基于16S rDNA高通量测序方法检测猪舍环境微生物群落多样性

Characterization of Microbial Community Diversities in Pig House Environments by 16S rDNA High-throughput Sequencing

[目的]研究猪舍环境微生物群落多样性,了解不同类型猪舍环境中细菌群落的结构差异以及潜在的致病菌属。[方法]利用空气沉降法采集规模化猪场妊娠猪舍、保育猪舍、分娩猪舍的环境微生物样本,每种类型猪舍选取3栋猪舍采样,共9个样本。采用Illumina Miseq技术,以细菌16S rDNA的V3~V4变异区为对象进行高通量测序;采用QIIME2软件对测序数据进行分析,比较不同类型猪舍环境微生物群落组成。[结果]在97%相似度阈值下9个样本共得到OTU 29 126个,涵盖31门66纲160目320科899属1 831种的细菌。分娩猪舍以及保育猪舍的Chao1指数、Shannon指数及谱系多样性指数整体高于妊娠猪舍。变形菌门(Proteobacteria)、拟杆菌门(Bacteroidota)、厚壁菌门(Firmicutes)和放线菌门(Actinobacteriota)为猪舍环境的四大优势菌群;变形菌门在3个类型的猪舍中相对丰度均最高,厚壁菌门、放线菌门以及拟杆菌门相对丰度在不同类型猪舍中差异较大。不动杆菌属(Acinetobacter)、棒杆菌属(Corynebacterium)、寡养单胞菌属(Stenotrophomonas)分别是分娩猪舍、妊娠猪舍以及保育猪舍中相对丰度最高的菌属。猪舍环境空气中存在创伤球菌属(Helcococcus)、链球菌属(Streptococcus)、军团菌属(Legionella)、沙雷菌属(Serratia)等多个对动物具有潜在致病力的菌属。[结论]猪舍环境微生物群落多样性丰富,分娩猪舍以及保育猪舍在细菌种类、系统进化多样性以及丰富程度上高于妊娠猪舍。研究发现的猪舍环境中潜在动物致病菌属为猪舍环境消毒的药物选择提供了依据。

[Objective]This study was conducted to characterize the microbial community diversities in pig house environments,to understand the structural differences of bacterial communities in different types of pig house environments,and to identify the potentially pathogenic bacterial genera.[Method]Environmental microbial samples were collected from pregnant sow houses,nursery pig houses and farrowing houses in a large-scale pig farm using air sedimentation method.Three houses were sampled for each type of pig house,with a total of 9 samples.Using Illumina Miseq technology,the high-throughput sequencing was performed targeting on the V3-V4 variant region of bacterial 16S rDNA.The sequencing data were analyzed by QIIME2 software to compare the composition of microbial communities in different types of pig house environments.[Result]At the similarity threshold of 97%,a total of 29126 OTUs were obtained from the 9 samples,covering 31 phyla,66 classes,160 orders,320 families,899 genera and 1831 species of bacteria.The Chao1 index,Shannon index and phylogenetic diversity index of the farrowing houses and nursery pig houses were generally higher than those of the pregnant sow houses.Proteobacteria,Bacteroidota,Firmicutes and Actinobacteriota were the four dominant bacterial groups at the phylum level in the pig house environments.The relative abundance of Proteobacteria was the highest in all three types of pig houses,while the relative abundance of Firmicutes,Actinobacteria and Bacteroidetes varied greatly among different types of pig houses.Acinetobacter,Corynebacterium and Stenotrophomonas were the genera with the highest relative abundance in farrowing houses,pregnant sow houses and nursery pig houses,respectively.There were multiple genera of bacteria with potential pathogenicity to animals,such as Helcococcus,Streptococcus,Legionella and Serratia,in the air of pig houses.[Conclusion]The pig house environments were rich in microbial community diversities. Farrowing houses and nursery pig houses had higher bacterial diversity, evolutionary diversity and abundance than the pregnant sow houses. The potentially pathogenic bacteria found in this study provided references for the selection of disinfection drugs used in pig house environments.