基于MiSeq分析川中黑山羊瘤胃细菌的多样性及群落结构

Analysis the bacterial diversity in rumen and their community structure from Chuanzhong black goat using MiSeq sequencing technology

采用MiSeq高通量测序技术分析川中黑山羊瘤胃细菌的多样性及菌群结构。选用3只140日龄健康公羊,其平均体质量为(15.53±0.21)kg,饲喂10 d后,于150日龄时采集瘤胃液(样品A),40 d后再次采集瘤胃液(样品F),提取瘤胃液细菌基因组DNA,对细菌16S rDNA序列V4区进行MiSeq测序。结果显示:1)从样品A与样品F中共获得高质量序列338 830条,聚类后得3 400个运算分类单位(OTU);2)样品A的α多样性指数高于样品F的,但其差异无统计学意义;3)门水平上,样品A最高相对丰度为拟杆菌门的(占总序列数的40.87%),其次为厚壁菌门的(27.19%),样品F最高相对丰度为拟杆菌门的(47.12%),其次为变形菌门的(19.99%),再次为厚壁菌门的(18.05%),样品A厚壁菌门的相对丰度极显著高于样品F的(P<0.01);4)在属水平上,样品A与样品F的最高相对丰度均为普雷沃氏菌属的(样品A的为25.54%,样品F的为27.67%),样品A中月形单胞菌属、丁酸弧菌属、瘤胃球菌属、琥珀酸弧菌属、琥珀酸菌属等的相对丰度显著高于样品F的(P<0.05)。试验结果表明,川中黑山羊瘤胃中相对丰度最高的菌门为拟杆菌门,相对丰度最高的菌属为普雷沃氏菌属,且两瘤胃样品中部分细菌相对丰度间的差异显著。

The study was designed to reveal the bacterial diversity in rumen and their community structure from Chuanzhong black goat using MiSeq sequencing technology. Three 140-day-old and weight of （15.53±0.21）kg Chuanzhong black goats were selected for collecting rumen liquid after normal feeding of 10 d （sample A）,after 40 d ,the rumen fluid was collected again（sample F）, respectively. Total DNA were extracted for amplifying V4 area in 16S rDNA, and their products were sequenced by IUumina MiSeq sequencing system. The results showed that： 1） A total of 338 830 high quality valid sequences from the sample A and the sample F, 3 400 operational taxonomic units were obtained. 2） The alpha diversity index of sample A was higher than that of sample F, however, their difference did not reach to statistical significance level. 3） At phylum level, the most abundant phylum in sample A was Bacteroidetes （accounted for 40.87% of the total sequences）, followed by Firrnicutes （it accounted for 27.19% of the total）; the most abundant phylum in sample F was Bacteroidetes （accounted for 47.12% of the total sequences） followed by Proteobacteria （it accounted for 19.99% of the total）, and Firmicutes （it accounted for 18.05% of the total）; the relative abundance of Firmicutes in sample A was very significantly higher than that in sample F （P 〈 0.01）. 4） At genus level, the most abundant genera was Prevotella （sample A was 25.54%, sample F was 27.67%）; the relative abundance of Selenomonas, Butyrivibrio, Ruminococcus, Succinivibrio and Succiniclasticum in sample A was significantly higher than that in sample F （P 〈 0.05）. In conclusion, Bacteroidetes was the most abundant phylum in the rumen bacterial community of Chuanzhong black goats, and Prevotella was the most abundant genus; there were significant difference between sample A and sample F.