Effects of social rearing systems on the gut microbiome of dairy calves before and after weaning.

Social housing may offer behavioral benefits for dairy calves but may also increase exposure to diverse microbes, including pathogens. Pre-weaned dairy calves are susceptible to gastrointestinal diseases, and it is unknown how social contact may impact the gut microbiome composition of dairy calves before and after weaning. This study aimed to investigate the effects of social rearing systems on the fecal microbiome of dairy heifer calves before and 3 d after weaning. The study was conducted at the University of Minnesota West Central Research and Outreach Center dairy in Morris, Minnesota. Dairy calves born from September to November 2020 were randomly assigned to one rearing system at birth: individual (IND, n = 18); group (GRP, n = 21); or dam-reared (DAM, n = 15). Calves were weaned at 63 d and housed in groups and comingled with other calves from the different treatments. Fecal samples were collected before and 3 d after weaning and sent for 16S rRNA short amplicon sequencing (V4 region). Gut microbiome sequence data were analyzed with Qiime2 and the R statistical interface for ecological analyses. Results showed a significant effect of the rearing system, weaning, and an interaction between the housing system and weaning on the calf fecal microbiome. Even though all treatments had different fecal microbiome compositions before weaning, particularly for analyses of presence/absence of taxa (Jaccard index), DAM raised calves showed the most distinctive microbiome and lower α diversity when compared with GRP and IND calves before weaning. DAM calves showed enrichment of Firmicutes, particularly before weaning, and enrichment of genera associated the fermentative metabolism and gut maturation, such as, Butyricicoccus, Megasphaera, Ruminococcus, Collinsella, and Sphaerochaeta. The GRP and IND calves had an enrichment of bacteria associated with solid feed intake, such as members of Prevotellaceae family before weaning. All calves showed a shift in their microbiome over weaning. After weaning, there were fewer microbiome compositional and diversity differences between treatments. Nevertheless, DAM calves maintained the most distinctive microbiome and unique features, such as lower enrichment of Prevotella and Bifidobacterium when compared with IND and GRP calves. In summary, results indicated that rearing calves in full contact with dams (therefore, having access to adult cattle and their environmental resources), may impact gut microbiome colonization and potentially accelerate gut maturation. However, those effects were less pronounced after weaning. The results also indicated the presence of beneficial bacteria in all treatment calves. Therefore, contact with adult cattle and their environmental resources appears to influence gut microbiome composition and maturation of dairy calves. Nevertheless, further studies, including functional analyses (shotgun metagenomics and metatranscriptomics, metabolomics, immune performance) considering different weaning strategies, feed intake, and environmental samples, as well as disease challenge models postweaning, would help elucidate the effects of social contact on the gut microbiome and health of dairy calves.