深龋微生物宏基因组测序结果比对不同数据库的研究

doi:10.13701/j.cnki.kqyxyj.2020.04.012

口腔医学研究 ›› 2020, Vol. 36 ›› Issue (4): 355-359.DOI: 10.13701/j.cnki.kqyxyj.2020.04.012

深龋微生物宏基因组测序结果比对不同数据库的研究

常婷^1,2, 周密^1,2, 李仪红³, 刘高霞^1,2*

1.华中科技大学同济医学院附属协和医院口腔医学中心湖北武汉 430022;
2.口腔颌面发育与再生湖北省重点实验室湖北武汉 430022;
3.纽约大学牙学院美国纽约 10010

收稿日期:2019-11-27 出版日期:2020-05-28 发布日期:2020-05-28
通讯作者: 刘高霞,E-mail: 2011xh0847@hust.edu.cn
作者简介:常婷(1978~ ),女,湖北黄石人,主治医师,博士,研究方向:口腔生物学。
基金资助:
国家自然科学基金青年项目(编号:81400503)

Metagenomic Analysis of Microbial Community Profiles in Deep Caries in Different Databases

CHANG Ting^1,2, ZHOU Mi^1,2, LI Yihong³, LIU Gaoxia^1,2*

1. Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
2. Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China;
3. New York University College of Dentistry, New York10010, USA

Received:2019-11-27 Online:2020-05-28 Published:2020-05-28

摘要/Abstract

摘要： 目的: 探讨深龋微生物宏基因组测序结果物种注释时比对不同数据库的差异。方法: 收集青少年第一恒磨牙深龋样本共16份,提取DNA后基因组高通量测序。测序结果分别比对NCBI nr数据库及HOMD数据库,分析应用不同数据库时深龋微生物组成的差异性。结果: 深龋微生物在纲分类水平上,两种数据库中相对丰度位于前10微生物均为放线菌纲、芽孢杆菌纲、拟杆菌纲、红蝽菌纲、Negativicutes纲、梭杆菌纲、梭菌纲、β-变形菌纲、黄杆菌纲和互养菌纲。在属分类水平上,两种数据库中相对丰度位于前10微生物均为乳杆菌属、放线菌属、欧氏菌属、普氏菌属、丙酸杆菌属、链球菌属、月形单胞菌属、棒杆菌属、纤毛菌属和类斯氏菌属。物种比例水平在两数据库中得到的数值有微小差异,但无明显统计学意义(P>0.05)。结论: 深龋样本宏基因组数据分别于NCBI nr和HOMD数据库注释后,微生物数量及结构无明显差异。

关键词: 深龋, 微生态, 宏基因组, 数据库

Abstract: Objective: To explore the annotation distinction of microbial taxa of human deep carious lesion in different databases. Methods: Sixteen deep carious samples were obtained from the first permanent molars of eight young adult patients. High-throughput metagenomic technology was used to sequence the microbial genomic DNA of each sample. The microbial composition and abundance at each taxon level were analyzed with both the NCBI nr database and HOMD database. Results: For the deep carious lesions, whether the NCBI nr database or HOMD database, the top 10 microbial taxa found at class rank were Actinobacteria, Bacilli, Bacteroidetes,Coriobacteriia, Negativicutes, Fusobacteriia, Clostridia, Betaproteobacteria, Flavobacteriia and Synergistia. At the genus rank, the top 10 microbial taxa identified from both databases were Lactobacillus, Actinomyces, Olsenella, Prevotella, Propionibacterium, Streptococcus, Selenomonas, Corynebacterium, Leptotrichia and Parascardovia. The abundance and percentage of the microbial taxa acquired from two databases were similar (P>0.05). Conclusion: The findings demonstrated that there was no significant statistical difference in microbial annotation analysis between the NCBI nr database and HOMD database for deep carious samples.

Key words: deep caries, microecology, metagenome, database

常婷, 周密, 李仪红, 刘高霞. 深龋微生物宏基因组测序结果比对不同数据库的研究[J]. 口腔医学研究, 2020, 36(4): 355-359.

CHANG Ting, ZHOU Mi, LI Yihong, LIU Gaoxia. Metagenomic Analysis of Microbial Community Profiles in Deep Caries in Different Databases[J]. Journal of Oral Science Research, 2020, 36(4): 355-359.

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深龋微生物宏基因组测序结果比对不同数据库的研究

Metagenomic Analysis of Microbial Community Profiles in Deep Caries in Different Databases

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