BBSRC Institute Strategic Programme: Microbes and Food Safety Partner Grant

The Microbes and Food Safety (MFS) ISP will provide an understanding of how microbial threats, such as pathogens and spoilage-causing bacteria, evolve and interact to affect food safety and develop strategies to reduce their impact on health and the economy. We take for granted that most of the food we eat in the UK is free from the risk of microbial pathogens but the Food Standards Agency (FSA) estimates that around 2.4 million cases of microbial foodborne illness occur every
year, costing in excess of £9 billion. There is also an economic threat of food waste through spoilage, increasing retail costs; up to 25% of food spoilage is due to the action of microbes. Our mission is to reduce human foodborne illness through improved food safety and to reduce waste due to food spoilage. To do so, we will address key food safety questions in three Themes: 1) what and where are the microbial threats in foods? 2) What are the factors associated with the survival and success of microbial threats? 3) How can we use this information to improve food safety and reduce food
waste?

Throughout this programme, we will focus on key organisms and issues of strategic importance for food safety, in which we will exploit and further develop our demonstrable expertise. These are Campylobacter, Salmonella, Listeria, Pseudomonas, antimicrobial resistance (AMR) and the identification of emerging microbial threats through the use of metagenome sequencing. As microbial threats such as pathogens and spoilage-causing bacteria exist as complex microbial communities
across the food chain, we focus not only on the key organisms of interest, but we will also study the other microbes present which may support their survival or persistence.

In Theme 1, MICROBIAL THREATS FROM FOODS IN ESTABLISHED AND EVOLVING FOOD SYSTEMS, we will identify what microbial threats are present in our food - particularly newer food types. Our aim is to understand how microbial threats spread and cause disease or food spoilage by studying the genetic diversity and dynamics of gene flow within populations of foodborne bacteria. In particular we will assess evolving microbial threats from foods associated with shifts in consumer preference, trading relationships and climate change.

In Theme 2, MICROBIAL SURVIVAL IN ESTABLISHED AND EVOLVING FOOD SYSTEMS, we will define the factors associated with the survival and success of microbial threats. Our aim is to understand microbial survival and adaptation better by understanding the lifestyle of the bacteria present, e.g. biofilms, community associations and/or metabolism without growth. To do this we will use our specialised core services, including informatics, sequencing and microscopy to investigate samples taken from throughout the food chain and also from human clinical samples.

In Theme 3, FLEXIBLE CAPABILITIES TO REDUCE FOOD SAFETY THREATS AND RESPOND TO EMERGING NATIONAL NEEDS, we will use the data generated in the first two themes to improve food safety and reduce food waste. We will work with our stakeholders within QIB, academia, government and industry to apply the scientific evidence derived from our fundamental research to improve the evaluation of future risk and to inform the control of threats to food safety and resilience. Our capability will remain flexible so that we can respond quickly to unexpected emerging national needs as required.

Our aim with this programme of work is, with our established stakeholders, to improve the production of safe and nutritious foods and reduce loss of food from spoilage through the delivery of scientific knowledge and acting as a knowledge and training hub for microbial food safety.

The focus of this contribution is the development of genome-scale metabolic models (GSMMs) of organisms of interest (Campylobacter and Salmonella are a focus but others may be developed). This will involve the application of existing analytical methods (e.g. those based on null-space analysis, linear programming [FBA and similar] and database mining) and the development of novel techniques and algorithms as may be needed.

Models will be informed by experimental data from the analysis of growth and metabolomic data generated across the ISP and will aim to include pangenome analysis to investigate community capabilities as well as just gaining insight about the survival strategies in single species.

The predictions which can be made from GSMMs are varied. For example, previous work has identified candidate genes for creation of defined knockouts, changes likely to arise from altering minimal or optimal media requirements, and identifying the metabolic rearrangements that an organism must undergo when faced with a change in environment or lifestyle (e.g. planktonic to biofilm transition).
All work will be in close collaboration with the QIB co-investigators (tasks 2.2 and 2.4), with a particular emphasis placed on experimental design as well as the interpretation of results. In addition to these activities, we will also provide training to relevant QIB staff in the theory and application of metabolic modelling and engage with their programming and IT teams to ensure efficient data sharing and longer-term development of modelling and other software.

Specific objectives are:
To help design experiments to produce relevant data and its subsequent interpretation
To build GSMMs of strains of interest
To expand models to incorporate communities
To make testable predictions based on the models
To refine GSMMs based on lab results
To train staff in metabolic modelling