鸭疫里默氏菌感染对鸭肠道菌群结构的影响

试验旨在分析鸭疫里默氏菌（RA）感染不同时期鸭肠道菌群结构变化规律,探讨鸭疫里默氏菌对鸭肠道微生物的影响及引起鸭致病的可能机制。采用细菌16S V4-V5区扩增通用引物,扩增鸭疫里默氏菌未感染组（鸭疫里默氏菌感染0 d组）,鸭疫里默氏菌感染后1、2、3、5、9和14 d的鸭直肠内容物样本DNA,将扩增得到的产物进行DNA建库后基于Ion S5^TMXL测序平台测序。测序得到的Raw Reads数据总量为4 710 688条序列,平均每个样本84 119条序列。共注释到数据库的操作分类单元（OTUs）数目为4 528。Alpha多样性分析结果表明,菌群多样性指数Shannon和Simpson在鸭疫里默氏菌感染组和未感染组间差异不显著（P>0.05）,菌群丰富度指数Chao1、Ace、Observed-species和PD-whole-tree在鸭疫里默氏菌感染后0~5 d逐渐降低,从5~14 d又逐渐增加,尤其在鸭疫里默氏菌感染后3和5 d均显著低于未感染组（P<0.05）。Beta多样性分析表明,未感染组与6个时间点的感染组间菌群差异均显著（P<0.05）,其中,未感染组与感染后3 d的物种差异最大,之后依次为感染后2、5、9、1和14 d。物种丰度聚类热图显示,在未感染组和不同时间感染组,物种丰度相对较高的微生物菌属均不同。在门水平,鸭疫里默氏菌感染组主要以厚壁菌门（Firmicutes）、unidentified-Bacteria、拟杆菌门（Bacteroidetes）、梭杆菌门（Fusobacteria）及变形菌门（Proteobacteria）为主;在属水平,Bacteroides在感染组和未感染组均为优势菌属,感染组中弯曲杆菌属（Campylobacter）和梭杆菌属（Fusobacterium）明显增加。本试验分析了鸭疫里默氏菌未感染组和感染不同时间组肠道菌群的差异,寻找到一些特征菌属,可为鸭疫里默氏菌的致病性研究提供理论依据。

Effect of Riemerella anatipestifer Infection on the Microflora of Ducks

The purpose of this study was to analyze the changes of intestinal microflora in ducks infected with Riemerella anatipestifer (RA) in different periods,and to explore the effect of Riemerella anatipestifer on intestinal microflora and the possible pathogenic mechanism.Using universal primers of 16S V4-V5 region of bacteria,the DNA of duck rectal contents in Riemerella anatipestifer uninfected group (Riemerella anatipestifer infected 0 day group) and Riemerella anatipestifer infected 1,2,3,5,9 and 14 days were amplified.The amplified products were sequenced on Ion S5^TMXL sequencing platform after DNA library construction.The total number of Raw Reads was 4 710 688,with an average of 84 119 sequences per sample.The total number of OTUs annotated to the database was 4 528.Alpha diversity analysis showed that Shannon and Simpson indexes had no significant difference between Riemerella anatipestifer infected groups and uninfected group (P>0.05).The indexes of Chao1,Ace,Observed-species and PD-whole-tree decreased gradually from 0 to 5 d after infection,and increased gradually from 5 to 14 d after infection,especially at 3 and 5 d after infection,which were significantly lower than those in uninfected group (P<0.05).Beta diversity analysis showed that there were significant differences between the uninfected group and the infected groups at 6 time points (P<0.05).The species difference between the uninfected group and 3 d after infection was the largest,followed by 2,5,9,1 and 14 d after infection.The cluster heat map of species abundance showed that the microbial genera with relatively high species abundance were different in the uninfected group and the infected groups at different time points.At the phylum level,Firmicutes,unidentified-Bacteria,Bacteroidetes,Fusobacteria and Proteobacteria were the main pathogens in Riemerella anatipestifer infection groups.At the genus level,Bacteroides was the dominant genus in all infected and uninfected groups.The number of Campylobacter and Fusobacterium in infected groups increased significantly.In this experiment,the intestinal microflora data of Riemerella anatipestifer uninfected group and different infection time groups were obtained.The differences between the infected group and uninfected group were analyzed and compared.Some characteristic bacteria were found,which could provide theoretical basis for the pathogenicity research of Riemerella anatipestifer.