Selective decline of bacteria colonizing the calf hindgut during colostrum to milk transition, with persistence of taxa correlating with host passive immunity

In neonate calves, the association between gut microbial colonization and passive immunity acquisition remains largely unknown. We evaluated the effect of transition from colostrum to milk on the hindgut microbiota, and the correlations between acquired passive immunity and this microbiome. In 14 Holstein calves, colostrum quality and host passive immunity were measured, feces were sampled when feeding colostrum and after transition to milk. Then, in eight calves displaying a wide range of passive immunity, the hindgut microbiota was evaluated with DNA sequencing; differential abundance was analyzed with Maaslin2. With transition from colostrum to milk, many initial bacterial colonizers did not survive; genus Ralstonia decreased, but Lactobacillus and Bacteroides increased. When feeding colostrum, the amount of immunoglobulins consumed positively correlated with abundance of Lactobacillaceae and Lachnospiraceae, but Escherichia-Shigella and Clostridium sensu stricto 1 correlated negatively with host passive immunity. After transition to milk, acquired passive immunity negatively correlated with Clostridium sensu stricto 1, Ralstonia, and Veillonella. Overall, many initial hindgut colonizers did not thrive during transition from colostrum to milk, homogenizing the bacterial profile with prevalence of milk digesters. Several bacterial taxa showed strong correlation with host passive immunity, suggesting an interplay between calf passive immunity acquisition and the colonizing microbiota.