Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

被引:290
作者
Liu, Bo [1 ,2 ]
Faller, Lina L. [3 ]
Klitgord, Niels [3 ]
Mazumdar, Varun [3 ]
Ghodsi, Mohammad [1 ,2 ]
Sommer, Daniel D. [1 ]
Gibbons, Theodore R. [1 ,4 ]
Treangen, Todd J. [1 ,10 ]
Chang, Yi-Chien [3 ]
Li, Shan [5 ]
Stine, O. Colin [5 ]
Hasturk, Hatice [8 ]
Kasif, Simon [3 ,7 ,9 ]
Segre, Daniel [3 ,6 ,7 ]
Pop, Mihai [1 ,2 ,4 ]
Amar, Salomon [3 ,11 ]
机构
[1] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA
[2] Univ Maryland, Dept Comp Sci, College Pk, MD 20742 USA
[3] Boston Univ, Bioinformat Program, Boston, MA 02215 USA
[4] Univ Maryland, Biol Sci Grad Program, College Pk, MD 20742 USA
[5] Univ Maryland, Sch Med, Dept Epidemiol & Publ Hlth, Baltimore, MD 21201 USA
[6] Boston Univ, Dept Biol, Boston, MA 02215 USA
[7] Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA
[8] Forysth Inst, Dept Periodontol, Cambridge, MA USA
[9] Harvard Massachusetts Inst Technol, Childrens Informat Program, Div Hlth Sci & Technol, Boston, MA USA
[10] Johns Hopkins Univ, Sch Med, McKusick Nathans Inst Genet Med, Baltimore, MD USA
[11] Boston Univ, Ctr Antiinflammatory Therapeut, Goldman Sch Dent Med, Boston, MA 02215 USA
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
ANTIBIOTIC-RESISTANCE PROFILE; PORPHYROMONAS-GINGIVALIS; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE; BACTERIAL DIVERSITY; GENETIC-ANALYSIS; FATTY-ACIDS; GENOME; PATHOGENS; IDENTIFICATION; PREVALENCE;
D O I
10.1371/journal.pone.0037919
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (similar to 2 lanes Illumina 76 bp PE) and high human DNA contamination ( up to similar to 90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.
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页数:16
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