2,625
Views
15
CrossRef citations to date
0
Altmetric
Original Article

The relationship between cigarette smoking and the tongue microbiome in an East Asian population

, , , , ORCID Icon, , , , , , , , & show all
Article: 1742527 | Received 12 Jul 2019, Accepted 17 Dec 2019, Published online: 25 Mar 2020

References

  • Chapple IL, Genco R; Working group 2 of the joint EFP/AAP workshop. Diabetes and periodontal diseases: consensus report of the joint EFP/AAP workshop on periodontitis and systemic diseases. J Periodontol. 2013;84(4 Suppl):S106–9.
  • Zhang X, Zhang D, Jia H, et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat Med. 2015;21(8):895–905.
  • Joshipura KJ, Hung HC, Rimm EB, et al. Periodontal disease, tooth loss, and incidence of ischemic stroke. Stroke. 2003;34(1):47–52.
  • Wu J, Peters BA, Dominianni C, et al. Cigarette smoking and the oral microbiome in a large study of American adults. ISME J. 2016;10(10):2435–2446.
  • Thomas AM, Gleber-Netto FO, Fernandes GR, et al. Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms. BMC Microbiol. 2014;14:250.
  • Yu G, Phillips S, Gail MH, et al. The effect of cigarette smoking on the oral and nasal microbiota. Microbiome. 2017;5(1):3.
  • Mason MR, Nagaraja HN, Camerlengo T, et al. Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome. PLoS One. 2013;8:e77287.
  • Blekhman R, Goodrich JK, Huang K, et al. Host genetic variation impacts microbiome composition across human body sites. Genome Biol. 2015;16:191.
  • Demmitt BA, Corley RP, Huibregtse BM, et al. Genetic influences on the human oral microbiome. BMC Genomics. 2017;18:659.
  • Sulyanto RM, Thompson ZA, Beall CJ, et al. The predominant oral microbiota is acquired early in an organized pattern. Sci Rep. 2019;9:10550.
  • Remen T, Pintos J, Abrahamowicz M, et al. Risk of lung cancer in relation to various metrics of smoking history: a case-control study in Montreal. BMC Cancer. 2018;18:1275.
  • Takahashi S, Tomita J, Nishioka K, et al. Development of a prokaryotic universal primer for simultaneous analysis of bacteria and archaea using next-generation sequencing. PLoS One. 2014;9(8):e105592.
  • Callahan BJ, McMurdie PJ, Rosen MJ, et al. DADA2: high-resolution sample inference from illumina amplicon data. Nat Methods. 2016;13(7):581–583.
  • Cole JR, Wang Q, Fish JA, et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42(Database issue):D633–642.
  • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–1797.
  • Dress AW, Flamm C, Fritzsch G, et al. Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol. 2008;3:7.
  • Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–1650.
  • Douglas GM, Maffei VJ, Zaneveld J, et al. PICRUSt2: an improved and extensible approach for metagenome inference. bioRxiv. 2019;672295. DOI:10.1101/672295.
  • Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14(9):755–763.
  • Barbera P, Kozlov AM, Czech L, et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst Biol. 2019;68(2):365–369.
  • Czech L, Barbera P, Stamatakis A. Methods for automatic reference trees and multilevel phylogenetic placement. Bioinformatics 2019; 35: 1151–1158.
  • Louca S, Doebeli M. Efficient comparative phylogenetics on large trees. Bioinformatics. 2018;34(6):1053–1055.
  • Caspi R, Altman T, Billington R, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2014;42(Database issue):D459–471.
  • Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol. 2009;5(8):e1000465.
  • Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71(12):8228–8235.
  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
  • McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.
  • Wickham H. ggplot2: elegant graphics for data analysis. NewYork (NY): Springer New York; 2009.
  • Mason MR, Preshaw PM, Nagaraja HN, et al. The subgingival microbiome of clinically healthy current and never smokers. ISME J. 2015;9(1):268–272.
  • Xu X, He J, Xue J, et al. Oral cavity contains distinct niches with dynamic microbial communities. Environ Microbiol. 2015;17(3):699–710.
  • Hall MW, Singh N, Ng KF, et al. Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity. NPJ Biofilms Microbiomes. 2017;3:2.
  • Kenney EB, Saxe SR, Bowles RD. The effect of cigarette smoking on anaerobiosis in the oral cavity. J Periodontol. 1975;46(2):82–85.
  • Teles FR, Teles RP, Sachdeo A, et al. Comparison of microbial changes in early re-developing biofilms on natural teeth and dentures. J Periodontol. 2012;83(9):1139–1148.
  • Asakawa M, Takeshita T, Furuta M, et al. Tongue microbiota and oral health status in community-dwelling elderly adults. mSphere. 2018;3(4):e00332–18.
  • Brock M, Maerker C, Schütz A, et al. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur J Biochem. 2002;269:6184–6194.
  • Mager DL, Haffajee AD, Socransky SS. Effects of periodontitis and smoking on the microbiota of oral mucous membranes and saliva in systemically healthy subjects. J Clin Periodontol. 2003;30(12):1031–1037.
  • Yan X, Yang M, Liu J, et al. Discovery and validation of potential bacterial biomarkers for lung cancer. Am J Cancer Res. 2015;5(10):3111–3122.
  • Qiao Y, Wu M, Feng Y, et al. Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls. Sci Rep. 2018;8(1):1597.
  • Flemer B, Warren RD, Barrett MP, et al. The oral microbiota in colorectal cancer is distinctive and predictive. Gut. 2018;67(8):1454–1463.
  • Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11(12):2639–2643.
  • Weiss S, Xu Z, Peddada S, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5(1):27.
  • McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10(4):e1003531.