The respiratory and fecal microbiota of beef calves from birth to weaning

Cattle are most susceptible to bovine respiratory disease (BRD) after feedlot placement. As a result, most research describing the respiratory microbiota of cattle has focussed on time periods when animals are in feedlots, or directly before their arrival. However, the development and growth of animals greatly depends on the establishment and maturation of their respiratory microbiota, which can also be affect by microbial signals from the gut. In this regard, the objective of this study was to evaluate the respiratory and gastrointestinal microbiota of beef calves from birth to weaning. A total of 30 synchronized pregnant cows, and their 30 calves at birth, were enrolled in the study. Deep nasal swabs and feces were collected from calves longitudinally, starting on the day of birth (day 1) and ending on the day of weaning (approximately 180 days of age). Nasopharyngeal, vaginal, and fecal samples were also collected from cows, and the microbiota of all samples were analysed using 16S rRNA sequencing. The fecal microbiota of calves was largely enriched with Lactobacillus during the first 8 weeks of life, before being displaced by genera associated with fibre digestion. The diversity of the calf fecal microbiota continuously increased throughout the study. In contrast, diversity of the calf respiratory microbiota generally decreased over time. On day 1, the calf respiratory microbiota was highly similar to the cow nasal microbiota, indicating colonization from cow contact shortly after birth. The microbial structure of the calf nasal microbiota remained similar to that of the cows, until day 180, when it diverged. This was largely driven by a decrease in Lactobacillus and an increase in genera typically associated with BRD, including Mannheimia, Pasteurella, and Mycoplasma. These three genera colonized calves early in life, though Mannheimia was initially transferred from the cow reproductive tract. Path analysis was used to model the interrelationships of calf respiratory and fecal microbiota. It was observed that respiratory Lactobacillus and fecal Ruminococcacea UCG005 negatively affected the relative abundance of Mannheimia and Pasteurella. Thus, the microbiota of both the respiratory and gastrointestinal tract may have important roles in antagonism of these genera, and overall calf health.