Differences in gut microbiome of Korean indigenous calves as driven by bovine rotavirus and bovine coronavirus infection

The gut microbiome of cattle suppresses pathogens and aids host immunity. However, the gut microbiome of newborn calves is still developing; therefore, diarrhea caused by pathogen infection is common. Rapid changes in the gut microbiome due to diarrhea have a significant impact on the health and growth of calves. Until recently, there have been few studies on the changes in the gut microbiome following infection with major digestive pathogens that cause diarrhea in Hanwoo (Korean indigenous cattle) calves. Therefore, this study was conducted to identify viral digestive pathogens that cause severe diarrhea in Hanwoo calves. Seven normal calves without diarrhea and eight calves with diarrhea were selected, and their feces were collected to analyze pathogens and the gut microbiome. Bovine rotavirus (BRV) and bovine coronavirus (BCoV) were detected in the feces of the calves with diarrhea. There was no significant difference in the alpha diversity of the microbiome between normal calves and calves infected with viruses; however, a significant decrease in NPShannon and Shannon indices and a significant increase in Simpson index were observed in calves infected with BRV compared to calves infected with BCoV. In addition, beta diversity of the microbiome differed distinctly between normal calves and calves infected with BRV or BCoV. At the class level, BRV infection increased <italic>Gammaproteobacteria</italic> and <italic>Actinobacteria</italic>, whereas BCoV infection increased <italic>Clostridia</italic> and decreased <italic>Bacilli</italic>. In addition, the abundance of <italic>Lactobacillus</italic> was significantly reduced upon infection with BRV and BCoV. In this study, we confirmed the differences in the gut microbiome based on viral pathogens causing diarrhea in Hanwoo calves. The results of pathogen-targeting research are expected to be helpful in preventing common pathogens in calves.