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Metabolomics for biomarker discovery: improving the health, performance and longevity of dairy cows by non-invasively detecting rumen pH.

Primary supervisor: Dr James McCaughern, Harper Adams University

Non-academic partner: Dr Jules Taylor-Pickard, Alltech

Project Title:

Metabolomics for biomarker discovery: improving the health, performance and longevity of dairy cows by non-invasively detecting rumen pH.

Project description:

One of the primary challenges associated with dairy cow nutrition is the provision of a diet that meets the cow’s nutrient requirements without compromising the ruminal ecosystem or the cow’s health. Forages and other feeds are initially fermented in the first stomach (or reticulo-rumen) by the resident microbial population, with microbial protein and volatile fatty acids being the primary end-products. The optimal pH for rumen microbial growth ranges from pH 6.0 to 6.5, but the rapid fermentation of sugars in grasses or starches in cereals can reduce ruminal pH to 5.8 or below. The resulting change in pH profile causes a disease known as subacute ruminal acidosis (SARA)1. The mean prevalence of SARA on UK dairy farms is ~26.2%2, and results in lower fibre digestibility, reduced intakes and milk yield, increased culling, and a higher carbon cost per litre of milk. Economically there is an estimated loss of approximately £340 per cow per lactation, excluding veterinary and increased culling costs3. Despite the importance to dairy cow health and welfare, diagnosis of the disease is problematic, requiring invasive techniques such inserting a needle through the reticulorumen wall (rumenocentesis), rumen cannulation or the use of rumen pH boluses, all of which are costly and difficult on-farm.


Metabolomics is a technique that utilises advanced analytical chemistry to provide researchers with a more complete picture of the animal’s phenotype at the metabolic level. This technology has been widely adopted in areas of crop science, but its application to non-invasively detect phenotypic changes due to diet in dairy cows has been limited4. This project aims to improve dairy cow health and performance by combining information generated from metabolomics with data from dairy cow feeding studies to identify novel metabolites (biomarkers) to detect and monitor SARA. Initial studies aim to profile metabotype changes in different biological sample types (e.g. milk, saliva, and faeces) from dairy cow feeding studies that have been completed and the samples banked. Subsequent studies will feed dairy cows with diets that vary in forage source (e.g. grass or maize silage), concentrate composition and level, or with additives, such as yeasts or buffers to control rumen pH, with the aim to validate these biomarkers and produce a non-invasive diagnostic test for SARA.


  1. Humer et al (2018) J Dairy Sci 101:872-888; 2. Atkinson (2014) Cattle Pract 22:1-9; 3. Stone (1999) USA; 4. Goldansaz et al (2017) 12:1-26.


Candidates are encouraged to contact Dr James McCaughern to discuss the project before applying if they wish to.

Contact: Dr James McCaughern, Harper Adams University


Deadline: 20 January 2023

To apply for a CASE studentship, please check your eligibility and complete the MIBTP application process.

Please ensure that you;

  • Apply directly to Harper Adams University.
  • Clearly state you are applying for a CASE project and stipulate the proejct title.