Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health.

A lack of information on the intestinal microbiome of neonatal calves prevents the use of microbial intervention strategies to improve calf gut health. This study profiled the taxonomic and functional composition of the small intestinal luminal microbiome of neonatal calves using whole genome sequencing of metagenome, aiming to understand the dynamics of microbial establishment during the early life. Despite highly individualized microbial communities, we identified two distinct taxonomic-based clusters from the collective luminal microbiomes comprising either a high level of Lactobacillus or Bacteroides Among the clustered microbiomes, Lactobacillus -dominant ileal microbiomes had significantly lower abundances of Bacteroides , Prevotella , Roseburia , Ruminococcus , and Veillonella compared to the Bacteroides -dominated ileal microbiomes. In addition, the upregulated ileal genes of the Lactobacillus -dominant calves were related to leukocyte and lymphocyte chemotaxis, the cytokine/chemokine-mediated signaling pathway, and inflammatory responses, while the upregulated ileal genes of the Bacteroides -dominant calves were related to cell adhesion, response to stimulus, cell communication and regulation of MAPK cascades. The functional profiles of the luminal microbiomes also revealed two distinct clusters consisting of functions related to either high protein metabolism or sulfur metabolism. A lower abundance of Bifidobacterium and a higher abundance of sulfur-reducing bacteria (SRB) were observed in the sulfur metabolism-dominant cluster (0.2±0.1%) compared to the protein metabolism-dominant cluster (12.6±5.7%), suggesting an antagonistic relationship between SRB and Bifidobacterium , which both compete for cysteine. These distinct taxonomic and functional clusters may provide a framework to further analyze interactions between the intestinal microbiome and the immune function and health of neonatal calves. Importance Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding on early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to develop dietary interventions to improve calf gut health. The use of metagenome sequencing based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the pre-weaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density and the abundance taxa and functions were observed. A correlation based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the microbiome and improve calf health.