Abstract
Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis.
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Acknowledgements
This work was supported by the International Science and Technology Cooperation Program of China (Grant Number: 2011DFA30940), the National Basic Research Program of China (‘973 Pilot Research Program’, Grant Number: 2011CB512108), National Key Technologies R&D Program of the Twelve Five-Year Plan, the Ministry of Science and Technology of China (Grant 2012BAI07B03), the National Natural Science Foundation of China (81170959, 30901689 and 81172579), Sichuan Provincial Department of science and technology project (2013SZ0039) and by Oklahoma Applied Research Support (OARS), Oklahoma Center for the Advancement of Science and Technology (OCAST), the State of Oklahoma through the Project AR11-035. We are also grateful to Tong Yuan, Xiaofei Lu, Feifei Liu, Qichao Tu, Zhou Shi, Kai Xue, Lei Cheng (OU researchers) and Arthur Escalas (PhD student of Université Montpellier) for their great help on this project.
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Li, Y., He, J., He, Z. et al. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J 8, 1879–1891 (2014). https://doi.org/10.1038/ismej.2014.28
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DOI: https://doi.org/10.1038/ismej.2014.28
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