Analysis of the intestinal flora of sucking goats with diarrhea by metagenomic Sequencing

Abstract Background: Diarrhea is one of the important diseases of sucking goats and seriously affects the survival rate of lambs. Many studies have been reported on the etiology of goat diarrhea, but the available information on the intestinal flora disorder in diarrheic goats was limited. Methods: To understand the impact of the gut microbes on goat health and to determine the changes in the intestinal flora of sucking goats with diarrhea, 13 fecal samples from 9 diarrheic lambs and 4 healthy lambs were collected and submitted to metagenomics analysis. Results: The data show that the intestinal flora of diarrheic goats was not only significant changed in the bacterial species, but also displayed abundances decrease in probiotics, such as Butyricicoccus pullicaecorum, Ruminococcus gnavus, Bacteroides fragilis, etc. Many harmful bacteria harboring in the intestinal flora and pathogenic bacteria invading from in vitro should be important bacteria that cause intestinal flora disorder. The most dominant harmful bacteria include Staphylococcus aureus, Lactococcus garvieae, Helicobacter pylori, Escherichia coli, Firmicutes bacterium, Bacteroides plebeius, etc. Conclusion: The intestine flora of sucking goats with diarrhea changed significantly in both species and abundance. Disorder of intestinal flora should be one of the important causes of diarrhea in sucking goats.