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

doi:10.13701/j.cnki.kqyxyj.2020.04.012

Journal of Oral Science Research ›› 2020, Vol. 36 ›› Issue (4): 355-359.DOI: 10.13701/j.cnki.kqyxyj.2020.04.012

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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

Abstract

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

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.

References

[1] 王兴.第四次全国口腔健康流行病学调查报告[M]. 北京:人民卫生出版社,2018:39.
[2] 朱玉娟,焦康礼,周建业,等.常用分子检测技术在儿童龋病微生物多样性研究中的应用[J].口腔医学研究, 2016, 32(2): 202-204.
[3] Munson MA, Banerjee A, Watson TF, et al. Molecular analysis of the microflora associated with dental caries [J] . J Clin Microbiol, 2004, 42(7): 3023-3029.
[4] Aas JA, Griffen AL, Dardis SR, et al. Bacteria of dental caries in primary and permanent teeth in children and young adults [J]. J Clin Microbiol, 2008, 46(4): 1407-1417.
[5] Lima KC, Coelho LT, Pinheiro IV, et al. Microbiota of dentinal caries as assessed by reverse-capture checkerboard analysis [J] . Caries Res, 2011, 45(1): 21-30.
[6] Tanner AC, Kressirer CA, Faller LL. Understanding caries from the oral microbiome perspective [J]. J Calif Dent Assoc, 2016, 44(7): 437-446.
[7] 徐欣, 何金枝, 周学东. 口腔微生物组在口腔精准医疗中的运用[J]. 国际口腔医学杂志, 2017, 44(6): 619-627.
[8] Gu S, Fang L, Xu X. Using SOAPaligner for short reads alignment [J]. Curr Protoc Bioinformatics, 2013, 44: 11.11.1-17.
[9] Luo R, Liu B, Xie Y, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler [J]. Gigascience, 2012, 1(1): 18.
[10] Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences [J] . Nucleic Acids Res, 2010, 38(12): e132.
[11] Fu L, Niu B, Zhu Z, et al. CD-HIT: accelerated for clustering the next-generation sequencing data [J]. Bioinformatics, 2012, 28(23): 3150-3152.
[12] Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND [J] . Nat Methods, 2015, 12(1): 59-60.
[13] Kuribayashi M, Kitasako Y, Matin K, et al. Intraoral pH measurement of carious lesions with qPCR of cariogenic bacteria to differentiate caries activity [J]. J Dent, 2012, 40(3): 222-228.
[14] Schulze-Schweifing K, Banerjee A, Wade WG. Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome [J]. Front Cell Infect Microbiol, 2014, 4: 164.
[15] Obata J, Takeshita T, Shibata Y, et al. Identification of the microbiota in carious dentin lesions using 16S rRNA gene sequencing [J]. PLoS One, 2014, 9(8): e103712.
[16] Zheng J, Wu Z, Niu K, et al. Microbiome of deep dentinal caries from reversible pulpitis to irreversible pulpitis [J]. J Endod, 2019, 45(3): 302-309.
[17] Escapa IF, Chen T, Huang Y, et al. New insights into human nostril microbiome from the expanded human oral microbiome database (eHOMD): a resource for the microbiome of the human aerodigestive tract [J]. mSystems, 2018, 3(6): e00187-18.

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

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