基于高通量测序技术对山羊盲肠细菌多样性的分析

【背景】由于反刍动物特殊的生理结构,以往研究者主要集中对其瘤胃微生物的结构与组成进行了大量研究,严重忽略了盲肠微生物在营养物质消化和肠道健康方面发挥的重要作用。【目的】采用高通量测序技术分析山羊盲肠细菌的多样性及菌群结构。【方法】选用12只10月龄健康母羊,其平均体重为20.70±1.60kg,饲喂20d后,采集每只山羊的盲肠内容物,提取微生物总DNA,用细菌通用引物对细菌16S rRNA基因的高可变区进行PCR扩增,利用Illumina MiSeq平台对扩增子进行高通量测序,并用QIIME等软件对测序序列进行生物信息学分析。【结果】山羊盲肠微生物测序共获得813 496条有效序列与6 883个OTU,并且稀释曲线和Coverage指数反映此次测序结果比较全面的覆盖了山羊盲肠微生物群落。α多样性和β多样性分析表明,山羊个体之间盲肠微生物的多样性存在差异。在门水平,各样品的优势菌门均为厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes);属水平,核心菌群由梭菌属(Clostridium)、瘤胃球菌属(Ruminococcus)和6个未分类的细菌组成。PICRUSt基因预测表明,山羊盲肠微生物以代谢功能为主,主要包括:碳水化合物代谢、氨基酸代谢、能量代谢和脂质代谢等。【结论】山羊盲肠与瘤胃细菌的多样性存在显著差异,与粪便微生物组成相似;与单胃动物相比,两者盲肠微生物的组成既有共性,也存在差异。

Analysis of cecum bacterial diversity of goat based on Illumina MiSeq sequencing

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.