Harnessing the gut microbiome to strengthen livestock resilience against carriage and infection by pathogens

Challenges

Infectious diseases continue to be a significant problem in farmed animals. Diseases such as enteritis, mastitis and uterine infections cause livestock suffering and financial losses for farmers. These issues are made more challenging by the rising prevalence of pathogens with antimicrobial resistance and the need to reduce antibiotic usage on farms. We need novel treatment options, therefore, to reduce the growth and prevalence of pathogens such as toxigenic Escherichia coli to reduce the burden of infectious disease in livestock.

One highly promising avenue is to harness the indigenous microbes (microbiome) of livestock to enhance their defence against invading pathogens. The microbiome protects the host animal via a range of activities, including stimulating the immune system and producing antimicrobial compounds that kill or impede disease-causing microbes. The susceptibility of animals to infectious diseases can therefore be heavily influenced by the composition of their gut microbiome. However, the microbiomes of livestock are complex, and many of the constituent species have either yet to be cultured or are vastly understudied. As a result, it is largely unknown what components of livestock microbiomes are likely to be the most active against pathogens, and that can be developed as novel therapeutic options. In this project, we are therefore aiming to identify livestock microbes, or their products, with inhibitory activity against a range of important pathogens.

Questions

Solutions

Infectious diseases, particularly when caused by antibiotic-resistant pathogens, are major problems in farmed animals. New treatment strategies are needed to reduce infections, and the use of antibiotics in farming environments. We aim to address this by harnessing animal intestinal and environmental microbiomes to boost defence. We will screen our diverse bacterial culture collections to identify health-associated microbes with potent activity against selected pathogens that cause significant economic and health impacts, including antibiotic-resistant strains. The approaches developed in this project also allow us to be responsive to new and emerging pathogens.

This project is:

• Identifying specific commensal microbes, and associated potential bioactives, from livestock microbiomes that suppress the growth of economically important animal pathogens, such as those that cause gastroenteritis and mastitis.
• Exploring mechanisms of action by these inhibitory gut commensal microbes and determine their potential for development as novel therapeutics by studying their genomes for beneficial and deleterious traits.
• Evaluating the ability of identified inhibitory gut microbes to reduce the carriage of pathogens in in-vitro models of the animal gut.

Thus, over the five-year span of this project, we are investigating microbiome links to resilience against infection by important livestock pathogens derived from distinct branches of life (including bacteria and fungi). By identifying candidate microbiome species with the greatest potential as alternative therapeutic targets, the novel information generated should inform attempts to develop new approaches to reduce and minimise the incidence of important disease-causing pathogens in animals.

Project Partners

Progress