Abstract:[Background] Due to the special physiological structure of ruminants, the previous researchers focused on the structure and composition of the rumen microbes, which seriously ignored the important role of cecum microorganism in nutrient digestion and intestinal health. [Objective] The study was designed to reveal the bacterial diversity in cecum and their community structure from goat using MiSeq sequencing technology. [Methods] Twelve 10-month-old and weight of 20.70±1.60 kg goats were selected for collecting cecum liquid after normal feeding, after 20 d, the cecum fluid from each goat was collected and then total genomic DNA was extracted from the cecum fluids. High variable region of bacterial 16S rRNA genes was amplified by PCR using bacterial universal primers. Analyzing amplicon sequence data on the Illumina MiSeq sequencing platform and biological information analysis using QIIME software were done. [Results] In this sequence, 813 496 effective sequences and 6 883 OTU were obtained, and according to the rarefaction curve and coverage index showed that the result of the sequencing was more comprehensive covering the cecum microorganism community of goats. Alpha diversity and beta diversity analysis showed that there were differences in cecum microbial diversity among goats. At the phylum level, the dominant bacteria were Firmicutes and Bacteroidetes, and the core genus was composed of Clostridium, Ruminococcus and unclassified bacteria of six. The cecum microbes of goats are mainly metabolizing function, including carbohydrate metabolism, amino acid metabolism, energy metabolism and lipid metabolism. [Conclusion] The diversity of bacteria in the cecum and rumen of goats was significantly different, similar to the composition of fecal microorganisms, and the composition of cecum microorganisms in both goats and single-gastric animals had similarities and differences.
