The teat skin microbiota of organic primiparous dairy cows is dynamic during the transition period.

Background: The transition period is a critical developmental period for dairy cows, during which the udder undergoes numerous physiological changes that can impact future cow health and performance. The teat skin is an important anatomical feature of the dairy cow, as it is continuously exposed to the environment, and also represents an important barrier against microbes that could invade the teat canal and mammary gland. Yet little is known about the temporal dynamics of the teat skin microbiota during the transition period. Therefore, the main objective of this study was to describe the temporal composition of the teat skin microbiota during the transition period in primiparous dairy cows using 16S rRNA sequencing.

Results: Teat skin swabs were collected throughout the transition period from 710 cows starting their first lactation on 5 certified organic dairy farms. Samples were collected bi-weekly beginning 8 weeks prepartum and then weekly for 4-5 weeks after calving. A total of 4827 teat skin swabs were collected and sequenced, and the resulting sequence data were analyzed by farm and time. Microbial richness, diversity and bacterial load changed dynamically as animals moved through late-stage gestation, parturition and lactation. However, the direction, timing and magnitude of these changes were unique to each farm. Principal component analysis revealed that the composition and structure of the teat skin microbiota also underwent a massive shift during the transition period, with significant differences between phases of the transition period, i.e., late-stage gestation, parturition and lactation. This trend was also observed when samples were categorized into community types using Dirichlet Multinomial Mixture models.

Conclusions: We observe that the teat skin microbiota comprises a diverse community of bacteria and archaea that experience large shifts in abundance and composition as cows move through the transition period. These shifts begin several weeks prior to calving and continue into the first few weeks postpartum, likely driven by a combination of changing environment, management and host physiology during the same period of time. The specific dynamics of these shifts seem to be fairly unique to each farm, which suggests that farm-level factors are important considerations for future work on the teat skin microbiota of transitioning first-lactation dairy cows.