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Simple Summary  The microbiota plays a pivotal role in the metabolism and health of animals. The gut microbiome is dynamically changed by various factors including age, diseases and diet. Before rumen development, most of the gut microbes are found in the colon. However, the diversification and functional changes in gut microbes of neonatal calves are not fully understood. Therefore, the aim of this study was to understand the dynamic changes in the fecal microbiome of pre-weaned calves using metagenomic analysis. We observed dynamic changes in the microbial composition during the pre-weaning period of neonatal dairy calves. In addition, we observed a drastic shift in the gut microbiome during diarrheal disease. Thus, the functions and composition of the fecal microbiome were significantly different between diarrheal cows and healthy cows at the same age. Overall, the study findings provide a strong insight into how aging and diarrhea affect the microbial communities of neonatal dairy calves. The results of study help develop strategies to improve early life gut microbiota being significantly relevant to the health status of dairy cows.    Abstract  Microbiota plays a critical role in the overall growth performance and health status of dairy cows, especially during their early life. Several studies have reported that fecal microbiome of neonatal calves is shifted by various factors such as diarrhea, antibiotic treatment, or environmental changes. Despite the importance of gut microbiome, a lack of knowledge regarding the composition and functions of microbiota impedes the development of new strategies for improving growth performance and disease resistance during the neonatal calf period. In this study, we utilized next-generation sequencing to monitor the time-dependent dynamics of the gut microbiota of dairy calves before weaning (1–8 weeks of age) and further investigated the microbiome changes caused by diarrhea. Metagenomic analysis revealed that continuous changes, including increasing gut microbiome diversity, occurred from 1 to 5 weeks of age. However, the composition and diversity of the fecal microbiome did not change after 6 weeks of age. The most prominent changes in the fecal microbiome composition caused by aging at family level were a decreased abundance of  Bacteroidaceae  and  Enterobacteriaceae  and an increased abundance of  Prevotellaceae . Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis indicated that the abundance of microbial genes associated with various metabolic pathways changed with aging. All calves with diarrhea symptoms showed drastic microbiome changes and about a week later returned to the microbiome of pre-diarrheal stage regardless of age. At phylum level, abundance of Bacteroidetes was decreased ( p = 0.09)  and that of Proteobacteria increased ( p  = 0.07) during diarrhea. PICRUSt analysis indicated that microbial metabolism-related genes, such as starch and sucrose metabolism, sphingolipid metabolism, alanine aspartate, and glutamate metabolism were significantly altered in diarrheal calves. Together, these results highlight the important implications of gut microbiota in gut metabolism and health status of neonatal dairy calves.

Dynamic Changes in Fecal Microbial Communities of Neonatal Dairy Calves by Aging and Diarrhea