| 摘要: |
| 为研究林麝粪便细菌的结构与组成,选取6只2~3岁的圈养条件相同且健康的公林麝,饲喂精粗比为2:8的饲粮,收集其新鲜粪便,提取其总DNA,然后用16S rRNA细菌通用引物进行PCR扩增,并用Illumina Miseq250PE测序平台,对扩增子进行Miseq双端测序。结果显示:1)借助Illumina Miseq250PE测序平台对样品进行测序,共获得85091条有效序列,5133个有效OTU。2)所得OTU经物种注释被归类为23个门,其中厚壁菌门(Firmicutes)(51.1%±19.9%)、拟杆菌门(Bacteroidetes)(35.6%±15.5%)、变形菌门(Proteobacteria)(5.2%±5.6%)和未分类菌门(*Unassigned)(2.2%±1.0%)为优势菌门,其总和达到菌群相对含量的94.1%;将其进一步分为240个菌属,其中18个为共享菌属,拟杆菌目(*Bacteroidales)(16.5%±10.2%)、瘤胃菌科(*Ruminococcaceae)(14.7%±13.8%)和梭菌目(*Clostridiales)(13.7%±3.9%)含量相对较高。3) OTUs稀释曲线均未达到平台期,说明测序深度不足以覆盖所有的菌群。4)非加权聚类图(PUGMA)显示样品B和E、C和F的菌群多样性相似度较高,而样品A和其他样品的相似度相对较低。由此可见,在正常状态下,健康林麝粪便分布有23个门类细菌群落,以Firmicutes、Bacteroidetes和Proteobacteria为优势菌群,进一步将林麝粪便细菌群落细分为240个属且发现林麝个体间菌群差异性较小且与其他草食动物优势菌群结构相似。 |
| 关键词: 林麝 菌群结构 OTU稀释曲线 共享菌群 |
| DOI：10.11841/j.issn.1007-4333.2016.02.12 |
| 投稿时间：2015-04-03 |
| 基金项目:四川省科技厅国际合作项目(2013HH0043) |
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| Exploring the diversity of musk deer fecal bacterial community |
|
ZHOU Mei-li1, WANG Li-zhi1, YAN Tian-hai1, YANG Ying2, XU Qin1, WANG Ji-wen1, GUO Wei1
|
| (1.Institute of Animal Nutrition, Sichuan Agricultural University, Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Ya'an 625014, China;2.Sichuan Institute of Musk Deer Breeding, Dujiangyan 611800, China) |
| Abstract: |
| To investigate the diversity of the male musk deer hindgut bacterial community,healthy musk deer (n=6;2-3 years of age) were fed using the diet consisting of 20% concentrate and 80% roughage ad libitum.Then we sampled flesh feces and extracted total DNA.The universal bacterial primers were used to amplify the V4-V5 region of 16S rRNA genes.We identified and characterized the overall fecal bacteria composition by all musk deer using the 16S rRNA high-throughput sequencing on the Illumina Miseq sequencing platform.Results showed that the sequencing data exhibited that the overall number of OTUs and valid reads using the Miseq sequencing of 16S rRNA gene reached 5133 OTUs (similarity ≥97%) and 85091 reads,respectively.In total,23 phyla were detected in the samples.Among them,the Firmicutes (51.1%±19.9%),Bacteroidetes (35.6%±15.5%),*Unassigned (2.2%±1.0%) and Proteobacteria(5.2%±5.6%)were the dominant phyla which consisted 94.1% of the overall bacteria community.At the genus level,240 genera could be found in all samples or part of samples.Among genera,the 18 shared genera were present in all fecal samples,and the *Bacteroidales (16.5%±10.2%)、*Ruminococcaceae (14.7%±13.8%)、*Clostridiales (13.7%±3.9%)are the predominant shared genera.The OTU rarefaction curves didn't reach the saturation plateau in the samples reflecting there were not enough coverage estimations.Furthermore,UPGMA analysis of the samples showed that the similarity of B and E、C and F bacteria communities were the highest.Therefore,our research revealed that hindgut bacteria communities from healthy musk deer fed using the basal diet were classified 23 phyla.Among them,Firmicutes,Bacteroidetes and Proteobacteria were regarded as the dominant hindgut bacteria phyla.Further genus-level analysis showed that 240 genera were discovered across all stool samples,18 genera of which were common bacteria communities.The similarity of hindgut bacteria distribution among different musk deer was relatively high,which was also similar with the dominant hindgut bacteria communities from the other herbivores. |
| Key words: musk deer structure of bacteria community OTU rarefaction curve shared bacteria community |
