Supporting data for "Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations"

The rumen of neonatal calves has limited functionality and establishing intestinal microbiota may play a crucial role in their health and performance. We aim to explore the temporal colonization of the gut microbiome and the benefits of early microbial intervention in newborn calves. We evaluated the impact of microbiota transplantation (MT) on metabolism and later milk production performance. We followed 36 newborn calves for two months and found that the composition and ecological interactions of their gut microbiomes likely reached maturity one month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction of Bacteroides species, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion, antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites. Our study provides metagenomic and metabolomic atlas of the temporal development of the gut microbiome in newborn calves. MT can alter the gut microbiome of newborns, leading to improved physiological status and later milk production. The data may help develop strategies to manipulate the gut microbiota during early life, which may be relevant to the health and production of newborn calves.