NE2202: The Equine Microbiome

(Multistate Research Project)

Status: Active


The stakeholders who will be served by the Equine Microbiome Multistate Research Project include: microbiome researchers, undergraduate and graduate students, horse owners/managers, veterinarians, equine industries (e.g., feed producers, nutritionists, behaviorists, competitors) equine enthusiasts (e.g., youth groups and spectators), and underserved communities (e.g., rural horse owners, undergraduate and graduate students with limited access to bioinformatics, biostatistics, or data resources).

The impact of the gut microbiome has been a popular press topic for human and animal care. Despite the popularity and availability of products purporting to positively impact health through modulating the gut microbiome, research to understand the details of the functional impact of the microbiome on horse health and disease is still in its infancy. A search of PubMed using the terms “equine” and “microbiome” yielded only 320 results. Publication in this area has increased exponentially since 2007.

This project will address the following needs to bridge the gaps between equine microbiome researchers, equine industries, students, and the public:

  • Advance the knowledgebase of equine microbiome science with robust, statistically significant sample numbers and diversity.
  • Communicate advances in microbiome science among researchers, students, and the public.
  • Refine and test protocols and standardized methods for researchers to enable collaboration, data sharing, and greater utilization of samples and data.
  • Provide translational connections between the equine gut microbiome and health parameters, nutrition, management, and performance that are based on research specific to horses.



The importance of this work is to establish a coordinated and collaborative network of equine microbiome researchers and to provide resources for students and the public that reflect the state of the science.

  The consequences of not establishing the Equine Microbiome Multistate Group are:

  • Confusion regarding the state of equine microbiome science among stakeholders leading to the spread of misleading information, poor purchasing and management decisions, uncertainty regarding efficacy of products and research strategies.
  • The continued lack of coordination among researchers, which is slowing the progress and efficiency of the science due to smaller sample sizes (horsekeeping is expensive relative to other species), inconsistent sampling and analysis protocols, inconsistent training of students, inability to share data.
  • Lack of understanding of the unique aspects of the equine microbiome and continued application of therapeutic and nutritional strategies from research on other species such as ruminants and humans that may be ineffective or have adverse effects on the unique equine gastro-intestinal tract.


The Equine Microbiome Multistate Group will leverage the depth of technical expertise, range of laboratory, sequencing, and animal facilities, diversity of horse herds, extensive archival sampling efforts, training capacities, and stakeholder support of each member institution. As a nation-wide effort, this group will maximize impact of data/samples for multiple studies, reach numbers needed for statistical power, mitigate geographic bias, and coordinate host and microbial connections.


  As a Multistate effort, this project will be able to:

  • Investigate the role of the microbiome in equine health by describing the structural and functional properties of the “normal” equine microbiome.
  • Test hypotheses of microbiome structure and function related to management, life stages, and disease states.
  • Build and test statistically rigorous models of host-microbiome interactions.
  • Establish a network for training students, outreach to the public, veterinary and equine industry education in microbiome science.
  • Create print and web-based resources for the equine community (public, education, veterinary and equine industry) to increase understanding of microbiome science and its applications to improving horse health and management.


  The likely impacts of successful completion of this work are:

  • For Researchers,
    1. The opportunity to work together to develop grant proposals and experimental collaborations to explore research questions focused on understanding the structure and function of the equine microbiome in health and disease. Through this multistate we will share expertise, horse samples, and technical assistance for basic and translational experimental approaches.
    2. The establishment of a shared database of metadata, sequence data and samples will increase the statistical power and efficiency of hypothesis testing and enable a baseline for the “normal” equine gut microbiome.
  • For Students,
    1. The shared database will provide opportunities to formulate and test hypotheses and increase research participation, especially for students from institutions with limited access to research facilities.
    2. Training in bioinformatics, biostatistics, microbial ecology, and host physiology will enable students to apply knowledge and techniques to real-world questions in the equine industry.
    3. The opportunity to participate in conferences and workshops around equine microbiome science will enable students to widen their network, practice presentation skills, and gain confidence in their futures as scientists.
  • For Veterinarians and Nutritionists,
    1. Equine microbiome insights will inform clinical practice, specifically understanding the impact of the microbiome on horse health and welfare and advice given to horse owners regarding management, feeding, and modulating the microbiome via pre/probiotics or antibiotics.
    2. Observations made by clinical veterinarians will provide essential questions and insights for microbiome researchers.
    3. Conference and workshop participation will enable veterinarians to share insights, clinical strategies, questions, and case studies.
    4. Creation of evidence-based web and print resources to translate equine microbiome science for better health outcomes.
    5. Equine nutritionists and feed manufacturers will gain insight to how the diet, microbiome, and equids interact with the potential to guide feeding recommendations and feed formulation for improved outcomes (health, welfare, and performance).
  • For Horse Owners and Enthusiasts,
    1. Greater understanding of the impacts of diet, management, and other factors on microbiome health, and ultimately the welfare of horses.
    2. Deeper knowledge of specific feed ingredients, pre/pro/postbiotics will enable horse owners to make informed decisions in purchasing horse care products, supplements, and feeds.
    3. Conference and workshop participation will help to dispel myths about the impacts of feeding and management practices on the microbiome, and promote equine welfare through communication of research based findings.
    4. Creation of evidence-based web and print resources to translate equine microbiome science for better management decisions.
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