家鸽粪便细菌多样性的高通量测序分析及其环境意义

Illumina sequencing of 16S rDNA tag revealed bacterial communities in pigeon feces and its environmental implication

[目的]研究家鸽粪便细菌群落组成与结构特征,明确鸽粪中病原微生物主要类群,探究鸽粪微生物多样性与环境风险之间的关系。[方法]以规模化养殖场家鸽粪便为试验材料,采用Illumina Mi Seq高通量测序方法分析了3个养殖场鸽粪(HP、WB和HH)细菌16S rDNA(V3V4)多样性及其环境意义。[结果]3个鸽粪样品共获得大约12万条有效序列,在Cutoff值为0.03水平上进行可操作分类单元(operational taxonomic unit,OTU)归类,HP、WB、HH分别有4 215、3 672和2 446个OTU类型,Shannon指数为5.00~6.17;VEN图比较分析表明,3个鸽粪样品中微生物种群组成较为一致,细菌共有13个门、31个纲、55个目、101个科和164个属,以拟杆菌门(Bacteroidetes)、变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)为主,覆盖了92%以上的物种数。优势菌属为Myroides、Pseudomonas、Sphingobacterium、Sporosarcina、Erysipelothrix、Oceanisphaer,约占总类群的48.5%~54.6%,且鸽粪中存在18.1%细菌16S rDNA序列未能归类。鸽粪中存在大量的好氧微生物,约占总类群的52%,然而,仅有11%的厌氧微生物。此外,发现鸽粪中含有Myroides、Sphingobacterium、Pseudomonas、Erysipelothrix、Acinetobacter 5种致病性微生物菌属。[结论]鸽粪中存在高度丰富的微生物多样性,有一定的传播禽类病原微生物的环境风险。

[ Objectives] The study was conducted to evaluate the bacterial community composition and structure in pigeon feces, clarify the dominant pathogenic microorganisms from pigeon feces, and account for the relationship between the microbial diversity of pigeon feces and environmental risk. [ Methods] Three fecal samples from large-scale pigeon farms（ HP ,WB and HH）were analyzed for bacterial diversity, using Illumina-based sequencing approach, and its environmental significance was elucidated. [ Results ] A number of 0. 12 million effective 16S rDNA V3V4 sequences were obtained from three pigeon fecal samples. These sequences were assigned to 4 215,3 672 and 2 446 OTU types in HP, WB and HH fecal samples at Cutoff of 0.03 distances, respectively. The Shan- non-Wiener index varied between 5.00 and 6.17. The Venn map was adopted to differentiate bacterial community relationships among different pigeon fecal samples, and it showed that the structure of bacterial communities, on the classification level of the phylum, in the three samples was very similar. All sequences were classified to 164 genera, which belonged to 13 phyla, 31 classes, 55 orders and 101 families. The dominant bacteria phylum in the pigeon feces were Bacteroidetes, Proteobacteria, Firmicutes, which accounts for 92% of all bacteria in pigeon feces. The dominant bacteria in the pigeon feces were Myroides, Pseudomonas, Sphingobacterium, Sporosarcina, Erysipelothrix, Oceanisphaer, accounting for 48.5% - 54.6% of the total group, and 18.1% proportion of bacterial 16S rDNA sequences were not classified. There were a large number of aerobic microorganisms in pigeon feces, which was about 52% of the total group, but, only 11% of the anaerobic microorganisms. Furthermore, five pathogenic bacteria,including Myroides, Sphingobacterium,Pseudomonas, Erysipelothrix, Acinetobacter had been detected. [ Conclusions ] The composition and abundance of the bacterial community in pigeon feces are significantly rich and have a potential risk of spreading poultry pathogenic microorganisms.