Review Topical Sections

Oral microbiome and health

  • The oral microbiome is diverse in its composition due to continuous contact of oral cavity with the external environment. Temperatures, diet, pH, feeding habits are important factors that contribute in the establishment of oral microbiome. Both culture dependent and culture independent approaches have been employed in the analysis of oral microbiome. Gene-based methods like PCR amplification techniques, random amplicon cloning, PCR-RELP, T-RELP, DGGE and DNA microarray analysis have been applied to increase oral microbiome related knowledge. Studies revealed that microbes from the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria, Neisseria, TM7 predominately inhabits the oral cavity. Culture-independent molecular techniques revealed the presence of genera Megasphaera, Parvimonas and Desulfobulbus in periodontal disease. Bacteria, fungi and protozoa colonize themselves on various surfaces in oral cavity. Microbial biofilms are formed on the buccal mucosa, dorsum of the tongue, tooth surfaces and gingival sulcus. Various studies demonstrate relationship between unbalanced microflora and development of diseases like tooth caries, periodontal diseases, type 2 diabetes, circulatory system related diseases etc. Transcriptome-based remodelling of microbial metabolism in health and disease associated states has been well reported. Human diets and habitat can trigger virus activation and influence phage members of oral microbiome. As it is said, “Mouth, is the gateway to the total body wellness, thus oral microbiome influences overall health of an individual”.

    Citation: Neetu Sharma, Sonu Bhatia, Abhinashi Singh Sodhi, Navneet Batra. Oral microbiome and health[J]. AIMS Microbiology, 2018, 4(1): 42-66. doi: 10.3934/microbiol.2018.1.42

    Related Papers:

    [1] Gaozhong Sun, Tongwei Zhao . Lung adenocarcinoma pathology stages related gene identification. Mathematical Biosciences and Engineering, 2020, 17(1): 737-746. doi: 10.3934/mbe.2020038
    [2] Pingping Song, Jing Chen, Xu Zhang, Xiaofeng Yin . Construction of competitive endogenous RNA network related to circular RNA and prognostic nomogram model in lung adenocarcinoma. Mathematical Biosciences and Engineering, 2021, 18(6): 9806-9821. doi: 10.3934/mbe.2021481
    [3] Yong Ding, Jian-Hong Liu . The signature lncRNAs associated with the lung adenocarcinoma patients prognosis. Mathematical Biosciences and Engineering, 2020, 17(2): 1593-1603. doi: 10.3934/mbe.2020083
    [4] Siqi Hu, Fang Wang, Junjun Yang, Xingxiang Xu . Elevated ADAR expression is significantly linked to shorter overall survival and immune infiltration in patients with lung adenocarcinoma. Mathematical Biosciences and Engineering, 2023, 20(10): 18063-18082. doi: 10.3934/mbe.2023802
    [5] Kunpeng Li, Zepeng Wang, Yu Zhou, Sihai Li . Lung adenocarcinoma identification based on hybrid feature selections and attentional convolutional neural networks. Mathematical Biosciences and Engineering, 2024, 21(2): 2991-3015. doi: 10.3934/mbe.2024133
    [6] Dongchen Lu, Wei Han, Kai Lu . Identification of key microRNAs involved in tumorigenesis and prognostic microRNAs in breast cancer. Mathematical Biosciences and Engineering, 2020, 17(4): 2923-2935. doi: 10.3934/mbe.2020164
    [7] Yanping Xie, Zhaohui Dong, Junhua Du, Xiaoliang Zang, Huihui Guo, Min Liu, Shengwen Shao . The relationship between mouse lung adenocarcinoma at different stages and the expression level of exosomes in serum. Mathematical Biosciences and Engineering, 2020, 17(2): 1548-1557. doi: 10.3934/mbe.2020080
    [8] Shuyi Cen, Kaiyou Fu, Yue Shi, Hanliang Jiang, Jiawei Shou, Liangkun You, Weidong Han, Hongming Pan, Zhen Liu . A microRNA disease signature associated with lymph node metastasis of lung adenocarcinoma. Mathematical Biosciences and Engineering, 2020, 17(3): 2557-2568. doi: 10.3934/mbe.2020140
    [9] Bijiong Wang, Yaodong Tang, Biyun Yu, Di Gui, Hui Xu . Expression of autophagy-related factor p62 for lung cancer diagnosis and prognosis: A systematic review and meta-analysis. Mathematical Biosciences and Engineering, 2019, 16(6): 6805-6821. doi: 10.3934/mbe.2019340
    [10] Jian Huang, Zheng-Fu Xie . Identification of SSBP1 as a prognostic marker in human lung adenocarcinoma using bioinformatics approaches. Mathematical Biosciences and Engineering, 2022, 19(3): 3022-3035. doi: 10.3934/mbe.2022139
  • The oral microbiome is diverse in its composition due to continuous contact of oral cavity with the external environment. Temperatures, diet, pH, feeding habits are important factors that contribute in the establishment of oral microbiome. Both culture dependent and culture independent approaches have been employed in the analysis of oral microbiome. Gene-based methods like PCR amplification techniques, random amplicon cloning, PCR-RELP, T-RELP, DGGE and DNA microarray analysis have been applied to increase oral microbiome related knowledge. Studies revealed that microbes from the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria, Neisseria, TM7 predominately inhabits the oral cavity. Culture-independent molecular techniques revealed the presence of genera Megasphaera, Parvimonas and Desulfobulbus in periodontal disease. Bacteria, fungi and protozoa colonize themselves on various surfaces in oral cavity. Microbial biofilms are formed on the buccal mucosa, dorsum of the tongue, tooth surfaces and gingival sulcus. Various studies demonstrate relationship between unbalanced microflora and development of diseases like tooth caries, periodontal diseases, type 2 diabetes, circulatory system related diseases etc. Transcriptome-based remodelling of microbial metabolism in health and disease associated states has been well reported. Human diets and habitat can trigger virus activation and influence phage members of oral microbiome. As it is said, “Mouth, is the gateway to the total body wellness, thus oral microbiome influences overall health of an individual”.


    Lung cancer are the most common causes of cancer-related deaths worldwide, which accounts for over 25% of all cancer-related deaths [1,2]. Lung cancer is classified into four main histological categories: lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), large cell lung carcinoma (LCLC) and small cell lung cancer (SCLC). Recent development in molecular targeted therapies have markedly improved the survival of individuals with LUAD.

    Risk stratification and survival estimation are very important to guide personalized treatment decision in patients with cancer. The principal clinical determinant in the therapeutics option and prognosis prediction for most solid tumors is tumor status, characterized by TNM staging system. However, there are heterogeneous clinical outcomes in patients sharing similar clinical features, indicating that TNM staging system is insufficient in risk stratification and the management of tumors could be improved by combining bio molecular signatures with traditional TNM staging system.

    miRNAs are short (approximately 18–24 nucleotides) noncoding RNAs and are common mechanisms of the posttranscriptional gene expression [3,4,5]. miRNAs play important roles in various process of tumor genesis and development [6,7]. They are highly conserved and their dysregulation are observed in all the types of tumors [6,7,8]. As miRNAs are very stable due to their resistance to RNase activity and to inferior circumstances [3], they can serve as cancer markers. Furthermore, the miRNA signature associated with survival outcome will be helpful to elucidate the mechanisms of miRNAs in lung cancer as well as develop novo therapeutics. In fact, a number of miRNAs have been characterized as promising molecule biomarkers for diagnosis, prediction of treatment efficacy, recurrence, metastasis and prognosis in patients with head and neck cancer [9,10], lung cancer [11,12,13,14,15,16,17], breast cancer [18,19,20,21], gastric cancer [22], pancreatic cancer [23], colorectal cancer [24,25], prostate cancer [26], cervical cancer [27,28] and bladder cancer [29].

    In our present study, a prognosis predicting model was constructed by a combination of miRNA expression profile and TNM classification parameters, and the prognostic model was visualized with a nomogram.

    The miRNA expression data (Data S1) and corresponding clinical information (Data S2) were downloaded from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/) at March 2019. There were 1881 miRNAs from 567 samples, including 521 LUAD tissues and 46 adjacent normal lung tissues, which were collected from patients with LUAD. Individuals with missing records in overall survival, endpoint event, sex, age at diagnosis, smoking history, TNM stages, cancer status, postoperative treatment, radiotherapy and treatment outcome, were excluded. Individuals whose survival time shorter than 2 months were also excluded, because they are likely to die from causes other than cancer. 460 individuals with LUAD were included in Cox regression analysis and randomly assigned into two distinct subetaoups, 306‐patient training set and 154‐patient validating set, at a ratio of 2:1, when visualizing the prognostic model with a nomogram.

    The expression data for miRNAs was normalized by log 2 transformation. Differential expression analysis between two groups (cancer vs control) was performed through Bayesian test with package ‘limma’ [30] for R (v3.6.3) [31] on the criteria of |log 2 FC (fold change)| ≥ 1 and P value < 0.05 [32,33,34].

    The differentially expressed miRNA data and clinical data were combined through function ‘merge’ in R. Then the possible prognostic value of differentially expressed miRNAs and clinicopathological parameters (194 differentially expressed miRNAs, T stage, N stage and Metastasis status) were assessed by univariate Cox regression analysis with R package ‘survival’ [35]. Subsequently, the candidate miRNAs and clinicopathological parameters with P value < 0.1 (41 miRNAs, T stage, N stage and Metastasis status) were further evaluated by multivariate Cox regression analysis with R package ‘survival’ [35].

    miRNA index was calculated by a linear combination of miRNA expression levels weighted by regression coefficient (β) from multivariate Cox regression analysis [10,11,12,19,21,25,28]. The formula was as follows: miR.index = βgene1 × exprgene1 + βgene2 × exprgene2 + … + βgenen × exprgenen, where “expr” indicated the expression levels of miRNA. With the median miR.index as the cutoff point, patients were stratified into two groups: low risk group (<median miR.index) and high risk group (>miR.index). Kaplan-Meier survival analysis was performed for the low and high risk groups with R package ‘survival’ [35] and ‘survminer’ [36].

    A nomogram was generated to visualize the effect of the miR.index and clinicopathological parameters on the survival of patients with LUAD in the training set, using R package ‘rms’ [37]. Subsequently, the prognostic model was tested by calculating the C-index and drawing the calibration curve in the training set and validating set, respectively.

    The aforementioned methods used in this study were illustrated in a flow diagram (Figure S1).

    The target genes of the identified prognostic miRNAs were predicted using miRTarBase (Release 7.0, http://miRTarBase.mbc.nctu.edu.tw/) bioinformatics analysis tools, which contains a great number of experimentally validated miRNA target genes. These target genes were then incorporated into Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis via the online bioinformatics tool, the Database for Annotation, Visualization, and Integrated Discovery (Release 6.8, https://david.ncifcrf.gov/).

    All statistical analyses were performed with R. Log-rank test was conducted to compare the difference for survival. Chi-square test was employed to test the clinicopathological parameters between the low risk and high risk groups. All statistical tests were two-tailed and P values < 0.05, except for P value < 0.1 in the univariate Cox regression analysis, were regarded as significant.

    Totally, 460 patients with LUAD were enrolled in the present study. The detailed clinicopathological characteristics of enrolled patients were shown in Data S3.

    A total of 194 differentially expressed (99 up-regulated and 95 down-regulated) miRNAs were identified between LUAD tissues and matched normal tissues, based on the cut-off criteria of (|log 2 FC| > 1.0 and P < 0.05). The differentially expressed miRNAs were presented in Data S4.

    A set of 41 miRNAs, T stage, N stage and Metastasis status, which had potential relationship to patient survival, were screened out by univariate Cox proportional hazards regression analysis (Data S5). These candidate miRNAs and TNM classification parameters were further verified by multivariate Cox proportional hazards regression analysis. Nine miRNAs (hsa-let-7i, hsa-mir-1976, hsa-mir-199a-1, hsa-mir-31, hsa-mir-3940, hsa-mir-450a-2, hsa-mir-4677, hsa-mir-548v and hsa‐mir‐6803) and N stage were identified as independent prognostic indicators for patients with LUAD (Data S6). Patients in low risk group had a superior overall survival compared to those in high risk group (89.4 months vs 38.2 months, P = 1e-08) (Figure 1). The demographic and clinicopathological characteristics between patients of the two groups were presented in Table 1. Among these nine miRNAs, hsa-mir-1976, hsa-mir-199a-1, hsa-mir-4677, hsa-mir-548v and hsa‐mir‐6803 were positively correlated with the overall survival, hsa-let-7i, hsa-mir-31, hsa-mir-3940 and hsa-mir-450a-2 were negatively correlated with the overall survival.

    Figure 1.  Patients in low risk group had a superior overall survival compared to those in high risk group.
    Table 1.  clinicopathological characteristics of patients finally included in the study stratified by miR.index.
    Overall Low Risk High Risk p
    460 230 230
    Sex (%) Female 243 (52.8) 127 (55.2) 116 (50.4) 0.35
    Male 217 (47.2) 103 (44.8) 114 (49.6)
    age (%) ≤ 66(Median) 229 (49.8) 116 (50.4) 113 (49.1) 0.852
    >66(Median) 158 (47.6) 84 (49.4) 74 (45.7)
    smoking_status (%) Never Smokers 62 (13.9) 40 (17.8) 22 (10.0) 0.055
    Former Smokers 273 (61.2) 130 (57.8) 143 (64.7)
    Current Smokers 111 (24.9) 55 (24.4) 56 (25.3)
    T (%) T1 158 (34.3) 83 (36.1) 75 (32.6) 0.52
    T2 243 (52.8) 122 (53.0) 121 (52.6)
    T3 42 (9.1) 19 (8.3) 23 (10.0)
    T4 17 (3.7) 6 (2.6) 11 (4.8)
    N (%) N0 303 (65.9) 158 (68.7) 145 (63.0) 0.231
    N1 90 (19.6) 39 (17.0) 51 (22.2)
    N2 65 (14.1) 31 (13.5) 34 (14.8)
    N3 2 (0.4) 2 (0.9) 0 (0.0)
    M (%) M0 442 (96.1) 225 (97.8) 217 (94.3) 0.092
    M1 18 (3.9) 5 (2.2) 13 (5.7)
    Stage (%) Stage Ⅰ 248 (54.5) 132 (58.1) 116 (50.9) 0.168
    Stage Ⅱ 112 (24.6) 54 (23.8) 58 (25.4)
    Stage Ⅲ 77 (16.9) 36 (15.9) 41 (18.0)
    Stage Ⅳ 18 (4.0) 5 (2.2) 13 (5.7)
    stage_event.system_version (%) 3rd 3 (0.7) 0 (0.0) 3 (1.3) 0.225
    4th 5 (1.1) 3 (1.3) 2 (0.9)
    5th 29 (6.3) 13 (5.7) 16 (7.0)
    6th 161 (35.0) 74 (32.2) 87 (37.8)
    7th 247 (53.7) 134 (58.3) 113 (49.1)
    Not Available 15 (3.3) 6 (2.6) 9 (3.9)
    Cancer_Status (%) Tumor Free 304 (74.5) 172 (81.9) 132 (66.7) 0.001
    With Tumor 104 (25.5) 38 (18.1) 66 (33.3)
    outcome (%) CR 273 (72.8) 162 (81.8) 111 (62.7) < 0.001
    PR 4 (1.1) 0 (0.0) 4 (2.3)
    SD 29 (7.7) 15 (7.6) 14 (7.9)
    PD 69 (18.4) 21 (10.6) 48 (27.1)
    POT (%) No 140 (34.5) 72 (34.3) 68 (34.7) 1
    Yes 266 (65.5) 138 (65.7) 128 (65.3)
    RT (%) No 56 (13.8) 23 (11.0) 33 (16.8) 0.12
    Yes 351 (86.2) 187 (89.0) 164 (83.2)
    T, tumor; N, node; M, metastasis; CR, complete response; PR, partial response; SD, stable disease; PD, progressive disease; POT, postoperative treatment; RT, radiation therapy.

     | Show Table
    DownLoad: CSV

    A total of 1757 target genes of the nine miRNAs were collected from the miRTarBase database (Data S7). The GO biological processes were mainly enriched in regulation of transcription, apoptotic process and response to heat or toxic substance (Data S8). The GO molecular function were linked to protein binding, transcription factor binding, nucleic acid binding and protein tyrosine kinase activity (Data S9). In addition, the KEGG pathways were significantly enriched in mRNA surveillance pathway, transcriptional misregulation in cancer, pathways in cancer, viral carcinogenesis and adherens junction (Data S10).

    A nomogram was generated to illustrate the relationship between prognostic indicators and the predicted survival outcomes of patients with LUAD. As shown in Figure 2, miR.index, T stage, N stage and Metastasis status were associated with survival. The clinicopathological parameters between the training set and validating set were well balanced (Table S1). The C-indexes were 0.68 and 0.72 in the training and validating set, respectively. The both C-indexes were close to or greater than 0.7, which confirmed the reliability of the model. Predictive accuracy of the model was further tested by calibration curves comparing actual 3 or 5-year overall survival (proportion) with predicted 3 or 5-year overall survival probability, both in the training and validating set (Figures S2–S5).

    Figure 2.  The 3 and 5-year survival probability for patients with LUAD predicted by the total points sumaried from miR.index, T stage, N stage and Metastasis status.

    LUAD is one of the most fatal malignancies worldwide [1,2]. The prognosis of patients with LUAD would be improved to some extent if tumor behavior could be predicted before initial treatment. Accurate prediction is definitely based on the clinicopathological characteristics, the identification of novel biomarkers and the elucidation of the precise molecular mechanisms underlying LUAD occurrence and development. The TNM staging system, based on the clinicopathological characteristics of cancer, is insufficient in risk stratification and prognosis prediction, and the prediction power could be enhanced when combined with molecular biomarkers.

    miRNAs are small non-coding RNAs that regulate gene expression [3,4,5]. They are involved in carcinogenesis and are presented as potential diagnostic or prognostic biomarkers in cancers [6,7]. Several miRNA markers have been identified for prediction of treatment outcome, recurrence, metastasis and prognosis in patients with cancers [9,10,11,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29], including LUAD [14,15,16]. Li et al determined that miR-101-1, miR-220a, miR-450a-2 and miR-4661 were related to survival outcome in patients with LUAD [14]. Lin et al proposed a four miRNAs signature (miR-148a-5p, miR-31-5p, miR-548v and miR-550a-5p) associated with prognosis in patients with LUAD [15]. Interestingly, the miRNA signatures obtained by various studies do not overlap, or just overlap partly, perhaps due to the variability in the methods used to identify differentially expressed miRNAs and screen out risky miRNAs. In most of the aforementioned studies, risk score or prognosis index were constructed with linear combination of miRNA expression levels multiplied by Cox regression coefficient (β). Bias is likely to occur when explain the contribution of risk score or prognosis index to survival, because there was significant difference among the expression levels of each individual miRNA. To avoid this possible bias, we normalized the expression levels of miRNAs by their quantile distribution. Lin et al removed miRNAs with expression levels of zero in ≥ 50% of the patients, because they thought the feasibility of implementation could be enhanced [15]. But to our opinion, some miRNAs downregulated in cancer could be missed when this part of the data was excluded in analysis.

    In our research, we identified nine miRNAs (hsa-let-7i, hsa-mir-1976, hsa-mir-199a-1, hsa-mir-31, hsa-mir-3940, hsa-mir-450a-2, hsa-mir-4677, hsa-mir-548v and hsa‐mir‐6803) associated with overall survival in patients with LUAD. Among them, miR-31, miR-450a-2 and miR-548v have been reported previously to be related to clinical outcome in patients with LUAD [14,15].

    To gain a deep understanding of the nine miRNAs, we obtained the target genes of these nine miRNAs, and predicted the biological functions and pathways associated with their targets using bioinformatics analysis. The target genes of the nine miRNAs were mainly enriched in key cancer-related biological processes and pathways, such as cell proliferation, cell differentiation, transcription regulation, cell transformation, cell cycle, response to drug and apoptosis. The results suggested that these miRNAs played an important role in the occurrence, development and prognosis of LUAD.

    Despite the potential ability of our model to predict prognosis in patients with LUAD, it had some limitations. The utility of different TNM staging system (3rd to 7th edition) and the incomplete records about treatment information (surgery, chemotherapy, radiotherapy and molecular targeted therapy) might cause biases in our analysis. Therefore, the prognostic value of the nine-miRNA signature is warranted for further validations.

    The prognostic model constructed with nine miRNA expression profile and TNM classification parameters can predict the survival in patients with LUAD, and the predictive power of the model are warranted for further validations.

    The authors want to thank professor Zhongxin Li for his kind help in revising the manuscript.

    The authors declare that there are no conflicts of interest.

    [1] Berger G, Bitterman R, Azzam ZS (2015) The human microbiota: the rise of an "empire". Rambam Maimonides Med J 6: 1–5.
    [2] Peek RM, Blaser MJ (2002) Helicobacter pylori and gastrointestinal tract adenocarcinomas. Nat Rev Cancer 2: 28–37. doi: 10.1038/nrc703
    [3] Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207–214. doi: 10.1038/nature11234
    [4] Charlson ES, Chen J, Custers-Allen R, et al. (2010) Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One 5: e15216. doi: 10.1371/journal.pone.0015216
    [5] Blaser MJ, Atherton JC (2004) Helicobacter pylori persistence: biology and disease. J Clin Invest 113: 321–333. doi: 10.1172/JCI20925
    [6] Roberts AP, Kreth J (2014) The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome. Front Cell Infect Mi 4: 124.
    [7] Kort R, Caspers M, Graff A, et al. (2014) Shaping the oral microbiota through intimate kissing. Microbiome 2: 41. doi: 10.1186/2049-2618-2-41
    [8] Willey JP (2008) Harley and Klein's Microbiology, In: Joanne MW, Linda MS, Christopher JW, 7 Eds., New York: McGraw-Hill Higher Education.
    [9] Wilson M (2008) The indigenous microbiota of the gastrointestinal tract, In: Wilson M, Author, Bacteriology of Humans: An Ecological Perspective, Oxford: Blackwell Publishing, 266–326.
    [10] Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Ann Rev Microbiol 55: 165–199. doi: 10.1146/annurev.micro.55.1.165
    [11] Gerald PC (2013) Oral microbiome homeostasis: The new frontier in oral care therapies. J Dent Oral Disord Ther 1: 3.
    [12] Joshi HM, Toleti RS (2009) Nutrition induced pleomorphism and budding mode of reproduction in Deinococcus radiodurans. BMC Res Notes 2: 123. doi: 10.1186/1756-0500-2-123
    [13] Dewhirst FE, Chen T, Izard J (2010) The human oral microbiome. J Bacteriol 192: 5002–5017. doi: 10.1128/JB.00542-10
    [14] Beck JD, Offenbacher S (2005) Systemic effects of periodontitis: epidemiology of periodontal disease and cardiovascular disease. J Periodontol 76: 2089–2100. doi: 10.1902/jop.2005.76.11-S.2089
    [15] Munson MA, Banerjee A, Watson TF, et al. (2004) Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 42: 3023–3029. doi: 10.1128/JCM.42.7.3023-3029.2004
    [16] Genco RJ, Grossi SG, Ho A, et al. (2005) A proposed model linking inflammation to obesity, diabetes, and periodontal infections. J Periodontol 76: 2075–2084. doi: 10.1902/jop.2005.76.11-S.2075
    [17] Joshipura KJ, Hung HC, Rimm EB, et al. (2003) Periodontal disease, tooth loss, and incidence of ischemic stroke. Stroke 34: 47–52. doi: 10.1161/01.STR.0000052974.79428.0C
    [18] Awano S, Ansai T, Takata Y, et al. (2008) Oral health and mortality risk from pneumonia in the elderly. J Dent Res 87: 334–339. doi: 10.1177/154405910808700418
    [19] Ford BJ, University of California Berkeley, Berkeley, 2008. Available from: http://www.ucmp.berkeley.eduhistoryleeuwenhoek.html.
    [20] Loesche WJ (1975) Chemotherapy of dental plaque infections. Oral Sci Rev 9: 65–107.
    [21] Wilson M (2005) Microbial inhabitants of humans: their ecology and role in health and disease, Cambridge: Cambridge University Press.
    [22] Alcaraz LD, Belda‐Ferre P, Cabrera‐Rubio R, et al. (2012) Identifying a healthy oral microbiome through metagenomics. Clin Microbiol Infec 18: 54–57.
    [23] Avila M, Ojcius DM, Yilmaz O (2009) The oral microbiota: living with a permanent guest. DNA Cell Biol 28: 405–411. doi: 10.1089/dna.2009.0874
    [24] Peterson J, Garges S, Giovanni M, et al. (2009) The NIH Human microbiome project. Gen Res 19: 2317–2323. doi: 10.1101/gr.096651.109
    [25] Mitreva M, Mardis ER (2009) Large-scale sequencing and analytical processing of ESTs, In: Parkinson J, Author, Expressed Sequence Tags (ESTs) Methods in Molecular Biology (Methods and Protocols), Humana Press, 153–187.
    [26] Qin J, Li R, Raes J, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59–65. doi: 10.1038/nature08821
    [27] Kreth J, Merritt J, Shi W, et al. (2005) Competition and coexistence between Streptococcus mutans and Streptococcus sanguinis in the dental biofilm. J Bacteriol 187: 7193–7203. doi: 10.1128/JB.187.21.7193-7203.2005
    [28] Jenkinson HF, Lamont RJ (2005) Oral microbial communities in sickness and in health. Trends Microbiol 13: 589–595. doi: 10.1016/j.tim.2005.09.006
    [29] Chalmers NI, Palmer RJ, Cisar JO, et al. (2008) Characterization of a Streptococcus sp.-Veillonella sp. community micromanipulated from dental plaque. J Bacteriol 190: 8145–8154.
    [30] Kleinberg I (2002) A mixed-bacteria ecological approach to understanding the role of the oral bacteria in dental caries causation: an alternative to Streptococcus mutans and the specific-plaque hypothesis. Crit Rev Oral Biol Med 13: 108–125. doi: 10.1177/154411130201300202
    [31] Davey M, Otoole GA (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev 64: 847–867. doi: 10.1128/MMBR.64.4.847-867.2000
    [32] Kreft JU (2004) Biofilms promote altruism. Microbiology 150: 2751–2760. doi: 10.1099/mic.0.26829-0
    [33] Irie Y, Parsek MR (2008) Quorum sensing and microbial biofilms. Curr Top Microbiol 322: 67–84.
    [34] Kolenbrander PE, Andersen RN, Blehert DS, et al. (2002) Communication among oral bacteria. Microbiol Mol Biol Rev 66: 486–505.
    [35] Kuramitsu HK, He X, Lux R, et al. (2007) Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 71: 653–670. doi: 10.1128/MMBR.00024-07
    [36] Kolenbrander PE (2000) Oral microbial communities: biofilms, interactions, and genetic systems. Annu Rev Microbiol 54: 413–437. doi: 10.1146/annurev.micro.54.1.413
    [37] McNab R, Ford SK, El-Sabaeny A, et al. (2003) LuxS-based signaling in Streptococcus gordonii: autoinducer 2 controls carbohydrate metabolism and biofilm formation with Porphyromonas gingivalis. J Bacteriol 185: 274–284. doi: 10.1128/JB.185.1.274-284.2003
    [38] Kreth J, Merritt J, Shi W, et al. (2005) Coordinated bacteriocin production and competence development: a possible mechanism for taking up DNA from neighbouring species. Mol Microbiol 57: 392–404. doi: 10.1111/j.1365-2958.2005.04695.x
    [39] van der Ploeg JR (2005) Regulation of bacteriocin production in Streptococcus mutans by the quorum-sensing system required for development of genetic competence. J Bacteriol 187: 3980–3989. doi: 10.1128/JB.187.12.3980-3989.2005
    [40] Webb JS, Givskov M, Kjelleberg S (2003) Bacterial biofilms: prokaryotic adventures in multicellularity. Curr Opin Microbiol 6: 578–585.
    [41] Antunes LCM, Ferreira RB, Buckner MM, et al. (2010) Quorum sensing in bacterial virulence. Microbiology 156: 2271–2282. doi: 10.1099/mic.0.038794-0
    [42] Jakubovics NS, Gill SR, Vickerman MM, et al. (2008) Role of hydrogen peroxide in competition and cooperation between Streptococcus gordonii and Actinomyces naeslundii. FEMS Microbiol Ecol 66: 637–644. doi: 10.1111/j.1574-6941.2008.00585.x
    [43] Edwards AM, Grossman TJ, Rudney JD (2006) Fusobacterium nucleatum transports noninvasive Streptococcus cristatus into human epithelial cells. Infect Immun 74: 654–662. doi: 10.1128/IAI.74.1.654-662.2006
    [44] Zhang G, Chen R, Rudney JD (2008) Streptococcus cristatus attenuates Fusobacterium nucleatum‐induced interleukin‐8 expression in oral epithelial cells. J Periodontal Res 43: 408–416. doi: 10.1111/j.1600-0765.2007.01057.x
    [45] Yilmaz O (2008) The chronicles of Porphyromonas gingivalis: the microbium, the human oral epithelium and their interplay. Microbiology 154: 2897–2903.
    [46] Bik EM, Long CD, Armitage GC, et al. (2010) Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J 4: 962–974. doi: 10.1038/ismej.2010.30
    [47] Trim RD, Skinner MA, Farone MB, et al. (2011) Use of PCR to detect Entamoeba gingivalis in diseased gingival pockets and demonstrate its absence in healthy gingival sites. Parasitol Res 109: 857–864. doi: 10.1007/s00436-011-2312-9
    [48] Bahrani-Mougeot FK, Paster BJ, Coleman S, et al. (2008) Diverse and novel oral bacterial species in blood following dental procedures. J Clin Microbiol 46: 2129–2132. doi: 10.1128/JCM.02004-07
    [49] Ghannoum MA, Jurevic RJ, Mukherjee PK, et al. (2010) Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 6: e1000713. doi: 10.1371/journal.ppat.1000713
    [50] Wang J, Gao Y, Zhao F (2016) Phage-bacteria interaction network in human oral microbiome. Environ Microbiol 18: 2143–2158. doi: 10.1111/1462-2920.12923
    [51] Baker JL, Bor B, Agnello M, et al. (2017) Ecology of the oral microbiome: beyond bacteria. Trends Microbiol 25: 362–374.
    [52] Wahida A, Ritter K, Horz HP (2016) The Janus-Face of bacteriophages across human body habitats. PLoS Pathog 12: e1005634. doi: 10.1371/journal.ppat.1005634
    [53] Pride DT, Salzman J, Haynes M, et al. (2012) Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J 6: 915–926. doi: 10.1038/ismej.2011.169
    [54] Ly M, Abeles SR, Boehm TK, et al. (2014) Altered oral viral ecology in association with periodontal disease. Mbio 5: e01133-14.
    [55] Arduino PG, Porter SR (2008) Herpes Simplex Virus Type 1 infection: overview on relevant clinic pathological features. J Oral Pathol Med 37: 107–121.
    [56] Wu YM, Yan J, Ojcius DM, et al. (2007) Correlation between infections with different genotypes of human cytomegalovirus and Epstein-Barr virus in subgingival samples and periodontal status of patients. J Clin Microbiol 45: 3665–3670.
    [57] Giacaman RA, Asrani AC, Gebhard KH, et al. (2008) Porphyromonas gingivalis induces CCR5-dependent transfer of infectious HIV-1 from oral keratinocytes to permissive cells. Retrovirology 5: 1. doi: 10.1186/1742-4690-5-1
    [58] Herzberg MC, Weinberg A, Wahl SM (2006) The oral epithelial cell and first encounters with HIV-1. Adv Dent Res 19: 158–166. doi: 10.1177/154407370601900128
    [59] Loning T, Ikenberg H, Becker J, et al. (1985) Analysis of oral papillomas, leukoplakias, and invasive carcinomas for human papillomavirus type related DNA. J Invest Dermatol 84: 417–420. doi: 10.1111/1523-1747.ep12265517
    [60] Kumaraswamy KL, Vidhya M (2011) Human papilloma virus and oral infections: an update. J Cancer Res 7: 120.
    [61] Pride DT, Salzman J, Relman DA (2012) Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ Microbiol 14: 2564–2576. doi: 10.1111/j.1462-2920.2012.02775.x
    [62] Abeles SR, Robles-Sikisaka R, Ly M, et al. (2014) Human oral viruses are personal, persistent and gender-consistent. ISME J 8: 1753–1767. doi: 10.1038/ismej.2014.31
    [63] Stevens RH, Porras OD, Delisle AL (2009) Bacteriophages induced from lysogenic root canal isolates of Enterococcus faecalis. Oral Microbial Immun 24: 278–284. doi: 10.1111/j.1399-302X.2009.00506.x
    [64] Pride DT, Salzman J, Haynes M, et al. (2012) Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J 6: 915–926. doi: 10.1038/ismej.2011.169
    [65] Lepp PW, Brinig MM, Ouverney CC, et al. (2004) Methanogenic Archaea and human periodontal disease. P Natl Acad Sci USA 101: 6176–6181. doi: 10.1073/pnas.0308766101
    [66] Matarazzo F, Ribeiro AC, Feres M, et al. (2011) Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects. J Clin Periodontol 38: 621–627. doi: 10.1111/j.1600-051X.2011.01734.x
    [67] Diaz PI, Chalmers NI, Rickard AH, et al. (2006) Molecular characterization of subject-specific oral microflora during initial colonization of enamel. Appl Environ Microb 72: 2837–2848. doi: 10.1128/AEM.72.4.2837-2848.2006
    [68] Smillie CS, Smith MB, Friedman J, et al. (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480: 241–244.
    [69] Yaron S, Kolling GL, Simon L, et al. (2000) Vesicle-mediated transfer of virulence genes from Escherichia coli O157: H7 to other enteric vacteria. Appl Environ Microb 66: 4414–4420. doi: 10.1128/AEM.66.10.4414-4420.2000
    [70] Mashburn-Warren LM, Whiteley M (2006) Special delivery: vesicle trafficking in prokaryotes. Mol Microbiol 61: 839–846. doi: 10.1111/j.1365-2958.2006.05272.x
    [71] Warburton PJ, Palmer RM, Munson MA, et al. (2007) Demonstration of in vivo transfer of doxycycline resistance mediated by a novel transposon. J Antimicrob Chemo 60: 973–980. doi: 10.1093/jac/dkm331
    [72] Seville LA, Patterson AJ, Scott KP, et al. (2009) Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA. Microb Drug Resist 15: 159–166. doi: 10.1089/mdr.2009.0916
    [73] Ciric L, Brouwer MS, Mullany P (2014) Minocycline resistance in an oral Streptococcus infantis isolate is encoded by tet (S) on a novel small, low copy number plasmid. FEMS Microbiol Lett 353: 106–115. doi: 10.1111/1574-6968.12410
    [74] Connell SR, Tracz DM, Nierhaus KH (2003) Ribosomal protection proteins and their mechanism of tetracycline resistance. Antimicrob Agents Ch 47: 3675–3681. doi: 10.1128/AAC.47.12.3675-3681.2003
    [75] Nasidze I, Li J, Quinque D, et al. (2009) Global diversity in the human salivary microbiome. Gen Res 19: 636–643. doi: 10.1101/gr.084616.108
    [76] Li Y, Ismail AI, Ge Y, et al. (2007) Similarity of bacterial populations in saliva from African-American mother-child dyads. J Clin Microbiol 45: 3082–3085.
    [77] Corby PM, Bretz WA, Hart TC (2007) Heritability of oral microbial species in caries-active and caries-free twins. Twin Res Hum Genet 10: 821–828. doi: 10.1375/twin.10.6.821
    [78] Edlund A, Santiago-Rodriguez TM, Boehm TK, et al. (2015) Bacteriophage and their potential roles in the human oral cavity. J Oral Microbial 7: 27423.
    [79] De Paepe M, Leclerc M, Tinsley CR, et al. (2014) Bacteriophages: an underestimated role in human and animal health? Front Cell Infect Mi 4: 39.
    [80] Dominguez-Bello MG, Costello EK, Contreras M, et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. P Natl Acad Sci USA 107: 11971–11975.
    [81] Holgerson PL, Harnevik L, Hernell O, et al. (2011) Mode of birth delivery affects oral microbiota in infants. J Dent Res 90: 1183–1188.
    [82] Holgerson PL, Vestman NR, Claesson R, et al. (2013) Oral microbial profile discriminates breastfed from formula-fed infants. J Pediatr Gastr Nutr 56: 127. doi: 10.1097/MPG.0b013e31826f2bc6
    [83] Vestman NR, Timby N, Holgerson PL, et al. (2013) Characterization and in vitro properties of oral lactobacilli in breastfed infants. BMC Microbiol 13: 1. doi: 10.1186/1471-2180-13-1
    [84] Baca P, Castillo AM, Liebana, MJ, et al. (2012) Horizontal transmission of Streptococcus mutans in school children. Med Oral Patol Oral 17: 495–500.
    [85] Stahringer SS, Clemente JC, Corley RP (2012) Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Res 22: 2146–2152.
    [86] Brook I, Gober AE (2008) Recovery of potential pathogens in the nasopharynx of healthy and otitis media-prone children and their smoking and nonsmoking parents. Ann Otol Rhinol Laryngol 117: 727–730.
    [87] Arcavi L, Benowitz NL (2004) Cigarette smoking and infection. Arch Intern Med 164: 2206–2216.
    [88] Tamashiro E, Xiong G, Anselmo-Lima WT, et al. (2009) Cigarette smoke exposure impairs respiratory epithelial ciliogenesis. Am J Rhinol Allergy 23: 117–122.
    [89] El Ahmer OR, Essery SD, Saadi AT, et al. (1999) The effect of cigarette smoke on adherence of respiratory pathogens to buccal epithelial cells. FEMS Immuno Med Microbiol 23: 27–36. doi: 10.1111/j.1574-695X.1999.tb01713.x
    [90] Sapkota AR, Berger S, Vogel TM (2010) Human pathogens abundant in the bacterial metagenome of cigarettes. Environ Health Perspect 118: 351–356.
    [91] Brook I, Gober AE (2005) Recovery of potential pathogens and interfering bacteria in the nasopharynx of smokers and nonsmokers. CHEST J 127: 2072–2075. doi: 10.1378/chest.127.6.2072
    [92] Winkelhoff AV, Bosch-Tijhof CJ, Winkel EG, et al. (2001) Smoking affects the subgingival microflora in periodontitis. J Periodontol 72: 666–671.
    [93] Fullmer SC, Preshaw PM, Heasman PA (2009) Smoking cessation alters subgingival microbial recolonization. J Dent Res 88: 524–528. doi: 10.1177/0022034509338676
    [94] Madhi SA, Adrian P, Kuwanda L, et al. (2007) Long-term effect of pneumococcal conjugate vaccine on nasopharyngeal colonization by Streptococcus pneumonia and associated interactions with Staphylococcus aureus and Haemophilus influenzae colonization in HIV-infected and HIV-uninfected children. J Infect Dis 196: 1662–1666. doi: 10.1086/522164
    [95] Regev-Yochay G, Trzciński K, Thompson CM, et al. (2006) Interference between Streptococcus pneumoniae and Staphylococcus aureus: in vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae. J Bacteriol 188: 4996–5001. doi: 10.1128/JB.00317-06
    [96] McNally LM, Jeena PM, Gajee K, et al. (2006) Lack of association between the nasopharyngeal carriage of Streptococcus pneumoniae and Staphylococcus aureus in HIV-1-infected South African children. J Infect Dis 194: 385–390.
    [97] Darveau RP (2010) Periodontitis: a polymicrobial disruption of host homeostasis. Nat Rev Microbiol 8: 481–490. doi: 10.1038/nrmicro2337
    [98] Armitage GC (1999) Development of a classification system for periodontal diseases and conditions. Ann Periodontol 4: 1–6.
    [99] Socransky SS, Haffajee AD, Cugini MA, et al. (1998) Microbial complexes in subgingival plaque. J Clin Periodontol 25: 134–144.
    [100] Kumar PS, Griffen AL, Barton JA, et al. (2003) New bacterial species associated with chronic periodontitis. J Dent Res 82: 338–344. doi: 10.1177/154405910308200503
    [101] Nyvad B, Kilian M (1987) Microbiology of the early colonization of human enamel and root surfaces in vivo. Eur J Oral Sci 95: 369–380. doi: 10.1111/j.1600-0722.1987.tb01627.x
    [102] Zijnge V, van Leeuwen MBM, Degener JE, et al. (2010) Oral biofilm architecture on natural teeth. PLoS One 5: e9321.
    [103] He XS, Shi WY (2009) Oral microbiology: past, present and future. Int J Oral Sci 1: 47. doi: 10.4248/ijos.09029
    [104] Yamada T, Takahashi-Abbe S, Abbe K (1985) Effects of oxygen on pyruvate formate-lyase in situ and sugar metabolism of Streptococcus mutans and Streptococcus sanguis. Infect Immun 47: 129–134.
    [105] Takahashi N, Nyvad B (2011) The role of bacteria in the caries process ecological perspectives. J Dent Res 90: 294–303.
    [106] Downes J, Mantzourani M, Beighton D (2011) Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata. Int J Syst Evol Microbiol 61: 25–29.
    [107] Kaur R, Gilbert SC, Sheehy EC, et al. (2013) Salivary levels of Bifidobacteria in caries free and caries active children. Int J Paediatr Dent 23: 32–38.
    [108] Munson MA, Pitt-Ford T, Chong B, et al. (2002) Molecular and cultural analysis of the microflora associated with endodontic infections. J Dent Res 81: 761–766.
    [109] Burne RA, Marquis RE (2000) Alkali production by oral bacteria and protection against dental caries. FEMS Microbiol Lett 193: 1–6. doi: 10.1111/j.1574-6968.2000.tb09393.x
    [110] Razavi A, Gmür R, Imfeld T, et al. (2007) Recovery of Enterococcus faecalis from cheese in the oral cavity of healthy subjects. Oral Microbiol Immun 22: 248–251. doi: 10.1111/j.1399-302X.2006.00349.x
    [111] Kampfer J, Gohring TN, Attin T, et al. (2007) Leakage of food borne Enterococcus faecalis through temporary fillings in a simulated oral environment. Int Endontic J 40: 471–477. doi: 10.1111/j.1365-2591.2007.01252.x
    [112] Raghavendran K, Mylotte JM, Scannapieco FA (2007) Nursing home‐associated pneumonia, hospital‐acquired pneumonia and ventilator‐associated pneumonia: the contribution of dental biofilms and periodontal inflammation. Periodontology 44: 164–177.
    [113] Scannapieco FA (1999) Role of oral bacteria in respiratory infection. J Periodontol 70: 793–802. doi: 10.1902/jop.1999.70.7.793
    [114] Vincent JL (1999) Prevention of nosocomial bacterial pneumonia. Thorax 54: 544–549. doi: 10.1136/thx.54.6.544
    [115] Gil-Perotin S, Ramirez P, Marti V, et al. (2012) Implications of endotracheal tube biofilm in ventilator-associated pneumonia response: a state of concept. Crit Care 16: 1–9.
    [116] Marik PE (2001) Aspiration pneumonitis and aspiration pneumonia. Engl J Med 344: 665–671. doi: 10.1056/NEJM200103013440908
    [117] Scannapieco FA (2013) The oral microbiome: its role in health and in oral and systemic infections. Clin Microbiol Newsl 35: 163–169. doi: 10.1016/j.clinmicnews.2013.09.003
    [118] Borgnakke WS, Ostalo PV, Taylor GW, et al. (2013) Effect of periodontal disease on diabetes: systematic review of epidemiologic observational evidence. J Periodontol 84: 135–152. doi: 10.1902/jop.2013.132001
    [119] Segata N, Haake SK, Mannon P, et al. (2012) Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13: R42. doi: 10.1186/gb-2012-13-6-r42
    [120] Anand PS, Nandakumar K, Shenoy KT (2006) Are dental plaque, poor oral hygiene, and periodontal disease associated with Helicobacter pylori infection? J Periodontol 77: 692–698. doi: 10.1902/jop.2006.050163
    [121] Whitmore SE, Lamont RJ (2014) Oral bacteria and cancer. PLoS Pathog 10: e1003933.
    [122] Atanasova KR, Yilmaz O (2014) Looking in the Porphyromonas gingivalis cabinet of curiosities: the microbium, the host and cancer association. Mol Oral Microbiol 29: 55–66. doi: 10.1111/omi.12047
    [123] Ahn J, Chen CY, Hayes RB (2012) Oral microbiome and oral and gastrointestinal cancer risk. Cancer Cause Control 23: 399–404. doi: 10.1007/s10552-011-9892-7
    [124] Kaur S, White S, Bartold PM (2013) Periodontal disease and rheumatoid arthritis a systematic review. J Dent Res 92: 399–408. doi: 10.1177/0022034513483142
    [125] Kamer AR, Dasanayake AP, Craig RG, et al. (2008) Alzheimer's disease and peripheral infections: the possible contribution from periodontal infections, model and hypothesis. J Alzheimers Dis 13: 437–449. doi: 10.3233/JAD-2008-13408
    [126] Ide M, Papapanou PN (2013) Epidemiology of association between maternal periodontal disease and adverse pregnancy outcomes-systematic review. J Clin Periodontol 40: S181–S194.
    [127] Zaura E, Keijser BJ, Huse SM, et al. (2009) Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol 9: 259.
    [128] Lazarevic V, Whiteson K, Hernandez D, et al. (2010) Study of inter-and intra-individual variations in the salivary microbiota. BMC Genomics 11: 523. doi: 10.1186/1471-2164-11-523
    [129] Moon JH, Lee JH (2016) Probing the diversity of healthy oral microbiome with bioinformatics approaches. BMB reports 49: 662. doi: 10.5483/BMBRep.2016.49.12.164
    [130] Baas-Becking LGM (1934) Geobiologie; of inleiding tot de milieukunde. WP Van Stockum & Zoon NV.
    [131] Loesche WJ (1969) Oxygen sensitivity of various anaerobic bacteria. Appl Microbiol 18: 723–727.
    [132] Ueki A, Akasaka H, Suzuki D, et al. (2006) Xylanibacter oryzae gen. nov., sp. nov., a novel strictly anaerobic, Gram negative, xylanolytic bacterium isolated from rice-plant residue in flooded rice-field soil in Japan. Int J Syst Evol Microbiol 56: 2215–2221.
    [133] Ausec L, Kraighera B, Mandic-Mulec I (2009) Differences in the activity and bacterial community structure of drained grassland and forest peat soils. Soil Biol Biochem 41: 1874–1881. doi: 10.1016/j.soilbio.2009.06.010
    [134] Castro HF, Classen AT, Austin EE, et al. (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microb 76: 999–1007. doi: 10.1128/AEM.02874-09
    [135] Contreras M, Costello EK, Hidalgo G, et al. (2010) The bacterial microbiota in the oral mucosa of rural Amerindians. Microbiology 156: 3282–3287. doi: 10.1099/mic.0.043174-0
    [136] Li K, Bihan M, Methé BA (2013) Analyses of the stability and core taxonomic memberships of the Human microbiome. PLoS One 8: e63139. doi: 10.1371/journal.pone.0063139
    [137] Zaura E, Nicu EA, Krom BP, et al. (2014) Acquiring and maintaining a normal oral microbiome: current perspective. Front Cell Infect Mi 4.
    [138] Galiminas V, Hall MW, Singh N, et al. (2014) Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators. Microbiome 2: 32.
    [139] Sun B, Zhou D, Tu J, et al. (2017) Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing. Biomed Res Int 2017: 8184160.
    [140] Hall MW, Singh N, Ng KF, et al. (2017) Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity. NPJ Biofilm Microbiome 3: 2. doi: 10.1038/s41522-016-0011-0
    [141] Takeshita T, Kageyama S, Furuta M, et al. (2016) Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study. Sci Rep 6: 22164. doi: 10.1038/srep22164
    [142] Li J, Quinque D, Horz HP, et al. (2014) Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa. BMC Microbiol 14: 316. doi: 10.1186/s12866-014-0316-1
    [143] Huse SM, Ye Y, Zhou Y, et al. (2012) A Core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One 7: e34242. doi: 10.1371/journal.pone.0034242
    [144] Gevers D, Knight R, Petrosino JF, et al. (2012) The human microbiome project: A community resource for the healthy human microbiome. PLoS Biol 10: e1001377. doi: 10.1371/journal.pbio.1001377
    [145] Walter J, Ley R (2011) The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol 65: 411–429. doi: 10.1146/annurev-micro-090110-102830
    [146] Xiao E, Mattos M, Vieira GHA, et al. (2017) Diabetes enhances IL-17 expression and alters the oral microbiome to increase its pathogenicity. Cell Host Microbe 22: 120–128. doi: 10.1016/j.chom.2017.06.014
    [147] Grover HS, Blaggana A, Jain Y, et al (2015) Detection and measurement of oral malodor in chronic periodontitis patients and its correlation with levels of select oral anaerobes in subgingival plaque. Contemp Clin Dent 6: S181–S187. doi: 10.4103/0976-237X.166825
    [148] Hoceini A, Khelil NK, Ben-Yelles I, et al. (2016) Caries-related factors and bacterial composition of supragingival plaques in caries free and caries active Algerian adults. Asian Pac J Trop Biomed 6: 720–726. doi: 10.1016/j.apjtb.2016.06.011
    [149] Horner-Devine MC, Lage M, Hughes JB, et al. (2004) A taxa-area relationship for bacteria. Nature 432: 750–753.
    [150] Reid NM, Addison SL, Macdonald LJ, et al. (2011) Biodiversity of active and inactive bacteria in the gut flora of wood-feeding huhu beetle larvae (Prionoplus reticularis). Appl Environ Microb 77: 7000–7006. doi: 10.1128/AEM.05609-11
    [151] Gong HL, Shi Y, Zhou L, et al. (2013) The composition of microbiome in larynx and the throat biodiversity between laryngeal squamous cell carcinoma patients and control population. PLoS One 8: e66476.
    [152] Chen T, Yu WH, Izard J, et al. (2010) The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database 2010.
    [153] Human Microbiome Jumpstart Reference Strains Consortium (2010) A catalog of reference genomes from the human microbiome. Science 328: 994–999.
    [154] Wang J, Qi J, Zhao H, et al. (2013) Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep 3: 1843. doi: 10.1038/srep01843
    [155] Raghunathan A, Ferguson HR, Bornarth CJ, et al. (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microb 71: 3342–3347. doi: 10.1128/AEM.71.6.3342-3347.2005
    [156] Dean FB, Hosono S, Fang L (2002) Comprehensive human genome amplification using multiple displacement amplification. P Natl Acad Sci USA 99: 5261–5266.
    [157] Chitsaz H, Yee-Greenbaum JL, Tesler G (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 29: 915–921. doi: 10.1038/nbt.1966
    [158] Bankevich A, Nurk S, Antipov D, et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455–477.
    [159] Lasken RS (2012) Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 10: 631–640. doi: 10.1038/nrmicro2857
    [160] Boschker HTS, Nold SC, Wellsbury P (1998) Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392: 801–805.
    [161] Radajewski S, Ineson P, Parekh NR, et al. (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649.
    [162] McLean JS (2014) Advancements toward a systems level understanding of the human oral microbiome. Front Cell Infect Mi 4: 98.
    [163] Peterson SN, Snesrud E, Liu J, et al. (2013) The dental plaque microbiome in health and disease. PLoS One 8: e58487.
    [164] Lourenço TGB, Heller D, Silva-Boghossian CM (2014) Microbial signature profiles of periodontally healthy and diseased patients. J Clin Periodontol 41: 1027–1036. doi: 10.1111/jcpe.12302
    [165] Farrell JJ, Zhang L, Zhou H, et al. (2011) Variations of oral microbiota are associated with pancreatic diseases including pancreatic cancer. Gut 61: 582–588.
    [166] Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, et al. (2012) The oral metagenome in health and disease. ISME J 6: 46–56. doi: 10.1038/ismej.2011.85
    [167] Duran-Pinedo AE, Chen T, Teles R, et al. (2014) Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis. ISME J 8: 1659–1672. doi: 10.1038/ismej.2014.23
    [168] Jorth P, Trivedi U, Rumbaugh K, et al. (2013) Probing bacterial metabolism during infection using high-resolution transcriptomics. J Bacteriol 195: 4991–4998. doi: 10.1128/JB.00875-13
    [169] Griffen AL, Beall CJ, Campbell JH, et al. (2012) Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J 6: 1176–1185.
    [170] Schulze-Schweifing K, Banerjee A, Wade WG (2014).Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome. Front Cell Infect Mi 4: 164.
    [171] Pushalkar S, Ji X, Li Y, et al. (2012) Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. BMC Microbiol 12: 144. doi: 10.1186/1471-2180-12-144
    [172] Liu B, Faller LL, Klitgord N, et al. (2012) Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One 7: e37919. doi: 10.1371/journal.pone.0037919
    [173] Xie G, Chain PSG, Lo CC, et al. (2010) Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Mol Oral Microbiol 25: 391–405.
    [174] Huson DH, Auch AF, Qi J, et al. (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377–386. doi: 10.1101/gr.5969107
    [175] Benitez-Paez A, Belda-Ferre P, Simon-Soro A, et al. (2014) Microbiota diversity and gene expression dynamics in human oral biofilms. BMC Genomics 15: 311.
    [176] Jorth P, Turner KH, Gumus P, et al. (2014) Metatranscriptomics of the human oral microbiome during health and disease. Mbio 5: e01012-14.
    [177] Maron PA, Ranjard L, Mougel C, et al. (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53: 486–493. doi: 10.1007/s00248-006-9196-8
    [178] Yakob M, Fuentes L, Wang MB, et al. (2014) Salivary biomarkers for detection of oral squamous cell carcinoma: current state and recent advances. Curr Oral Health Rep 1: 133–141. doi: 10.1007/s40496-014-0014-y
    [179] Barnes VM, Ciancio SG, Shibly O, et al. (2011) Metabolomics reveals elevated macromolecular degradation in periodontal disease. J Dent Res 90: 1293–1297. doi: 10.1177/0022034511416240
    [180] Arrais JP, Rosa N, Melo J, et al. (2013) Oral Card: a bioinformatic tool for the study of oral proteome. Arch Oral Biol 58: 762–772.
  • This article has been cited by:

    1. Zhiqiang Wang, Fan Hu, Ruijie Chang, Xiaoyue Yu, Chen Xu, Yujie Liu, Rongxi Wang, Hui Chen, Shangbin Liu, Danni Xia, Yingjie Chen, Xin Ge, Tian Zhou, Shuixiu Zhang, Haoyue Pang, Xueni Fang, Yushuang Zhang, Jin Li, Kaiwen Hu, Yong Cai, Development and Validation of a Prognostic Model to Predict Overall Survival for Lung Adenocarcinoma: A Population-Based Study From the SEER Database and the Chinese Multicenter Lung Cancer Database, 2022, 21, 1533-0346, 153303382211332, 10.1177/15330338221133222
    2. Zhichao Lin, Wenhai Huang, Zehua Xie, Yongsheng Yi, Zumei Li, Expression, Clinical Significance, Immune Infiltration, and Regulation Network of miR-3940-5p in Lung Adenocarcinoma Based on Bioinformatic Analysis and Experimental Validation, 2022, Volume 15, 1178-7074, 6451, 10.2147/IJGM.S375761
    3. Zhenghua Liu, Shize Yang, Siyu Zhou, Shiyao Dong, Jiang Du, Prognostic Value of lncRNA DRAIC and miR-3940-3p in Lung Adenocarcinoma and Their Effect on Lung Adenocarcinoma Cell Progression, 2021, Volume 13, 1179-1322, 8367, 10.2147/CMAR.S320616
    4. Beata Smolarz, Adam Durczyński, Hanna Romanowicz, Krzysztof Szyłło, Piotr Hogendorf, miRNAs in Cancer (Review of Literature), 2022, 23, 1422-0067, 2805, 10.3390/ijms23052805
  • Reader Comments
  • © 2018 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索

Metrics

Article views(18349) PDF downloads(1843) Cited by(164)

Figures and Tables

Figures(3)  /  Tables(1)

/

DownLoad:  Full-Size Img  PowerPoint
Return
Return

Catalog