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Metagenomic Investigation of Cow Reproductive Biology and Ecology

Periodic Reporting for period 1 - MICROBE (Metagenomic Investigation of Cow Reproductive Biology and Ecology)

Reporting period: 2018-05-28 to 2020-05-27

Ireland has the fastest growing dairy industry in the EU and is expected to produce 41% more milk in 2026 compared with 2016. Dairy cows with poor fertility cows pose a substantial challenge to achieving this target. Milk production in Ireland is seasonal due to changes in pasture growth throughout the year. Cows calve in February and March; lactate until December when they are “dried off”; and are non-lactating until the birth of a new calf initiates a new lactation cycle. Reproductive performance is evaluated as the proportion of the herd that calves in the first six weeks of the calving season. The current average of 65% in dairy herds is considerably below the target of 90%. This means 35% of cows produce milk for only 230 to 270 days each year instead of the optimum 305 days. Endometritis is an inflammatory disease of the endometrium lining the uterus, and is a leading cause of failed pregnancy establishment. The disease affects ~30% of cows, increases embryo mortality by 25%, and costs the EU and USA dairy industries €2 billion annually.

The endometrium and microbiota (population of microbes) are usually in a state of symbiosis when the cow is either receptive to pregnancy or pregnant. This symbiosis is disrupted (dysbiosis) at calving when pathogens such as Fusobacterium necrophorum and Trueperella pyogenes populate the uterus and produce inflammatory, pore-forming toxins or virulence factors that damage the endometrium. This may explain why endometritis has long term negative effects on embryo survival, but the mechanisms of how endometrium-microbe interactions affect embryo survival are unknown. Presently, mechanisms linking the uterine microbiota to embryo survival have not been elucidated. Cows offer many advantages as an animal model to study the function of the uterine microbiota: bovine uterine biology and pregnancy development are well characterized; and the uterus is relatively accessible through non-invasive sampling.

The objectives of this project were to (1) examine endometrium-bacteria interactions at the level of the transcriptome and metagenome, and test the hypothesis that such interactions are responsive to genomic selection for fertility; (2) isolate and culture specific uterine microbes from two genotypes of dairy cows divergent in fertility; and (3) use ex-vivo tissue culture systems to validate novel functional mechanisms by which uterine bacteria isolated from cows divergent in genetic merit for fertility interact with the oviduct and endometrium during sperm transport and embryo development.
Uterine and vaginal swabs were collected from Elite-genotype and National Average-genotype Holstein Friesian cows and New Zealand-genotype and Danish-genotype Jersey cows at one week and nine weeks after calving. DNA was extracted from the swabs and sequenced using Illumina shotgun sequencing technology to derive a metagenomic profile for each sample. The uterine microbial population had greater diversity in cows that required assistance at calving compared with cows that calved unassisted. The uterine and vaginal microbial composition was significantly different between dairy cow genotypes and breeds. Also, the vaginal microbial population after calving was significantly different in cows that subsequently developed the uterine diseases metritis and endometritis compared with cows that remained healthy.
The dissemination strategy included a number of activities such as lectures, conference presentations, open day events, discussion group meetings, and webinars. Accordingly, information about the project was disseminated in the following ways: 1) Delivered lectures on uterine health and the uterine microbiome to Cork Institute of Technology Agri-Bioscience students, 2) Organised and promoted the Next Generation Breeding and Reproduction village at the Teagasc Moorepark 2019 Open Day, 3) Delivered presentations on the latest developments in dairy cow reproduction to veterinarian and farmer discussion groups, 4) Delivered training updates to Teagasc dairy advisors, 5) Discussed treatments for uterine disease and other opportunities to improve dairy cow fertility with farmers at the Johnstown Castle Winter milk event and during the Teagasc Dairy Breeding webinar series, 6) Delivered an oral presentation at the Microbiomes Underpinning Agriculture Conference, 7) Submitted the metagenome sequence data to an open-access database, 8) Commenced preparation of manuscripts to be published as open-access.
This action has generated the largest and most comprehensive dataset of uterine and vaginal metagenomes in cattle to date, using state of the art whole genome sequencing technology. Analysis of the sequence data has revealed within and between breed differences in the microbial population – a novel finding that suggests the existence of host-microbe interactions in the bovine reproductive system. Additional analysis has identified bacterial pathogens in cows with uterine disease for which new treatments may be developed. Furthermore, the host organization is ideally positioned to fully exploit the sequence data. The research carried out during this action has set the stage for the development of novel, next generation diagnostic tools for uterine disease. Specifically, the Fellow has already commenced a novel project to evaluate the performance of a portable, rapid DNA sequencer for which the samples and sequence generated by the MICROBE project will be used. If successful, veterinarians could screen for uterine or vaginal pathogens present after calving but before clinical symptoms of disease have manifested, which would facilitate preemptive treatment. We expect that the work carried out in this action will lead to improvements in dairy cow health and fertility. These improvements in disease diagnostics and therapeutic use will be necessary to achieve a 50% reduction in antimicrobial use, as targeted in the EU’s “From farm to fork” strategy.
Overview of MICROBE project