The first few weeks of a foal's life are a critical period for the development of its gut microbiome - the complex community of microorganisms that supports digestion, immunity and overall health. Researchers are now taking a closer look at where those microbes come from, and a new DNA sequencing technique could accelerate progress.
Scientists from the Horse Microbiome Research Group at the University of Surrey have demonstrated that Oxford Nanopore sequencing offers a rapid and affordable way of profiling bacterial communities in horses. Led by Dr Joy Leng and published in the Journal of Medical Microbiology, the study provides the technological foundation for the Alborada Well Foal 2 project, which is investigating how mares help establish the microbiome of their newborn foals.
The research follows on from the original Alborada Well Foal Study, which showed that the composition of the gut microbiome during early life may influence the future health and athletic performance of Thoroughbred racehorses. One particularly important finding was that foals treated with antibiotics during their first four weeks of life were more likely to experience poorer health and performance later on, highlighting how easily the developing microbiome can be disrupted.
The new project aims to answer two important questions. Firstly, how do mares pass beneficial bacteria to their foals? Secondly, if antibiotics are essential during early life, can their impact on the developing gut microbiome be reduced?
To find out, researchers will collect faecal, milk, saliva and skin samples from mares before and after foaling, together with faecal samples from their foals during the first 60 days of life. By comparing the bacterial communities found at these different sites, they hope to identify the main sources of the microbes that first colonise the foal's gut.
The study will also develop a laboratory model of the foal gut microbiome to investigate how different antibiotic treatments alter bacterial populations. This will allow potential protective strategies, including prebiotics, probiotics and postbiotics, to be evaluated before they are used in the field.
A key feature of the project is the use of Oxford Nanopore long-read sequencing. Unlike conventional short-read sequencing, which analyses DNA as thousands of small fragments that must later be reconstructed using sophisticated computing, long-read sequencing reads much longer stretches of DNA directly as they pass through microscopic nanopores. The portable MinION Mk1D device can be operated within a standard laboratory, while user-friendly analysis software makes the technology far more accessible than traditional sequencing platforms.
To evaluate the approach, the researchers analysed bacterial DNA from faeces, saliva, milk and skin samples collected from Thoroughbred mares and foals during a pilot study. The technique successfully identified distinct bacterial communities at each anatomical site, with results closely matching those reported previously using conventional sequencing.
Perhaps most impressively, complete microbiome profiles were generated within just three days at a cost of around £30 per sample, substantially reducing both the time and expense involved.
Although this was a relatively small pilot study, it demonstrates that Oxford Nanopore sequencing can provide reliable, rapid and cost-effective microbiome analysis across a range of equine tissues. As the Alborada Well Foal 2 project continues, the technology is expected to provide valuable insights into how mares seed their foals with beneficial microbes and may ultimately help identify practical ways of protecting the developing microbiome when antibiotic treatment is unavoidable.
For more details, see:
Leng, J., Tait, C., Alsubaie, B., Van Vliet, A. H. M., Sells, P., La Ragione, R. M., & Proudman, C. (2026).
Rapid bacterial community profiling of equine faecal, skin, milk and saliva samples using Oxford Nanopore long-read 16S rRNA amplicon sequencing.
Journal of medical microbiology, 75(7), 002176.
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