Nine research themes have been identified where the role of microbiological research is crucial to help meet the challenges of ensuing global food security and safety.

For each of the nine research themes, the Microbiology Society has summarised core challenges that arise from some of the main drivers underpinning the goal of ensuring food security and safety. From these core challenges key research priorities have been identified. The Society recognises that any proposed solutions to food security and safety will require multidisciplinary, multinational teams to effectively meet the global challenges of our future food supply. Funds need to be committed to support microbiology research programmes, which have the potential to deliver solutions to these global challenges.

1. Soil health and nutrient cycling
2. Plant–microbe dynamics
3. Crop pathogens
4. Gut microbiology in farm animals
5. Animal pathogens
6. Food spoilage
7. Food safety and human diseases
8. Waste reduction and management
9. Novel methods

1. Soil health and nutrient cycling

The potential of plants to achieve their theoretical experimental yields is critically dependent upon the potential of the soil in which they are grown. Healthy soils contain a high abundance of diverse micro-organisms (10⁹–10¹⁰ cells per gram), including many thousand species of bacteria, fungi, algae, protozoa and viruses, most of which have yet to be identified and less than 10% of which can be currently classified. These microbes carry out vital life-sustaining functions, including cycling of nutrients such as carbon, nitrogen and phosphorus, and promoting plant growth; many microbial pathogens are also present. Soil microbes live in highly diverse communities that interact with each other, plants and the environment in complex ways. Because most of the microbes cannot be cultured, we still have little understanding of these interactions.

Core challenges

Exploit the recent advances in genomics and advanced biochemical techniques, which provide the necessary diagnostic tools, to understand the links between microbial community composition, activity and soil ecosystem processes.

Key research priorities

• To determine the effect of external factors on soil microbial communities and their functions, such as decomposition and nutrient cycling. External factors should include:
  
   - Physical factors, such as agricultural practices, for example tillage, crop rotation and fertilisation, including the use of non-chemical forms such as manure or green waste composts. These factors have been demonstrated to have effects on soil biota and associated functions. Mycorrhizal fungi are known to have a reduced or altered diversity under conventional agriculture compared to reduced tillage, organic or more natural systems and little information is available relating to the function of different species under different agricultural systems. Nitrogen cycling microbial groups are known to be affected by similar changes in practice, but in contrasting directions where increased flux through the nitrogen cycle driven by fertilisation results in high levels of greenhouse gas emission from agricultural systems. Our understanding of these and other soil groups is hampered by the difficulty of working in soil, mainly due to system complexity, including the highly multifunctional nature of most soil species and low culturability.
  
   - Chemical factors, such as use of fertilisers and how this relates to run off.
  
   - Environmental factors, such as drought and increased temperature due to climate change.
   
• To understand the impact of the plant and the plant genotype on soil microbial communities, in particular the effect of plant exudates on the communities. The plant provides an opportunity to manipulate the soil system in perhaps its most active habitat, the rhizosphere. Recent evidence demonstrates differences in the microbial community structure of the rhizosphere both within and between plant species. It is a high priority to gain an understanding of the functional consequences of these differences. Of particular interest is the role that plant breeding has had in shifting communities of microbes colonising the root.
   
• To understand the role that microbes play in nutrient cycling, for example the role of soil microbes in nitrate leaching, which is a major environmental problem, and in the recovery of phosphorous from sewage and waste water.
   
• Research needs to make use of new tools, such as genomics and metagenomics linking to functional tools, to assess the linkage between community characters and activity. Additionally, there is an increased requirement to develop and apply simple methods to assess soil quality. 

2. Plant–microbe dynamics

Many complex crop–microbe interactions occur at all stages of crop growth from seed to product; they can be beneficial, harmful or neutral. Relationships that range from mutualistic, where both plant and microbe benefit, to parasitic, where the microbe receives some benefit from the interaction at the expense of the host, can all be considered as part of the complex symbiotic ecology. Pathogenic interactions occur when host plant cells are actively killed by the microbe to facilitate exploitation (see Theme 3 – Crop pathogens, p. 20). Some micro­organisms transition through several different relationships with plants during their life-cycles, and manipulating them in any one relationship will benefit from understanding the transition state triggers. This has implications for pathogen control, where application of fungicides may best be implemented at non-pathogenic stages. An example of an interaction that is neutral for the plant, but disastrous for human health is the carriage of food-borne pathogens. There has been a recent increase in cases of food-borne illness associated with plant-associated transmission of food-borne pathogens, for example the recent Escherichia coli O104 outbreak in Germany that was associated with contaminated seeds and affected over 3,500 people, more than 1,000 of these seriously.

Many microbes, in particular mycorrhizal fungi, rhizobia and viral, bacterial and fungal endophytes, confer direct benefits on their host plants in return for resources, such as carbon. These relationships are little exploited, especially in our major crops. Similarly, the role of host plant diversity in maintaining microbial stability in crop systems and the cost of microbes to crop productivity need to be determined. However, agronomic approaches may need to be changed to optimise these associations.

Core challenges

To understand the nature and control of signals that trigger and change plant–microbe interactions and to develop strategies to exploit these trigger signals to favour more symbiotic, mutualistic states in microbial life-cycles. A need also exists to enhance the efficacy of mycorrhizal, rhizobial and endophytic associations with plants in stable, diverse communities. These challenges need to be investigated in several microbe–crop associations required for food security.

Key research priorities

• Understand what triggers make microbes enter the different stages of their life-cycles in relation to their hosts and to determine whether these control mechanisms are environmentally driven (for example by temperature) or come from plant signals.
   
• Develop a greater understanding of beneficial plant–microbe interactions and how these can be enhanced and/or exploited by shifting microbial community structures towards stable, benign states (rather than eliminating detrimental microbes), and to understand the food safety implications of the dynamics of the association of animal, including human pathogens with plants.
   
• Enhance the function and host range of mycorrhizal fungi and rhizobia, which associate with roots, and provide plants with mineral nutrients and fixed nitrogen, respectively, in exchange for carbon.
   
• Identify and exploit endophytes (bacteria viruses or fungi that live within plants) that confer tolerance to stresses.
   
• Deploy diversity, particularly traits that reduce epidemic severity, at all scales from within crops to geographical regions to keep microbial populations stable and benign, and reduce opportunities for new pathogens.
   
• Reduce the transmission of human food-borne pathogens on plant materials (also reduce the carriage of spoilage microbes).
   
• Determine the cost of different plant–microbe relationships to non-target effects such as yield in crops and how this might be manipulated in crop health through novel treatments, including resistance priming with elicitors (analogous to immunisation).

3. Crop pathogens

Crop production continues to be lost to pests and diseases; for four major world crops, actual losses are estimated at £150bn, with potential losses (without crop protection) at £275bn [12]. Disease control measures (for example crop resistance to pathogens, fungicides, rotation) reduce crop losses and help to alleviate food shortages, but their implementation needs to be optimised. Changes in climate and pathogen populations may increase the severity of crop disease epidemics and further threaten food security, especially for those farming in marginal environments.

Core challenges

To understand the causes of crop diseases and their impacts on food security, including the role and production of mycotoxins, and develop strategies to intervene in situations where crop losses may occur. To guide government and industry strategies by using models to predict the effects of changes such as climate change, movement of pathogens and changing agricultural practices on crop–disease interactions. To identify and exploit sources of durable resistance, particularly utilising crop and pathogen genomic data.

Key research priorities

• Develop strategies to limit movement of invasive plant pathogens by identifying and monitoring routes of entry into new areas and implementing legislative controls, including destruction of infected plants and plant products.
   
• Exploit crop and pathogen genomic data to identify essential, invariant pathogenicity effectors likely to lead to identification of receptors and thereby durable crop resistance.
   
• Identify durable crop resistance against pathogens that is robustly expressed when exposed to various stress factors (abiotic or biotic).
   
• Exploit new methods for monitoring pathogen populations (for example combining air sampling with molecular diagnostics) to detect changes in pathogen populations (for example species movement, change in pathogen range, fungicide resistance, new races) so that control strategies for existing and emerging pathogens can be developed.
   
• Develop more accurate predictions of impacts of changes in climate, environmental and agricultural practices on losses from specific crop diseases, to identify those diseases that will increase/decrease in importance to guide government/industry strategies for adaptation.
   
• Understand the role of crop disease control in climate change mitigation (decreasing greenhouse gases). It is estimated that use of fungicides on UK arable crops currently saves 1.6 Mt CO₂ equiv. per season.

4. Gut microbiology in farm animals

The complex and diverse microbial population in the gut of farm animals, consisting of archaea, bacteria, protozoa and fungi, plays a central role in increasing the production of high-value human food from farmed livestock. At a global scale, livestock farming contributes up to 18% of total greenhouse gas emissions [18]. In Europe, livestock-related methane emissions result from the fermentation in the digestive tract of ruminant animals (70%) and in animal waste (30%). Thus in order to improve the greenhouse gas balance of farming, there is a requirement to reduce methane production by ruminants and to improve digestive efficiency to reduce excreta. It is also becoming obvious that microbial transformations in the gut can lead to the production of breakdown products (for example conjugated linoleic acids form during fatty acid biohydrogenation in the rumen) that are beneficial to human health. Ruminant production systems will increasingly focus on better use of lignocellulosic biomass either from waste material or forages grown on land not suitable for direct cropping, and must be optimised to reduce the production of greenhouse gases and to produce products which promote human health. The microbiota of all livestock is important in the retention of energy from the diet as well as the development of the immune system. Understanding the microbial communities and activities underlying these processes is therefore essential to ensure the efficient use of raw materials and maturation of host defences. In monogastric farm animals, microbiological studies have and will continue to lead to increased digestive efficiency and reduced pathogen transfer into the food chain.

Core challenges

To improve our understanding of the interactions between farm animals and the microbes that live within them in order to increase productivity and promote human health while reducing the environmental and welfare impacts associated with livestock agriculture.

Key research priorities

• To develop novel methods to modify the gut microbial community to decrease the production of greenhouse gases from farmed livestock.
   
• To analyse metagenomic and metabolomic data to understand the constituents and activities of the microbiota of livestock in totality and in situ to improve digestive efficiency.
   
• To improve the efficiency of forage (current and novel forages produced in response to climate change) and by-product usage in farmed livestock to decrease the competition between farmed livestock and humans for feedstuffs.
   
• To understand how microbial transformations occurring in the gut influence the health-giving properties of food derived from animal sources.
   
• To understand how the indigenous microbiota protects against invading microbes, for example by defining the microbes and constituents thereof that mediate competitive exclusion and the maturation of mucosal immunity.
   
• To understand how the genetic make-up of the animal interacts with the microbial population in the gut and how this might be matched to available feedstuffs to maximise productivity and minimise environmental impact.

5. Animal pathogens

Infectious diseases are a major threat to the productivity and welfare of food-producing animals and to pollinating insects. Such diseases constrain trade, the prosperity of rural and developing communities and our ability to feed a global population that is growing in size and affluence. Improvements in animal health and productivity will ease demands on raw materials, including crops and agricultural land on which humans also rely. The intensification of animal production, together with an expected narrowing of genetic diversity of food-producing animals, is likely to lead to an increase in the burden of animal diseases and may see the emergence of new pathogens. The situation is exacerbated by the spread of resistance to antimicrobial agents among animal pathogens (which also blunts weapons used to treat human infections) as well as a decline in the rate of discovery of novel drugs and a decline in the facilities and expertise required to address challenges to animal health. Around 70% of human infectious diseases that have emerged in the last six decades have their origins in animals [14], and the vast scale of animal production suggests that new zoonoses will arise in the future. In addition to economically important endemic animal diseases, such as bovine tuberculosis, mastitis and respiratory and enteric diseases, the UK is threatened continually by ‘exotic’ pathogens, including emerging vector-borne diseases as a consequence of environmental change. Introduction of such exotic pathogens can profoundly affect trade, as evidenced by the impact of UK epidemics of foot-and-mouth disease, and erode public confidence in food, as with mad cow disease. Control of infectious diseases of animals is most effective when vaccination is used together with state-of-the-art diagnosis and surveillance. Advances in gene sequencing, the immunology of food-producing animals and the ability to manipulate microbial genomes will provide new opportunities for diagnosis and control of animal pathogens.

Core challenges

To develop, improve and implement methods for the rapid diagnosis and control of the approximately 80 infectious diseases of food-producing animals and fish and pollinating insects recognised by the World Health Organization for Animal Health as being of global or regional significance [23].

Key research priorities

• For many important infectious diseases of food-producing animals, fish and pollinating insects, improved methods for rapid and specific diagnosis, including simple on-farm tests, are needed to speed up detection and provide a network of global intelligence on the spread of infectious diseases.
   
• To aid analysis of risk, targeting of resources and control measures, and the development of effective control strategies, an understanding is needed of the molecular basis of host–pathogen interactions with emphasis on identification of:
  
   - mechanisms of pathogen colonisation and persistence;
   - mechanisms of host or tissue tropism of pathogens;
   - virulence determinants and the basis of pathology;
   - mechanisms of innate and adaptive immunity to pathogens;
   - factors influencing transmission between hosts, including the role of wildlife;
   - factors influencing pathogen evolution and the emergence of new pathogens;
   - components of pathogens that can be targeted by drugs, or which are suitable for inclusion into vaccines;
   - the effect of co-infections with different micro-organisms (including indigenous microbes) on the outcome of infection.
   
• To determine the effects of climate/environmental change on the dynamics of disease transmission and geographical spread.
   
• The development of new disease control strategies, including pre-and probiotics, immuno­stimulants and medicinal plant or microbial products. Research into probiotics for aquatic organisms is increasing with the demand for environment-friendly aquaculture.
   
• Development of disease-resistant animals by selective breeding or transgenesis based on knowledge of pathogen biology.

6. Food spoilage

Food spoilage may be defined as any change that renders food unfit or unsafe for human consumption. Microbiological spoilage is a significant problem with respect to the shelf life of raw and processed foods (meat, fish and vegetable products) and is a key contributor to food waste. Future food security will necessitate that less food is wasted. More than 25% of the food that is bought is wasted because of delays in the food chain, poor storage and human behaviour [16]. Contamination and spoilage may occur at any stage along the food chain from harvest to retail, where bacteria, yeasts and moulds cause microbial spoilage. An area of concern is the safety of ready-to-eat meals that use diverse sources of ingredients in support of an expanding value-added market within the UK.

Core challenges

A central issue is the adaptation of communities of microbes to specific environments, both pre-and post­harvest. The globalisation of food production with, for example, legislation and guidelines that apply in the UK not necessarily applying elsewhere, could give rise to new hazards, and the centralisation of post-harvest storage and processing mean that any problem can effect a wide number of consumers across national borders. Until it is understood how these organisms survive and adapt to conditions at harvest, during storage and processing, then microbial spoilage will remain a barrier to the efficient use of food and potential source of infection. Adaptation is also an important consideration in terms of the detection of pathogens that can reside within mixed communities below detection limits, or in a ‘non-detectable’ state. There is a need to consolidate and standardise methods for understanding microbial contamination or growth on pre-and post-harvest foods.

Key research priorities

• Understanding microbial ecology of pre-and post-harvest produce, and how these microbial populations can affect shelf life and food quality.
   
• To be able to track microbial spoilage and pathogen sources in order to predict pre-and post­harvest hazards to inform farmers and food processors on storage and process control measures.
   
• The development of rapid diagnostics to allow for correct species and strain identification from within mixed microbial communities and develop databases for the food source attribution of microbes.
   
• Develop an understanding of how to optimise the food chain, improve shelf life and produce intelligent packaging.

7. Food safety and human diseases

Food-borne illnesses are a serious global problem and a need exists to improve food safety while improving consumer choice and the welfare and productivity of animals. The World Health Organization estimates that worldwide food-borne and water-borne diarrhoeal diseases taken together kill about 2.2 million people annually [24]. In the UK, it is estimated that about 1 million people suffer a food-borne illness of which 20,000 receive hospital treatment, and there are over 500 deaths. This cost to the UK economy in 2009 was about £2bn [15]. Such infections can have life-threatening consequences and vaccines or treatments for most food-borne pathogens are lacking or ineffective. The evolution of food-borne microbes has been punctuated by the emergence of new problems, for example Salmonella enterica serovar Enteritidis phage type 4, responsible for an on-going pandemic associated with egg contamination, and Shiga toxin-producing E. coli, which first manifested as E. coli O157 in the early 1980s and more recently in an unusual ‘hybrid’ O104 strain that infected over 3,500 people in Germany in 2011, killing 50 and producing life-threatening conditions in over a quarter of patients. Other threats have grown over time: cases of Campylobacter (mainly poultry-associated) now account for the majority of food-borne illness, with around 724,000 infections [25] estimated to have occurred in the UK during 2010 and around 65% of chickens on retail sale being contaminated [26]. Listeria monocytogenes infections (usually associated with ready-to-eat produce) also raise concern due to the high level of mortality. Infection can be fatal in one-third of cases in susceptible individuals [10]. The proportion of all food-borne outbreaks due to fresh fruit and vegetables contaminated with animal excreta, for example by using untreated manure, has increased significantly in recent years. Large-scale outbreaks can produce political and trade implications over and above the public health cost.

Core challenges

To enhance the microbiological safety of food it is necessary to minimise contamination of food supply chains by pathogens and to eradicate or control any pathogens that are present. It is necessary to identify all routes by which pathogens contaminate each food supply chain and to define the activities of microbes throughout in order to target new and effective control strategies to reduce microbial persistence and transmission. Moreover, improved tools are needed to identify emerging pathogens and assess the zoonotic and epidemic potential of microbes found in food-producing animals and the environment.

Key research priorities:

• To understand pathogen biology throughout the food chain in order to develop and refine strategies that reduce transmission/persistence of pathogens in the food chain, and in turn human disease.
   
• Define the nature, frequency and consequences of genetic exchange and variation in food-borne microbes to aid assessment of risk and targeting of control strategies.
   
• To understand the role of husbandry practices, diet and health of food-producing animals in the carriage of zoonotic pathogens.
   
• Define the transmission pathways of food-borne pathogens with emphasis on the points of entry of pathogens into food supply chains and the persistence and activities of microbes in varied production niches.
   
• Development of effective food-processing approaches based on improved understanding of pathogen biology and quantitative microbiology to improve food safety and to extend shelf life and quality of food.
   
• Development of improved methods to detect food-borne microbes and assess the risk they pose, including rapid detection of viable or infectious agents, for example in non-culturable states.

8. Waste reduction and management

Waste occurs at all points along the food chain. This includes those parts, such as straw or animal slurry, ancillary to the food itself, losses due to spoilage in the field and during processing, losses due to perceived low quality and domestic food waste. While other themes are concerned with reduction of waste, this theme deals with what to do with waste created.

At least half of food grown is discarded before and after it reaches consumers. It is estimated that in the UK one-third to half of landfill waste comes from the food sector. Landfill releases greenhouse gases, in particular methane, which contribute to climate change. The Waste Hierarchy (in order of preference: Prevention, Re­use, Recycle, Other recovery, Disposal) states the common sense and now legal approach to waste disposal, the specific method being dependent on the nature of the waste. In the context of food security and safety, waste can be converted into products for further use (for example animal feed, compost) or sources of energy (for example biogas in anaerobic digestion, bioethanol in refineries, or burned directly in power plants). The production of ethanol, butanol and other foods from food waste helps reverse the trend of using agricultural resources to produce biofuel rather than food. However, it is important to remove pathogens from waste in order to prevent them re-entering the food chain, and where possible reduce spoilage microbes.

Microbiology is central to most of these processes. The modification and exploitation of food wastes using microbiological routes may be considered as part of a biorefinery process in which high-value components may be initially extracted from the waste prior to exploiting the residue.

Core challenges

The core microbiological challenges of waste management concern optimisation and matching of microbial processes to specific waste streams. This is another example of where we need much better understanding of the ecology of microbial communities.

Key research priorities

• Improved production of cell-wall-degrading enzymes from microbial sources for the commercial disassembly of plant structures. At the moment, enzymes used in cell wall saccharification are still overly expensive.
   
• Microbial optimisation of waste treatment. The sequence of microbiological processes underlying anaerobic digestion requires further investigation to improve the production of methane and reduce the problems caused by heterogeneous wastes, and to ensure safety.
   
• Removal of pathogens (and reduction of spoilage microbes) from plant and animal waste to prevent them re-entering the food chain.
   
• Generation of useful products from food waste through the use of targeted microbial degradation.
   
• Reduction in methane release through better control of microbiology in landfills.

9. Novel methods

The development and application of novel methods can revolutionise the approaches taken by industry and academia to study and address issues affecting food safety and security. These new methods are very diverse and include practical methods to rapidly detect, study and manipulate microbial genomes; the development and use of microbes as biocontrol agents to control crop pests; modelling-based systems that can improve the understanding of the effects of changes in food production and processing and how these affect microbiological risks in the food chain; methods of remote sensing that can be used in surveillance, tracking and monitoring on both local, national or global levels; development in information collection and analysis systems that allow the recording and assessment of large amounts of complex multi-dimensional data to allow logical and valid conclusions to be drawn.

Core challenges

The core challenges are to understand what novel methods are becoming available and how these could be employed within the food chain to help in the understanding and improvement of food safety and security issues. Key are the developments in ’omics technologies that allow a detailed study of the microbial genome, an insight into microbial diversity within foods and the potential to develop rapid detection methods for new pathogens. This requires an ability to handle and analyse large amounts of information with suitable bioinformatics approaches. Continuing with information handling and analysis approaches, the development of modelling systems that will enable prediction of the effects of changes to food production procedures would allow for better risk assessment and identification of potential new hazards.

Key research priorities

• Development, use and application of ’omics technologies to study and understand microbial diversity and interactions within the food chain. This will include ‘active’ organisms, stressed ‘non-culturable’ organisms, and organisms containing or with the ability to produce compounds that will affect food safety and security. This includes an ability to assign roles to particular genes. This will allow the identification of the complete microflora contained within foods and allow us to understand their interactions, which will have effects on safety (through competition of pathogens with other innocuous microflora) and shelf life (more accurate identification of spoilage flora will allow development of effective strategies for their elimination). Additionally, such methods could allow metabolic modelling of nutrient cycling and metabolism in complex microbial communities in soil and the plant rhizosphere.
   
• Development of technologies that would allow rapid implementation of simple (potentially point of use) tests for a range of organisms that may be new/novel animal or plant pathogens. Tests allow for rapid identification, helping with control of these organisms and increasing safety within the food chain.
   
• Development of suitable data handling, management and analysis systems (hardware and software) to help us to data-mine, analyse and understand results from the large amounts of data produced by current and future novel methods. This will allow the fast analysis of complex datasets, yielding results such as identification of microbial communities and identification of particular genes within organisms that could encode either beneficial or negative microbial effects.
   
• Study and use of microbial biocontrol agents for crop pests (for example use of fungi or Bt toxin to control insects). This would allow an effective control of pests without the use of chemical pesticides, thus reducing the use of chemical pesticides in agriculture.
   
• Development of modelling and risk-based approaches that could be used to predict the effects of changes in food production methods, or indeed how extraneous events could affect food safety and security, for example climate change effects across large geographical areas.