Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life

The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (<i>n</i> = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (<i>n</i> = 57) and nasal (<i>n</i> = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by <i>Bacteroidaceae</i> (40%; relative abundance), <i>Ruminococcaceae</i> (13%), and <i>Lachnospiraceae</i> (10%), with changes in diversity (Kruskal-Wallis; <i>p</i> < 0.05) and composition (PERMANOVA; <i>p</i> < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured <i>Moraxellaceae</i> (49%), <i>Mycoplasmataceae</i> (16%), and <i>Pasteurellaceae</i> (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (<i>p</i> < 0.05). NST metrics (Kruskal-Wallis; <i>p</i> > 0.01) and DMM (PERMANOVA; <i>p</i> < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.