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Molecular Diagnosis for Bacteria and Fungi of the Reproductive Tract

mares and foals

Our understanding of the microbiome, especially the fungal community, is very limited in the equine reproductive tract. The molecular diagnostic methods to characterize the microbiome of both bacteria and fungi, namely next generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR), are now available for clinical use in veterinary medicine and has several advantages over the standard culture method.

These molecular diagnostic tests are able to detect the presence of bacteria even those that are difficult to culture, bacterial DNA detection can be done even in animals that are being treated with antibiotics, and be able to detect disruption of the normal microbiome also known as dysbiosis. One important bottleneck for fully realizing the diagnostic potential of these molecular diagnostic test is the accurate interpretation of the microbiome and the changes that are associated with endometritis and infertility. Therefore, the goal of this study is to characterize the uterine microbiome of mares in health and disease.

In collaboration with MicrogenVet, the Cheong lab is seeking to enroll a number of apparently healthy mares that are to be bred and compare the microbiome of the mares that clear intrauterine fluid effectively post-breeding with mares that develop persistent breeding induced endometritis, as well as to compare the microbiome of mares that become pregnant from the breeding with mares that fail to conceive.

A secondary goal of this study is to determine if NGS and qPCR can be used to support treatment decision primarily related to identifying the efficacy of treatment.

Eligibility: Any mare that has a uterine sample collected pre-breeding.

Compensation: Advanced molecular diagnostics will be provided at a reduced cost

Owner Responsibilities:  We will ask to collect an initial uterine sample prior to breeding and possibly a sample of the semen used, and for mares that develop persistent breeding induced endometritis, a follow-up uterine sample. We will follow-up via phone for data pertaining to outcomes of breeding attempts and treatments.

Principal Investigator: Dr. Soon Hon Cheong, DVM, PhD

Contact: Please contact Dr. Cheong at 607.253.3100 or email at or