remove tags map to a reference genome create an insertion site plot file Continued updates and releases have been made since the first release in 2022 with the latest in february 2025. These have increased functionality and accuracy |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | Used by groups around the world for analysis of transposon insert site data |
| URL | https://github.com/quadram-institute-bioscience/QuaTradis |
| Description | Discussion with a leading producer of raw pet food |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion with a leading producer of raw pet food to implement phage antimicrobials to improve the safety of product. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Discussion with representative from the British Retail Consortium |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Discussion with representative from the British Retail Consortium to identify potential implementation of phage antimicrobials to combat bacterial pathogens in the food chain |
| Year(s) Of Engagement Activity | 2024 |
| Description | Food Safety Research Network Community meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Participation in the Food Safety Research Network Community meeting in Birmingham in February 2024 to network to exchange knowledge on approaches to improve food safety and disseminate our activities in the use of phage as antimicrobials and the impact of copper on Salmonella in pigs. Potential applications and needs of industry were established. Contacts for further discussion were identified. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Knowledge exchange with UKHSA enteric pathogen surveillance team |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Meeting to share analysis of surveillance data that adds value to UKHSA core activities to improve public health |
| Year(s) Of Engagement Activity | 2025 |
| Description | MicrobeZoo |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | We have created the 'MicrobeZoo' an immersive activity where participants are 'shrunk' then transit through different environments (soil, gut, water) to explore in an interactive way how microbes impact each of these. This has been shown the the Norwich Science festival and will be toured at latitude festival, royal norfolk show and Royal Society summer exhibition |
| Year(s) Of Engagement Activity | 2026 |
| Description | Norwich Science Festival 2024 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Developed and ran a stand at the Norwich Science Festival communicating the differences between 'good' and 'bad' microbes |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://norwichsciencefestival.co.uk/whats-on/nrp-explorium-2024?start_time=2024-02-21T10.30 |
| Description | PhD training week |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | As part of a 6-week training block, we developed and ran hands-on bioinformatics training focused upon mapping and variant calling in comparative genomics. Students have reported use of taught techniques in their PhDs. |
| Year(s) Of Engagement Activity | 2022,2023,2024 |
| URL | https://mmbdtp.github.io/modules/comparative-genomics/programme/ |
| Description | Radio Cambridgeshire interview |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Radio interview to discuss importance of microbiology research to the general public |
| Year(s) Of Engagement Activity | 2024,2025 |
| Description | TV interview about launch of the Centre for Microbial Interactions |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview on ITV news discussing the launch of the Centre for Microbial Interactions (led by Webber) to represent the strength and importance of microbiology research from the Norwich Research Park |
| Year(s) Of Engagement Activity | 2025 |
| Description | The NIHR Health Protection Research Unit in Genomics and Enabling Data Conference 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The NIHR Health Protection Research Unit in Genomics and Enabling Data Conference 2024 |
| Year(s) Of Engagement Activity | 2024 |