基于高通量测序的鼠类肠道细菌群落多样性分析

目的探明鼠类肠道细菌群落组成和多样性。方法分离鼠类完整肠道并提取总DNA,利用Oxford Nanopore Technologies公司(MK1C)的纳米孔单分子测序技术对其肠道细菌16S rRNA的全区序列进行测序,统计肠道细菌的操作分类单元(operational taxonomic unit,OTU)数量,分析其物种组成、丰度及Alpha、Beta多样性。结果获得鼠类肠道细菌16S rRNA优质序列1161377条,根据序列相似性进行聚类分析获得1484个OTUs。共注释到24个门,48个纲,113个目,241个科和534个属;在门分类水平上,以厚壁菌门Firmicutes和变形菌门Proteobacteria为优势门类;在属分类水平上,优势属为肠球菌Enterococcus、乳酸杆菌Lactobacillus和葡萄球菌Staphylococcus,其丰度分别为38.7%,17.65%和7.48%。Alpha多样性分析结果显示,鼠类肠道细菌的观测物种数、Chao1指数、Shannon指数和Simpson指数分别为1484、1825.77、3.91和0.058。Beta多样性分析结果显示臭鼬和小家鼠肠道菌群组成最接近,而黄胸鼠和小家鼠肠道菌群组成相差最大。结论鼠类肠道细菌菌群整体多样性比较丰富,可为有效评估鼠传疾病传播风险提供依据。

Diversity analysis of rodents gut bacteria based on high throughput sequencing

Objective To reveal the gut microbial community structure and diversity in guts of rodents.Methods The total gut DNA was extracted from the rodents.The whole 16 S rRNA sequence of intestinal bacteria was sequenced with nanopore single molecule sequencing technology of Oxford nanopore technologies(mk1 c).The number of operational taxonomic units(OTUs)of intestinal bacteria was counted,and the species composition,abundance,alpha and beta diversity were analyzed.Results A total of 1161377 valid 16 S rRNA sequences were obtained,and 1484 OTUs were obtained by cluster analysis based on sequence similarity.There were 24 phyla,48 classes,113 orders,241 families and 534 genera annotated;Firmicutes and Proteobacteria were the dominant phyla at the phylum level;Enterococcus,Lactobacillus and Staphylococcus were the dominant genera at the genus level,and their abundances were 38.7%,17.65%and 7.48%.Alpha diversity analysis showed that the number of species,Chao1 index,Shannon index and Simpson index were 1484,1825.77,3.91 and 0.058 respectively.The results of beta diversity analysis showed that the intestinal microflora structure of Mephitis mephitis and Mus musculus was the most similar,while the intestinal microflora structure of Rattus flavipectus and Mus musculus was the most different.Conclusion The overall diversity of intestinal bacterial flora of rats is relatively rich,which provides a basis for the effective assessment of the risk of transmission of rat borne diseases.