利用Illumina MiSeq测序平台分析肉鸡盲肠微生物多样性
Diversity of the cecal microbiome of broiler chicken based on Illumina MiSeq sequencing platform

为对肉鸡盲肠微生物的多样性进行探索，选取15只饲养在相同条件下的科宝-500肉鸡，利用Illumina MiSeq测序平台与Qiime等16s rRNA序列分析工具在22日龄时采集盲肠内容物进行研究。结果显示：1）测序共获得359 158条有效序列与3 210个OTU，并且由稀释曲线可以证明此次测序结果比较全面的覆盖了肉鸡盲肠微生物群落。2）各样品菌群之间存在差异，得到序列的数量以及菌群多样性差别较大。3）通过核心菌群分析可知，4个共享菌群在门水平上分别为：拟杆菌门Bacteroidetes（70.0%±12.1%）、厚壁菌门Firmicutes（25.4%±11.2%）、变形菌门Proteobacteria（4.3%±3.7%）和蓝菌门Cyanobacteria（0.3%±0.5%）。4）有益菌群如乳酸杆菌属Lactobacillus、双歧杆菌属Bifidobacterium虽然存在于盲肠微生物中，但相对丰度不高。5）PICRUSt分析盲肠菌群对应的基因功能发现：功能转运、嘌呤代谢、DNA修复重组蛋白、氧化磷酸化和甲烷代谢等基因功能丰度最高。由此可见，个体差异虽然对肉鸡盲肠微生物结构影响较大，但是仍然存在不少共性。
Tools of 16s Rrna (Illumina MiSeq sequencing platform and Qiime) were used to investigate the diversity of broiler's cecal microbiome.Chicken were raised in the same condition,15 healthy individuals were sacrificed to harvest their cecal samples at 22 days old.The results showed that:1) 359 158 sequences and 3 210 OTU were collected after sequencing and according to the Shannon-Wiener curve,the sequencing data was reliable for overall bacterial of the cecum.2) Differences mainly in sequencing number and the diversity of the microbiota were detected between samples.3) According to the core microbiota analysis,4 shared bacteria in phylum are Bacteroidetes(70.0%±12.1%),Firmicutes(25.4%±11.2%),Proteobacteria(4.3%±3.7%)and Cyanobacteria(0.3%±0.5%).4) Beneficial bacterial such as Lactobacillus,Bifidobacterium were detected in chicken cecum but the relative abundance was low by comparison.5) PICRUSt analysis was performed to show that abundance of the functional genes such as transporters,purine metabolism,DNA repair and recombination proteins,oxidative phosphorylation and methane metabolism were relatively high.Despite the differences among individual animals,lots of similarities were discovered in cecal microbiome among the samples.