The timely acquisition of high-quality colostrum is a proven factor in promoting intestinal health in young calves, including supporting epithelial function, host metabolism, immune development, and microbial colonization. Mucosal microbial colonization is influenced by the birth environment and local factors (ex. temperature, pH, host epithelia types, etc.) We studied the impact of colostrum on the choreography of the neonatal calf microbiome. Twelve healthy, male Holstein calves were separated from their dams immediately following birth, fed 4 liters of aseptically collected, high-quality colostrum, and housed, monitored, and fed separately for the remainder of the experiment. Postpartum maternal udder and vaginal scrapings were sampled. Fecal samples were collected throughout the experiment. Three animals were euthanized for necropsy, and intestinal samples were collected after colostrum administration (day 1), and progressively during the trial (days 3, 7, and 21). The V3-V4 region of the microbial 16S rRNA gene was sequenced from digesta, mucosal scrapings, and feces. Mean diversity indices were highest in maternal udder (mean 217 OTUs) and vaginal scrapings (mean 152 OTUs), followed by colostrum samples. In calf samples, diversity increased over time in all locations; duodenal (mean 122 OTUs) and proximal jejunal samples (mean 217 OTUs) had the highest diversity. Calf duodenal, middle jejunal, and ileal (day 7) digesta samples, and fecal samples were most similar to maternal colostrum samples using Bray-Curtis dissimilarity. When clustering with multidimensional scaling (MDS) by OTU abundance, there was some clustering by location of sample: intestinal samples, stomach samples, and maternal samples clustered somewhat together, respectively. The proximal jejunum had the highest diversity at the phylum level, and contained phyla Acidobacteria and Actinobacteria, which were not observed in abundance elsewhere. Firmicutes increased along the digestive tract (proximal to distal), along which Bacteroidetes and Proteobacteria decreased, the latter of which was much higher in mucosal scrapings (P < 0.05). Shifts in community diversity were observed in the first few days after birth, and neither digesta nor mucosal microbiota had distinguished themselves by 21 days (LDA, PERMANOVA, ANOSIM). A large proportion of genera in colostrum, udder, vagina, and intestinal samples could not be classified. In combination, these results indicate that colostrum contributes significantly to the trajectory of the intestinal microbiome of the young calf. Further studies are needed to identify the mechanism and clinical significance of these results, and to explore the identity and importance of the unknown taxa.
Keywords: host-associated microbiome