Abstract
Housing strategies to alleviate the negative effects of heat stress on the performance of pre-weaned dairy calves have become a focus of research in recent years. Experiments evaluating such strategies have focused on thermoregulatory responses, behavior, and performance. To date, no experiments have evaluated their effects on the microbiota of the upper respiratory tract. Understanding this relationship is crucial for assessing its impact on respiratory health, disease susceptibility, and calf well-being. We conducted an experiment to characterize nasal microbiota from calves housed outdoors, under a naturally ventilated barn, with and without the provision of fans. The experiment was conducted in a commercial dairy in southern GA. Male Holstein calves (n = 60) were assigned randomly at birth (day 0) to 1 of 3 treatments: hutch outdoors with 50% of its area covered with plywood (control = 20), hutch in an open-sided barn with no supplemental cooling (SH = 21), and hutch in an open-sided barn with ceiling fans (SHF = 19), and followed until 68 d of age. Following the removal of obvious debris from the nostrils, nasal swabs were collected from all calves on week 5 (35 ± 8.9 d) and 9 (63 ± 3.2 d) of life and qPCR and 16S rRNA sequencing was performed. Treatment did not affect total bacterial 16S gene copy numbers or alpha diversity (i.e., Shannon and Simpson indexes) at 5 or 9 wk of age. We observed differences, however, in the nasal microbiome structure at weeks 5 and 9 among treatments, with variations in the mean relative abundance (MRA) of certain bacterial genera. On week 5, SHF treatment had reduced MRA of Mycoplasma compared with control and SH treatments and greater MRA of Acinetobacter than calves in the SH treatment. On week 9, control calves had reduced MRA of Escherichia compared with SHF calves and greater Moraxella MRA compared with those in the SH and SHF treatments. We observed differences in nasal microbiome structure of pre-weaned dairy calves as a result of housing strategy. While the results presented herein suggest a potential link between housing conditions and the risk of respiratory disease, further research is necessary to investigate this hypothesis. Improved understanding of the impact of housing environment on respiratory health as well as on heat stress could help producers make informed management decisions to improve calf health and well-being.