Notes

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3. John Travis, “All the World’s a Phage: Viruses That Eat Bacteria Abound—And Surprise,” Science News 164, no. 2 (2003): 26, https://www.sciencenews.org/article/all-worlds-phage.

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7. Thomas Abrahamsson, Hedvig Jakobsson, Anders Andersson, et al., “Low Diversity of the Gut Microbiota in Infants with Atopic Eczema,” The Journal of Allergy and Clinical Immunology 129, no. 2 (2012): 434–440, 440 e431–432, doi: 10.1016/j.jaci.2011.10.025.

8. Kaarina Kukkonen, Erkki Savilahti, Tari Haahtela, et al., “Probiotics and Prebiotic Galacto-Oligosaccharides in the Prevention of Allergic Diseases: A Randomized, Double-Blind, Placebo-Controlled Trial,” The Journal of Allergy and Clinical Immunology 119, no. 1 (2007): 192–198, doi: 10.1016/j.jaci.2006.09.009.

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10. Mogens Kilian, Iain Chapple, M. Hannig, et al., “The Oral Microbiome—An Update for Oral Healthcare Professionals,” British Dental Journal 221, no. 10 (2016): 657–666, doi: 10.1038/sj.bdj.2016.865.

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12. William Wade, “Unculturable Bacteria—The Uncharacterized Organisms That Cause Oral Infections,” Journal of the Royal Society of Medicine 95, no. 2 (2002): 81–83, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1279316.

13. Michael Rappé and Stephen Giovannoni, “The Uncultured Microbial Majority,” Annual Review of Microbiology 57 (2003): 369–394, doi: 10.1146/annurev.micro.57.030502.090759.

14. Floyd Dewhirst, Tuste Chen, Jacques Izard, et al., “The Human Oral Microbiome,” Journal of Bacteriology 192, no. 19 (2010): 5002–5017, doi: 10.1128/JB.00542–10.

15. “Microbiology by Numbers,” Nature Reviews Microbiology 9 (2011): 628, doi: 10.1038/nrmicro2644.

16. Arianna DeGruttola, Daren Low, Atsushi Mizoguchi, et al., “Current Understanding of Dysbiosis in Disease in Human and Animal Models,” Inflammatory Bowel Diseases 22, no. 5 (2016): 1137–1150, doi: 10.1097/MIB.0000000000000750.

17. Ingegerd Johansson, Ewa Witkowska, B. Kaveh, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries,” Journal of Dental Research 95, no. 1 (2016): 80–86, doi: 10.1177/0022034515609554.

18. Arianna DeGruttola, et al., “Current Understanding of Dysbiosis in Disease in Human and Animal Models.”

19. C. Lee Ventola, “The Antibiotic Resistance Crisis: Part 1: Causes and Threats” P & T40, no. 4 (2015): 277–283, https://www.ncbi.nlm.nih.gov/pubmed/25859123.

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26. Ibid.

27. Ibid.

28. Izabela Struzycka, “The Oral Microbiome in Dental Caries,” Polish Journal of Microbiology / Polskie Towarzystwo Mikrobiologow = The Polish Society of Microbiologists 63, no. 2 (2014): 127–135, https://www.ncbi.nlm.nih.gov/pubmed/25115106.

29. Jinzhi He, Yan Li, Yangpei Cao, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases,” Folia Microbiologica 60, no. 1 (2015): 69–80, doi: 10.1007/s12223-014-0342-2.

30. Jukka Meurman and Iva Stamatova, “Probiotics: Contributions to Oral Health,” Oral Diseases 13, no. 5 (2007): 443–451, doi: 10.1111/j.1601–0825.2007.01386.x.

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32. Ruiqing Wu, Dunfang Zhang, Eric Tu, et al., “The Mucosal Immune System in the Oral Cavity—An Orchestra of T Cell Diversity,” International Journal of Oral Science 6, no. 3 (2014): 125–132, doi: 10.1038/ ijos.2014.48.

33. Jukka Meurman, et al., “Probiotics: Contributions to Oral Health.”

34. Ruiqing Wu, et al., “The Mucosal Immune System in the Oral Cavity—An Orchestra of T Cell Diversity.”

35. Koichi Shudo, Hiroshi Fukasawa, Madoka Nakagomi, et al., “Towards Retinoid Therapy For Alzheimer’s Disease,” Current Alzheimer Research 6, no. 3 (2009): 302–311, doi: 10.2174/156720509788486581.

36. Alessio Fasano, “Leaky Gut and Autoimmune Diseases,” Clinical Reviews in Allergy and Immunology 42, no. 1 (2012): 71–78, doi: 10.1007/s 12016-011-8291-x.

37. Hiroshi Kiyono, et al., “The Mucosal Immune System: From Dentistry to Vaccine Development.”

38. Magali Noval Rivas and Talal Chatila, “Regulatory T Cells in Allergic Diseases,” The Journal of Allergy and Clinical Immunology 138, no. 3 (2016): 639–652, doi: 10.1016/j.jaci.2016.06.003.

39. Deirdre Devine, et al., “Modulation of Host Responses by Oral Commensal Bacteria.

40. Alessio Fasano, “Zonulin, Regulation of Tight Junctions, and Autoimmune Diseases,” Annals of the New York Academy of Sciences 1258, no. 1 (2012): 25–33, doi: 10.1111/j.1749-6632.2012.06538.x.

41. Alessio Fasano, “Leaky Gut and Autoimmune Diseases,” Clinical Reviews in Allergy and Immunology 42. no. 1 (2012): 71–78, doi: 10.1007/s12016-011-8291-x.

42. Alessio Fasano and Terez Shea-Donohue, “Mechanisms of Disease: The Role of Intestinal Barrier Function in the Pathogenesis of Gastrointestinal Autoimmune Diseases,” Nature Clinical Practice 2, no. 9 (2005): 416–422, doi: 10.1038/ncpgasthep0259.

43. Mogens Kilian, et al., “The Oral Microbiome—An Update for Oral Healthcare Professionals.”

44. Floyd Dewhirst, et al., “The Human Oral Microbiome.”

45. Ibid.

46. I. Cho and M. J. Blaser, “The Human Microbiome: At the Interface of Health and Disease,” Nature Reviews Genetics 13, no. 4 (2012): 260–70.

47. Y. J. Huang, B. J. Marsland, S. Bunyavanich, et al., “The Microbiome in Allergic Disease,” The Journal of Allergy and Clinical Immunology 139, no. 4 (2017): 1099–1110.

48. Nicola Segata, Susan Kinder Haake, Peter Mannon, et al., “Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples,” Genome Biology 13, no. 6 (2012): R42, doi: 10.1186/gb-2012-13-6-r42.

49. Purnima Kumar and Matthew Mason, “Mouthguards: Does the Indigenous Microbiome Play a Role in Maintaining Oral Health?” Frontiers in Cellular and Infection Microbiology 6, no. 5 (2015): 35, doi: 10.3389/fcimb.2015.00035.

50. B. Wilson and K. Whelan, “Prebiotic Inulin-Type Fructans and Galacto-Oligosaccharides,” Journal of Gastroenterology and Hepatology 32, suppl. no. 1 (2017): 64–68.

51. Thomas Auchtung, Tatiana Fofanova, Christopher Stewart, et al., “Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi,” mSphere 3, no. 2 (2018), doi: 10.1128/mSphere.00092-18.

52. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases.”

53. Anna Edlund, Tasha Santiago-Rodriguez, Tobias Boehm, et al., “Bacteriophage and Their Potential Roles in the Human Oral Cavity,” Journal of Oral Microbiology 7, no. 27423 (2015), doi: 10.3402/jom. v7.27423.

54. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases”

55. Ingegerd Johansson, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries.”

56. Elizabeth Thursby and Nathalie Juge, “Introduction to the Human Gut Microbiota,” The Biochemical Journal 474, no. 11 (2017): 1823–1836, doi: 10.1042/BCJ20160510.

57. P. Lif Holgerson, L. Harnevik, O. Hernell, et al., “Mode of Birth Delivery Affects Oral Microbiota in Infants,” Journal of Dental Research 90, no. 10 (2011): 1183–1188, doi: 10.1177/0022034511418973.

58. Elizabeth Thursby, et al., “Introduction to the Human Gut Microbiota.”

59. P. Lif Holgerson, et al., “Mode of Birth Delivery Affects Oral Microbiota in Infants.”

60. Y. J. Huang, et al., “The Microbiome in Allergic Disease.”

61. Katherine Gregory, Buck Samuel, Pearl Houghteling, et al., “Influence of Maternal Breast Milk Ingestion on Acquisition of the Intestinal Microbiome in Preterm Infants,” Microbiome 4, no. 68 (2016): 68, doi: 10.1186/s40168-016-0214-x.

62. Camilia Martin, Pei-Ra Ling, and George Blackburn, “Review of Infant Feeding: Key Features of Breast Milk and Infant Formula,” Nutrients 8, no. 5 (2016): 279, doi: 10.3390/nu8050279.

63. Rodney Donlan, “Biofilms: Microbial Life on Surfaces,” Emerging Infectious Diseases 8, no. 9 (2002): 881–890, doi: 10.3201/eid0809.020063.

64. Floyd Dewhirst, et al., “The Human Oral Microbiome.”

65. Rodney Donlan, “Biofilms: Microbial Life on Surfaces.”

66. Ibid.

67. Melissa Miller and Bonnie Bassler, “Quorum Sensing in Bacteria,” Annual Review of Microbiology 55 (2001): 165–199, doi: 10.1146/annurev.micro.55.1.165.

68. B. Wilson, et al., “Prebiotic Inulin-Type Fructans and Galacto-Oligosaccharides.”

69. Joanne Slavin, “Fiber and Prebiotics: Mechanisms and Health Benefits,” Nutrients 5, no. 4 (2013): 1417–1435, doi: 10.3390/nu5041417.

70. Floyd Dewhirst, et al., “The Human Oral Microbiome.”

71. Ingegerd Johansson, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries.”

72. Maria Cagetti, Stefano Mastroberardino, Egle Milia, et al., “The Use of Probiotic Strains in Caries Prevention: A Systematic Review,” Nutrients 5, no. 7 (2013): 2530–2550, doi: 10.3390/nu5072530.

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74. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases.”

75. Izabela Struzycka, “The Oral Microbiome in Dental Caries.”

76. Ibid.

77. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases.”

78. E. A. Grice and J. A. Segre, “The Human Microbiome: Our Second Genome,” Annual Review of Genomics and Human Genetics 13 (2012): 151–71.

79. Ingegerd Johansson, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries.”

80. Ibid.

81. Ensanya Ali Abou Neel, et al., “Demineralization-Remineralization Dynamics in Teeth and Bone.”

82. Ingegerd Johansson, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries.”

83. Clifton Bingham and Malini Moni, “Periodontal Disease and Rheumatoid Arthritis: The Evidence Accumulates for Complex Pathobiologic Interactions,” Current Opinion in Rheumatology 25, no. 3 (2013): 345–353, doi: 10.1097/BOR.0b013e32835fb8ec.

84. Karen Schwarzberg, Rosalin Le, Balambal Bharti, et al., “The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease,” PLoS ONE 9, no. 1 (2014): e86708, doi: 10.1371/journal.pone.0086708.

85. J. Henry Clarke, “Toothaches and Death,” Journal of the History of Dentistry 47, no. 1 (1999): 11–13, doi: https://ohsu.pure.elsevier.com/en/publications/toothaches-and-death-2.

86. S. Porter and C. Scully, “Oral Malodour (Halitosis),” BMJ 333, no. 7569 (2006): 632–635, doi: 10.1136/bmj.38954.631968.AE.

87. Ibid.

88. Walter Loesche, “Microbiology of Dental Decay and Periodontal Disease,” in Medical Microbiology, 4th ed., edited by Samuel Baron (Galveston, TX: University of Texas Medical Branch at Galveston; 1996).

89. Ingegerd Johansson, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries.”

90. Maria Cagetti, et al., “The Use of Probiotic Strains in Caries Prevention: A Systematic Review.”

91. Clifton Bingham, et at., “Periodontal Disease and Rheumatoid Arthritis: The Evidence Accumulates for Complex Pathobiologic Interactions.,”

92. E. A. Grice, et al., “The Human Microbiome: Our Second Genome.”

93. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases.”

94. Nicola Segata, et al., “Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples.,”

95. Ibid.

96. Ingegerd Johansson, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries.”

97. Michael Docktor, Bruce Paster, Shelly Abramowicz, et al., “Alterations in Diversity of the Oral Microbiome in Pediatric Inflammatory Bowel Disease,” Inflammatory Bowel Diseases 18, no. 5 (2012): 935–942, doi: 10.1002/ibd.21874.

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99. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases.”

100. Hiroshi Kiyono, et al., “The Mucosal Immune System: From Dentistry to Vaccine Development.”

101. Nicola Segata, et al., “Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples.”

102. Ibid.

103. Izabela Struzycka, “The Oral Microbiome in Dental Caries.”

104. Yoshio Yamaoka, “Mechanisms of Disease: Helicobacter Pylori Virulence Factors,” Nature Reviews Gastroenterology & Hepatology 7, no. 11 (2010): 629–641, doi: 10.1038/nrgastro.2010.154.

105. Marjorie Walker and Nicholas Talley, “Review Article: Bacteria and Pathogenesis of Disease in the Upper Gastrointestinal Tract—Beyond the Era of Helicobacter Pylori,” Alimentary Pharmacology & Therapeutics 39, no. 8 (2014): 767–779, doi: 10.1111/apt.12666.

106. Aaron Thrift, Nirmala Pandeya, Kylie Smith, et al., “Helicobacter Pylori Infection and the Risks of Barrett’s Oesophagus: A Population-Based Case-Control Study,” International Journal of Cancer 130, no. 10 (2012): 2407–2416, doi: 10.1002/ijc.26242.

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108. Chun-Ling Jia, Guang-Shui Jiang, Chun-Hai Li, et al., “Effect of Dental Plaque Control on Infection of Helicobacter Pylori in Gastric Mucosa,” Journal of Periodontology 80, no. 10 (2012): 1069–1073, doi: 10.1902/jop.2009.090029.

109. Siew Ng, Hai Yun Shi, Nima Hamidi, et al., “Worldwide Incidence and Prevalence of Inflammatory Bowel Disease in the 21st Century: A Systematic Review of Population-Based Studies,” The Lancet 390, 10114 (2018): 2769–2778.

110. Andrew Yu, Louis Cabanilla, Eric Qiong Wu, et al., “The Costs of Crohn’s Disease in the United States and Other Western Countries: A Systematic Review,” Current Medical Research and Opinion 24, no. 2 (2008): 319–328, doi: 10.1185/030079908X260790.

111. Michael Docktor, et al., “Alterations in Diversity of the Oral Microbiome in Pediatric Inflammatory Bowel Disease,”

112. Kewir Nyuyki and Quentin Pittman, “Toward a Better Understanding of the Central Consequences of Intestinal Inflammation,” Annals of the New York Academy of Sciences 1351, no. 1 (2015): 149–154, doi: 10.1111/nyas.12935.

113. Michael Docktor, et al., “Alterations in Diversity of the Oral Microbiome in Pediatric Inflammatory Bowel Disease,”

114. Ibid.

115. Fernanda Brito, Cyrla Zaltman, Ana Teresa Pugas Carvalho, et al., “Subgingival Microflora in Inflammatory Bowel Disease Patients with Untreated Periodontitis,” European Journal of Gastroenterology & Hepatology 25, no. 2 (2012): 239–45, doi: 10.1097/MEG.0b013e32835a2b70.

116. Stephan Vavricka, Christine Manser, Sebastian Hediger, et al., “Periodontitis and Gingivitis in Inflammatory Bowel Disease: A Case-Control Study,” Inflammatory Bowel Diseases 19, no. 13 (2013): 2768–2777, doi: 10.1097/01.MIB.0000438356.84263.3b.

117. Clifton Bingham, et at., “Periodontal Disease and Rheumatoid Arthritis: The Evidence Accumulates for Complex Pathobiologic Interactions.,”

118. Bradley Bale, Amy Doneen, and David Vigerust, “High-Risk Periodontal Pathogens Contribute to the Pathogenesis of Atherosclerosis,” BMJ Postgraduate Medical Journals 93, no. 1098 (2017): 215–220, https://pmj.bmj.com/content/93/1098/215

119. Ibid.

120. Stefan Reichert, Axel Schlitt, V. Beschow, et al., “Use of Floss/Interdental Brushes is Associated with Lower Risk for New Cardiovascular Events among Patients with Coronary Heart Disease,” Journal of Periodontal Research 50, no. 2 (2015): 180–188, doi: 10.1111/jre.12191.

121. Curtis Steyers III and Francis Miller Jr., “Endothelial Dysfunction in Chronic Inflammatory Diseases,” International Journal of Molecular Sciences 15, no. 7 (2014): 11324–11349, doi: 10.3390/ijms150711324.

122. Bradley Bale, et al., “High-Risk Periodontal Pathogens Contribute to the Pathogenesis of Atherosclerosis.,”

123. Herbert Cobe, “Transitory Bacteremia,” Oral Surgery, Oral Medicine, and Oral Pathology 7, no. 6 (1954): 609–615, doi: 10.1016/0030-4220(54)90071-7.

124. Bradley Bale, et al., “High-Risk Periodontal Pathogens Contribute to the Pathogenesis of Atherosclerosis.”

125. Jukka Meurman, “Oral Microbiota and Cancer,” Journal of Oral Microbiology 2 (2010), doi: 10.3402/jom.v2i0.5195.

126. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases.”

127. Jukka Meurman, “Oral Microbiota and Cancer.”

128. Bradley Bale, et al., “High-Risk Periodontal Pathogens Contribute to the Pathogenesis of Atherosclerosis.,”

129. Embriette Hyde, Fernando Andrade, Zalman Vaksman, et al., “Metagenomic Analysis of Nitrate-Reducing Bacteria in the Oral Cavity: Implications for Nitric Oxide Homeostasis,” PLoS ONE 9, no. 3 (2014): e88645, doi: 10.1371/journal.pone.0088645.

130. Jinzhi He, et al., “The Oral Microbiome Diversity and Its Relation to Human Diseases.,”

131. Clifton Bingham, et at., “Periodontal Disease and Rheumatoid Arthritis: The Evidence Accumulates for Complex Pathobiologic Interactions.”

132. Vilana Araujo, Iracema Melo, and Vilma Lima, “Relationship between Periodontitis and Rheumatoid Arthritis: Review of the Literature,” Mediators of Inflammation 2015 (2015): 259074, doi: 10.1155/2015/259074.

133. Clifton Bingham, et at., “Periodontal Disease and Rheumatoid Arthritis: The Evidence Accumulates for Complex Pathobiologic Interactions.,”

134. Vilana Araujo, et al., “Relationship between Periodontitis and Rheumatoid Arthritis: Review of the Literature.,”

135. YiPing Weng Han, Xueyan Wang, “Mobile Microbiome: Oral Bacteria in Extra-Oral Infections and Inflammation.” Journal of Dental Research 92, no. 6 (2013): 485–491, doi: 10.1177/0022034513487559.

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137. Clifton Bingham, et at., “Periodontal Disease and Rheumatoid Arthritis: The Evidence Accumulates for Complex Pathobiologic Interactions,”

138. Vilana Araujo, et al., “Relationship between Periodontitis and Rheumatoid Arthritis: Review of the Literature,”

139. Muhammad Nazir, “Prevalence of Periodontal Disease, Its Association with Systemic Diseases and Prevention,” International Journal of Health Sciences 11, no. 12 (2017): 72–80.

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141. Ibid.

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145. Gian Paolo Littarru, Ryo Nakamura, Lester Ho, et al., “Deficiency of Coenzyme Q 10 in Gingival Tissue from Patients with Periodontal Disease,” Proceedings of the National Academy of Sciences of the United States of America 68, no. 10 (1971): 2332–2335, http://www.ncbi.nlm.nih.gov/pubmed/5289867.

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147. Anirban Chatterjee, Abhishek Kandwal, Nidhi Singh, et al., “Evaluation of Co-Q10 Anti-Gingivitis Effect on Plaque Induced Gingivitis: A Randomized Controlled Clinical Trial,” Journal of Indian Society of Periodontology 16, no. 4 (2012): 539-542, doi: 10.4103/0972–124X.106902.

148. Ingegerd Johansson, et al., “The Microbiome in Populations with a Low and High Prevalence of Caries.”

149. Thomas Auchtung, et al., “Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi.”

150. Stefan Reichert, et al., “Use of Floss/Interdental Brushes is Associated with Lower Risk for New Cardiovascular Events among Patients with Coronary Heart Disease.”

151. D. Belstrom, M. Sembler-Moller, M. Grande, et al. “Impact of Oral Hygiene Discontinuation on Supragingival and Salivary Microbiomes,” JDR Clinical & Translational Research 3, no. 1 (2017): 57–64, doi: 10.1177/2380084417723625.

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156. Jukka Meurman, et al., “Probiotics: Contributions to Oral Health.”

157. M. Seminario-Amez, et al., “Probiotics and Oral Health: A Systematic Review.”

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