Abstract
Despite the significant influence of the microbial communities that inhabit the ruminant's gastrointestinal tract on their health and production, the study of the composition and variations in sheep and goats gut microbiome is limited. The present study investigated the faecal microbiomes of sheep and goats at 6 and 12 months of age using Illumina MiSeq, targeting the 16S rRNA gene V3-V4 region sequences. Firmicutes (95.37%; 93.01%) and Proteobacteria (62.03%; 26.83%) were the core bacterial phyla in goats and sheep, respectively. The core bacterial genera were Lysinibacillus, Escherichia, Anaerocolumn, Clostridium, Streptococcus, Anaerocolumna, Tissierella, Muricomes, Enterococcus, and Bifidobacterium. At the age of 12 months, the complexity and diversity of the bacterial species presented at a high level. In conclusion, the composition of the fecal microbiota showed no substantial differences between sheep and goats at the phylum level, whereas the diversity of the bacterial genera and species increased with age.