Comparative metagenomic analysis of small ruminants' fecal microbiota

Abstract Background Ruminant's gastrointestinal tract inhabits complex microbial communities that influence several aspects of their development and health. Due to the limited knowledge of the fecal microbial population of sheep and goats, the current study aimed to determine the core fecal microbiota of sheep and goats at different ages. Metagenomic analysis was performed by Illumina MiSeq targeting the V3-V4 region of the 16S rRNA genes. Fecal samples were collected from sheep and goats aged 6 months and 12 months, obtained from a single farm. The fecal bacterial composition of both species was investigated at the phylum, class, order, family, and genus levels. Observed Species, Chao1, and Shannon indices were calculated to measure the microbial diversity.Results The core phyla of sheep and goats were Firmicutes (>93.01% in sheep, >95.37% in goat), followed by Proteobacteria (>26.83%in sheep, >62.03% in goat). At the genus level, a total of 36 genera were identified. Of these, 10 genera were identified in both sheep and goats including Escherichia (>40.12%), Clostridium (19.38%), Enterococcus (>5.03%), Lysinibacillus (>76.95%) Streptococcus (>2.83%), Anaerocolumna (>1.63%), Anaerotignum (>35.95%), Muricomes (>0.99%), Tissierella (>0.91%) and Bifidobacterium (>0.51%). Alpha diversity indices indicated that the highest level for the complexity of species diversity was detected in sheep fecal samples at 12 months of age.Conclusion Fecal bacterial metagenomic analysis of sheep and goats showed no significant differences in the microbiota composition on the phyla level. There was an increase in microbiota diversity with age at the genus level. Although analyzing the bacterial composition and diversity is important, further studies on their poten­tial functionality are required.