Human Microbiome: When a Friend Becomes an Enemy

Archivum Immunologiae et Therapiae Experimentalis

Volumn 63, Issue 4, 2015, Pages 287-298

  Muszer, Magdalena ^a   Noszczyńska, Magdalena ^a   Kasperkiewicz, Katarzyna ^a   Skurnik, Mikael ^b,c  

^a UNIVERSITY OF SILESIA   (Poland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

Author keywords

Bacteria; Health; Homeostasis; Microbiome

Indexed keywords

ACNE; ATHEROSCLEROSIS; ATOPIC DERMATITIS; AUTISM; CARDIOVASCULAR SYSTEM; DIGESTIVE SYSTEM; DIGESTIVE SYSTEM CANCER; DISEASE ASSOCIATION; HEALTH; HOMEOSTASIS; HOST PATHOGEN INTERACTION; HUMAN; IMMUNE SYSTEM; INFLAMMATORY BOWEL DISEASE; INSULIN DEPENDENT DIABETES MELLITUS; INTEGUMENTARY SYSTEM; INTESTINE FLORA; MICROFLORA; MULTIPLE SCLEROSIS; NERVOUS SYSTEM; NONHUMAN; OBESITY; PATHOGEN LOAD; PSORIASIS; REVIEW; RHEUMATOID ARTHRITIS; SKIN FLORA; SYMBIOSIS; ACNE VULGARIS; GASTROINTESTINAL TUMOR; IMMUNOLOGY; MICROBIOLOGY; SKIN;

ACNE VULGARIS; ARTHRITIS, RHEUMATOID; ATHEROSCLEROSIS; AUTISTIC DISORDER; DERMATITIS, ATOPIC; DIABETES MELLITUS, TYPE 1; GASTROINTESTINAL NEOPLASMS; HOMEOSTASIS; HUMANS; IMMUNE SYSTEM; INFLAMMATORY BOWEL DISEASES; MICROBIOTA; MULTIPLE SCLEROSIS; OBESITY; PSORIASIS; SKIN;

EID: 84938289994     PISSN: 0004069X     EISSN: 16614917     Source Type: Journal    
DOI: 10.1007/s00005-015-0332-3     Document Type: Review

References (117)

1. Ackerman J (2012) The ultimate social network. Sci Am 306:38–43
2. Adams JB, Johansen LJ, Powell LD et al (2011) Gastrointestinal flora and gastrointestinal status in children with autism-comparisons to typical children and correlation with autism severity. BMC Gastroenterol 11:22
3. Alexeyev OA, Jahns AC (2012) Sampling and detection of skin Propionibacterium acnes: current status. Anaerobe 18:479–483
4. Arumugam M, Raes J, Pelletier E et al (2011) Enterotypes of the human gut microbiome. Nature 473:174–180
5. Atarashi K, Tanoue T, Oshima K et al (2013) Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500:232–236
6. Babu SD, Jayanthi V, Devaraj N et al (2006) Expression profile of mucins (MUC2, MUC5AC and MUC6) in Helicobacter pylori infected pre-neoplastic and neoplastic human gastric epithelium. Mol Cancer 5:10
7. Bäckhed F, Manchester J, Semenkovich C et al (2007) Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA 104:979–984
8. Baumgart M, Dogan B, Rishniw M et al (2007) Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum. ISME J 1:403–418
9. Bek-Thomsen M, Lomholt HB, Kilian M (2008) Acne is not associated with yet-uncultured bacteria. J Clin Microbiol 46:3355–3360
10. Benach JL, Li E, McGovern MM (2012) A microbial association with autism. MBio 3(1):e00012–e00019
11. Benn CS, Thorsen P, Jensen JS et al (2002) Maternal vaginal microflora during pregnancy and the risk of asthma hospitalization and use of antiasthma medication in early childhood. J Allergy Clin Immunol 110:72–77
12. Bik EM, Eckburg PB, Gill SR et al (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 103:732–737
13. Binek M (2012) Mikrobiom człowieka—zdrowie i choroba. Postepy Mikrob 51:27–36
14. Boerner BP, Sarvetnick NE (2011) Type 1 diabetes: role of intestinal microbiome in humans and mice. Ann NY Acad Sci 1243:103–118
15. Bojar RA, Holland KT (2004) Acne and Propionibacterium acnes. Clin Dermatol 22:375–379
16. Boltin D, Niv Y (2012) Ghrelin, Helicobacter pylori and body mass: is there an association? Isr Med Assoc J 14:130–132
17. Boudeau J, Glasser AL, Masseret E et al (1999) Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn’s disease. Infect Immun 67:4499–4509
18. Brandl K, Plitas G, Schnabl B et al (2007) MyD88-mediated signals induce the bactericidal lectin RegIII gamma and protect mice against intestinal Listeria monocytogenes infection. J Exp Med 204:1891–1900
19. Caesar R, Fåk F, Bäckhed F (2010) Effects of gut microbiota on obesity and atherosclerosis via modulation of inflammation and lipid metabolism. J Intern Med 268:320–328
20. Callard RE, Harper JI (2007) The skin barrier, atopic dermatitis and allergy: a role for Langerhans cells? Trends Immunol 28:294–298
21. Capone KA, Dowd SE, Stamatas GN et al (2011) Diversity of the human skin microbiome early in life. J Invest Dermatol 131:2026–2032
22. Chen YE, Tsao H (2013) The skin microbiome: current perspectives and future challenges. J Am Acad Dermatol 69:143–155
23. Chung KT, Stevens SE Jr, Cerniglia CE (1992) The reduction of azo dyes by the intestinal microflora. Crit Rev Microbiol 18:175–190
24. Collins SM, Bercik P (2009) The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease. Gastroenterology 136:2003–2014
25. Conteduca V, Sansonno D, Lauletta G et al (2013) H. pylori infection and gastric cancer: state of the art (review). Int J Oncol 42:5–18
26. Critchfield JW, van Hemert S, Ash M et al (2011) The potential role of probiotics in the management of childhood autism spectrum disorders. Gastroenterol Res Pract 2011:161358
27. Cryan JF, O’Mahony SM (2011) The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterol Motil 23:187–192
28. Dave M, Higgins PD, Middha S et al (2012) The human gut microbiome: current knowledge, challenges and future directions. Transl Res 160:246–257
29. De Angelis M, Piccolo M, Vannini L et al (2013) Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One 8:e76993
30. Desvarieux M, Demmer RT, Rundek T et al (2005) Periodontal microbiota and carotid intima-media thickness: the Oral Infections and Vascular Disease Epidemiology Study (INVEST). Circulation 111:576–582
31. Diaz-Heijtz R, Wang S, Anuar F et al (2011) Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA 108:3047–3052
32. Dietert RR, Dietert JM, DeWitt JC (2011) Environmental risk factors for autism. Emerg Health Threats J 4:7111
33. Dorca-Arévalo J, Soler-Jover A, Gibert M et al (2008) Binding of epsilon-toxin from Clostridium perfringens in the nervous system. Vet Microbiol 131:14–25
34. Dorca-Arévalo J, Martin-Satué M, Blasi J (2012) Characterization of the high affinity binding of epsilon toxin from Clostridium perfringens to the renal system. Vet Microbiol 157:179–189
35. Ebringer A, Rashid T, Wilson C (2010) Rheumatoid arthritis, Proteus, anti-CCP antibodies and Karl Popper. Autoimmun Rev 9:216–223
36. Fahlén A, Engstrand L, Baker BS et al (2012) Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin. Arch Dermatol Res 304:15–22
37. Fava F, Danese S (2011) Intestinal microbiota in inflammatory bowel disease: friend of foe? World J Gastroenterol 17:557–566
38. Fei N, Zhao L (2012) An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J 7:880–884
39. Finegold SM (2011) Desulfovibrio species are potentially important in regressive autism. Med Hypotheses 77:270–274
40. Finegold SM, Molitoris D, Song Y et al (2002) Gastrointestinal microflora studies in late-onset autism. Clin Infect Dis 35(Suppl 1):S6–S16
41. Finegold SM, Dowd SE, Gontcharova V et al (2010) Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16:444–453
42. Franczuk A, Jagusztyn-Krynicka EK (2012) Rola mikroflory jelit w indukcji choroby Leśniowskiego-Crohna w świetle programu badań Human Microbiome Project. Postepy Mikrob 51:257–264
43. Frank DN, St Amand AL, Feldman RA et al (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 104:13780–13785
44. Gaetti-Jardim E Jr, Marcelino SL, Feitosa AC et al (2009) Quantitative detection of periodontopathic bacteria in atherosclerotic plaques from coronary arteries. J Med Microbiol 58(Pt 12):1568–1575
45. Gao Z, Tseng CH, Strober BE et al (2008) Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One 3:e2719
46. 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
47. Gonzalez A, Stombaugh J, Lozupone C et al (2011) The mind-body-microbial continuum. Dialogues Clin Neurosci 13:55–62
48. Grice EA, Segre JA (2011) The skin microbiome. Nat Rev Microbiol 9:244–253
49. Grice EA, Kong HH, Conlan S et al (2009) Topographical and temporal diversity of the human skin microbiome. Science 324:1190–1192
50. Gripenberg-Lerche C, Zhang L, Ahtonen P et al (2000) Construction of urease-negative mutants of Yersinia enterocolitica serotypes O:3 and O:8: role of urease in virulence and arthritogenicity. Infect Immun 68:942–947
51. Harley IT, Karp CL (2012) Obesity and the gut microbiome: striving for causality. Mol Metab 1:21–31
52. Holmes E, Li JV, Athanasiou T et al (2011) Understanding the role of gut microbiome–host metabolic signal disruption in health and disease. Trends Microbiol 19:349–359
53. Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336:1268–1273
54. Hot A, Miossec P (2011) Effects of interleukin (IL)-17A and IL-17F in human rheumatoid arthritis synoviocytes. Ann Rheum Dis 70:727–732
55. Hsiao EY, McBride SW, Hsien S et al (2013) Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155:1451–1463
56. Human Microbiome Project Consortium (2012a) Structure, function and diversity of the healthy human microbiome. Nature 486:207–214
57. Human Microbiome Project Consortium (2012b) A framework for human microbiome research. Nature 486:215–221
58. Huycke MM, Gaskins HR (2004) Commensal bacteria, redox stress and colorectal cancer: mechanisms and models. Exp Biol Med 229:586–597
59. Iebba V, Aloi M, Civitelli F et al (2011) Gut microbiota and pediatric disease. Dig Dis 29:531–539
60. Ivanov I, Atarashi K, Manel N et al (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139:485–498
61. Iwase T, Uehara Y, Shinji H et al (2010) Staphylococcus epidermidis esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature 465:346–349
62. Jaff MR, Dale RA, Creager MA et al (2009) Anti-chlamydial antibiotic therapy for symptom improvement in peripheral artery disease: prospective evaluation of rifalazil effect on vascular symptoms of intermittent claudication and other endpoints in Chlamydia pneumoniae seropositive patients (PROVIDENCE-1). Circulation 119:452–458
63. Kinnebrew MA, Ubeda C, Zenewicz LA et al (2010) Bacterial flagellin stimulates Toll-like receptor 5-dependent defense against vancomycin-resistant Enterococcus infection. J Infect Dis 201:534–543
64. Kobayashi KS, Chamaillard M, Ogura Y et al (2005) Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract. Science 307:731–734
65. Kong HH (2011) Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends Mol Med 17:320–328
66. Kong HH, Segre JA (2012) Skin microbiome: looking back to move forward. J Invest Dermatol 132(Pt 2):933–939
67. Kong HH, Oh J, Deming C et al (2012) Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 22:850–859
68. Koren O, Knights D, Gonzalez A et al (2013) A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol 9:e1002863
69. Lai Y, Di Nardo A, Nakatsuji T et al (2009) Commensal bacteria regulate Toll-like receptor 3-dependent inflammation after skin injury. Nat Med 15:1377–1382
70. Lee YK, Mazmanian SK (2010) Has the microbiota played a critical role in the evolution of the adaptive immune system? Science 330:1768–1773
71. Lee YK, Menezes JS, Umesaki Y et al (2011) Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc Natl Acad Sci USA 108(Suppl 1):4615–4622
72. Ley RE (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26:5–11
73. Ley RE, Bäckhed F, Turnbaugh P et al (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102:11070–11075
74. Ley RE, Turnbaugh PJ, Klein S et al (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444:1022–1023
75. Livingston M, Loach D, Wilson M et al (2010) Gut commensal Lactobacillus reuteri 100-23 stimulates an immunoregulatory response. Immunol Cell Biol 88:99–102
76. Louis P (2012) Does the human gut microbiota contribute to the etiology of autism spectrum disorders? Dig Dis Sci 57:1987–1989
77. Mazmanian SK, Liu CH, Tzianabos AO et al (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122:107–118
78. Mazmanian SK, Round JL, Kasper DL (2008) A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453:620–625
79. Morgan XC, Tickle TL, Sokol H et al (2012) Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13:R79
80. Morgan XC, Segata N, Huttenhower C (2013) Biodiversity and functional genomics in the human microbiome. Trends Genet 29:51–58
81. Muhlestein J (2003) Antibiotic treatment of atherosclerosis. Curr Opin Lipidol 14:605–614
82. Ochoa-Repáraz J, Mielcarz DW, Ditrio LE et al (2009) Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis. J Immunol 183:6041–6050
83. Parracho HM, Bingham MO, Gibson GR et al (2005) Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J Med Microbiol 54(Pt 10):987–991
84. Proctor LM (2011) The Human Microbiome Project in 2011 and beyond. Cell Host Microbe 10:287–291
85. Pull SL, Doherty JM, Mills JC et al (2005) Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc Natl Acad Sci USA 102:99–104
86. Rashid T, Ebringer A (2007) Ankylosing spondylitis is linked to Klebsiella—the evidence. Clin Rheumatol 26:858–864
87. Ravel J, Blaser MJ, Braun J et al (2014) Human microbiome science: vision for the future. Bethesda, MD, July 24–26, 2013. Microbiome doi: 10.1186/2049-2618-2-16
88. Reddy BS, Simi B, Patel N et al (1996) Effect of amount and types of dietary fat on intestinal bacterial 7 alpha-dehydroxylase and phosphatidylinositolspecific phospholipase C and colonic mucosal diacylglycerol kinase and PKC activities during stages of colon tumor promotion. Cancer Res 56:2314–2320
89. Rolig AS, Cech C, Ahler E et al (2013) The degree of Helicobacter pylori-triggered inflammation is manipulated by preinfection host microbiota. Infect Immun 81:1382–1389
90. Romano-Keeler J, Weitkamp JH, Moore DJ (2012) Regulatory properties of the intestinal microbiome effecting the development and treatment of diabetes. Curr Opin Endocrinol Diabetes Obes 19:73–80
91. Rooks MG, Garrett WS (2011) Sharing the Bounty. The Scientist. http://www.the-scientist.com/?articles.view/articleNo/30764/title/Sharing-the-Bounty/. Accessed 13 December 2013
92. Rumah KR, Linden J, Fischetti VA et al (2013) Isolation of Clostridium perfringens type B in an individual at first clinical presentation of multiple sclerosis provides clues for environmental triggers of the disease. PLoS One 8:e76359
93. Sandler RH, Finegold SM, Bolte ER et al (2000) Short-term benefit from oral vancomycin treatment of regressive-onset autism. J Child Neurol 15:429–435
94. Scher JU, Abramson SB (2011) The microbiome and rheumatoid arthritis. Nat Rev Rheumatol 7:569–578
95. Schön MP, Boehncke WH (2005) Psoriasis. N Engl J Med 352:1899–1912
96. Sekirov I, Russell SL, Antunes LC et al (2010) Gut microbiota in health and disease. Physiol Rev 90:859–904
97. Snel J, Hermsen CC, Smits HJ et al (1998) Interactions between gut-associated lymphoid tissue and colonization levels of indigenous, segmented, filamentous bacteria in the small intestine of mice. Can J Microbiol 44:1177–1182
98. Stecher B, Chaffron S, Kappeli R et al (2010) Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog 6:e1000711
99. Stepankova R, Tonar Z, Bartova J et al (2010) Absence of microbiota (germ-free conditions) accelerates the atherosclerosis in ApoE-deficient mice fed standard low cholesterol diet. J Atheroscler Thromb 17:796–804
100. Tlaskalová-Hogenová H, Štěpánková R, Kozáková H et al (2011) The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases. Cell Mol Immunol 8:110–120
101. Toivanen P (2003) Normal intestinal microbiota in the aetiopathogenesis of rheumatoid arthritis. Ann Rheum Dis 62:807–811
102. Tomida S, Nguyen L, Chiu BH et al (2013) Pan-genome and comparative genome analyses of Propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. MBio 4:e00003–e00013
103. Trivedi B (2012) Microbiome: the surface brigade. Nature 492:S60–S61
104. Troy E, Kasper D (2010) Beneficial effects of Bacteroides fragilis polysaccharides on the immune system. Front Biosci 15:25–34
105. Turnbaugh PJ, Bäckhed F, Fulton L et al (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213–223
106. Ursell LK, Metcalf JL, Parfrey LW et al (2012) Defining the human microbiome. Nutr Rev 70(Suppl 1):S38–S44
107. Vaarala O (2011) The gut as a regulator of early inflammation in type 1 diabetes. Curr Opin Endocrinol Diabetes Obes 18:241–247
108. Vannucci L, Stepankova R, Grobarova V et al (2009) Colorectal carcinoma: importance of colonic environment for anti-cancer response and systemic immunity. J Immunotoxicol 6:217–226
109. Wang L, Christophersen CT, Sorich MJ et al (2013) Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder. Mol. Autism 4:42
110. Webster GF (2002) Acne vulgaris. BMJ 325:475–479
111. Weisenseel P, Prinz JC (2005) Incidental detection of S. pyogenes DNA in psoriatic skin by PCR. Arch Dermatol Res 296:573–576
112. Wen L, Ley RE, Volchkov PY et al (2008) Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455:1109–1113
113. Williams BL, Hornig M, Parekh T et al (2012) Application of novel PCR-based methods for detection, quantitation and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances. MBio 3(1):e00211–e00261
114. Wright SD, Burton C, Hernandez M et al (2000) Infectious agents are not necessary for murine atherogenesis. J Exp Med 191:1437–1442
115. Wu HJ, Wu E (2012) The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes 3:4–14
116. Wylie KM, Truty RM, Sharpton TJ et al (2012) Novel bacterial taxa in the human microbiome. PLoS One 7:e35294
117. Yap IK, Angley M, Veselkov KA et al (2010) Urinary metabolic phenotyping differentiates children with autism from their unaffected siblings and age-matched controls. J Proteome Res 9:2996–3004