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Deciphering the relationship between early life gut microbiomes and the risk of post weaning diarrhoea in piglets

   Bristol Veterinary School

About the Project

Pig production is an efficient and potentially sustainable source of high-quality animal protein. In commercial production early, abrupt weaning of piglets is associated with dysbiosis of the intestinal microbiome, precipitating a range of enteric bacterial and viral infections including toxigenic diarrheoa and oedemic disease caused by Escherichia coli. Together these diseases represent a significant welfare issue and lead to reduced productivity and economic loss. The use of antimicrobials to control these diseases is being phased out and there is a clear need for alternative approaches to minimise the impact on production and welfare.

In this project we will look at the relationship between piglet weaning and the intestinal microbiome at group and farm level and correlate this to outcome (health & productivity) in both standard and higher welfare production systems. Such an approach will allow us better to understand how dysbiosis of the microbiome varies between groups of piglets both within and between farms; provide an evidence base for best practice; and inform potential microbial-based interventions such as probiotics.

Aims and objectives

The proposal has three main objectives:

  1. Identify the key microbial taxa associated with favourable and unfavourable responses to weaning, towards developing targeted microbial interventions such as probiotics and prebiotics.
  2. Determine the extent of differing production systems and environments on development of the intestinal microbiome of the pig and risk of post-weaning diarrhoea.
  3. Seek to determine the role of group ‘pen’ effects in development of the microbiome and the extent this may underpin variation within susceptibility to infection and capacity for the individual animal to thrive.


Twenty pig units will be recruited to the study from the South West and East Anglia, representing both standard and higher welfare systems (n=10 each). On each farm the scholar will gather pooled faecal samples from repeated representative pens (n=5) pre- and post-weaning, and process the samples for microbial 16S rRNA amplicon sequencing and qPCR for a panel of pathogens implicated in post-weaning diarrhoea (PWD). Performance data including growth rates, disease incidence and mortality rates will be collected for each corresponding pen and at the farm level. Resulting compositional microbiome data will be integrated with performance data and pathogen levels to identify gut microbiota, or consortia thereof, which are associated with reduced incidence of PWD and its causative agents both pre- and post-weaning. Farm level comparisons will be performed to identify management practices associated with improved outcomes and ‘protective’ microbiome phenotypes.

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This project will be based in Bristol Veterinary School.

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