The human microbiome and autoimmunity

Current Opinion in Rheumatology

Volumn 25, Issue 2, 2013, Pages 234-240

  Proal, Amy D ^a   Albert, Paul J ^b   Marshall, Trevor G ^c  

^a Autoimmunity Research Foundation   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c MURDOCH UNIVERSITY   (Australia)

Author keywords

autoantibodies; autoimmune disease; immunopathology; interactome; metagenome; molecular mimicry; VDR nuclear receptor

Indexed keywords

CATHELICIDIN; GLIOTOXIN; OLMESARTAN; POLYPEPTIDE ANTIBIOTIC AGENT; RHEUMATOID FACTOR; TOLL LIKE RECEPTOR 2; VITAMIN D;

ALGORITHM; ALZHEIMER DISEASE; ASPERGILLUS FUMIGATUS; AUTOIMMUNITY; CHRONIC FATIGUE SYNDROME; COMORBIDITY; DISEASE SEVERITY; ENVIRONMENTAL FACTOR; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; HEALTH CARE QUALITY; HUMAN; IMMUNE RESPONSE; IMMUNOPATHOLOGY; INNATE IMMUNITY; MICROBIOME; MOLECULAR MIMICRY; MYCOBACTERIUM TUBERCULOSIS; OBESITY; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN INTERACTION; PSORIASIS; RANDOMIZED CONTROLLED TRIAL (TOPIC); REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; ULCERATIVE COLITIS;

ADJUVANTS, IMMUNOLOGIC; AUTOANTIBODIES; AUTOIMMUNE DISEASES; AUTOIMMUNITY; FAMILY; FEMALE; HOST-PATHOGEN INTERACTIONS; HUMANS; IMMUNITY, INNATE; INFECTION; MALE; METAGENOME; MODELS, IMMUNOLOGICAL; MOLECULAR MIMICRY; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, CALCITRIOL;

EID: 84873357099     PISSN: 10408711     EISSN: 15316963     Source Type: Journal    
DOI: 10.1097/BOR.0b013e32835cedbf     Document Type: Review

References (60)

1. Lasken RS. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 2012; 10:631-640.
2. Pflughoeft KJ, Versalovic J. Human microbiome in health and disease. Annu Rev Pathol 2012; 7:99-122.
3. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486:207-214.
4. Qin J, Li R, Raes J, et al. A human gut microbial genecatalogueestablished by metagenomic sequencing. Nature 2010; 464:59-65.
5. Turnbaugh PJ, Ley RE, Hamady M, et al. The human microbiome project. Nature 2007; 449:804-810.
6. Smillie CS, Smith MB, Friedman J, et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 2011; 480:241-244.
7. Pagani I, Liolios K, Jansson J, et al. The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012; 40:D571-D579.
8. Pride DT, Salzman J, Haynes M, et al. Evidence of a robust resident bacter-iophage population revealed through analysis of the human salivary virome. ISME J 2012; 6:915-926.
9. DiGiulio DB, Romero R, Amogan HP, et al. Microbial prevalence, diversityand abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS One 2008; 3:e3056.
10. Blainey PC, Milla CE, Cornfield DN, Quake SR. Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Sci Transl Med 2012; 4:153ra30.
11. Moriyama K, Ando C, Tashiro K, et al. Polymerase chain reaction detection of bacterial 16S rRNAgene in human blood. Microbiol Immunol 2008; 52:375-382.
12. Loo RL, Chan Q, Brown IJ, et al. A comparison of self-reported analgesic use and detection of urinary ibuprofen and acetaminophen metabolites by means of metabonomics: the INTERMAP Study. Am J Epidemiol 2012; 175:348-358.
13. Clamp M, Fry B, Kamal M, et al. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci US A 2007; 104:19428-19433.
14. Goodacre R. Metabolomics of a superorganism. J Nutr 2007; 137:S259-S266.
15. Xu Y, Xie J, Li Y, et al. Using a cDNA microarray to study cellular gene expression altered by Mycobacterium tuberculosis. Chin Med J 2003; 116:1070-1073.
16. Goh KI, Cusick ME, Valle D, et al. Thehuman disease network. Proc Natl Acad Sci US A 2007; 104:8685-8690.
17. Ramchandran L, Shah NP. Proteolytic profiles and angiotensin-I converting enzyme and alpha-glucosidase inhibitory activities of selected lactic acid bacteria. J Food Sci 2008; 73:M75-M81.
18. Giongo A, Gano KA, Crabb DB, et al. Toward defining the autoimmune microbiomefortype 1 diabetes. ISME J 2010; 5:82-91.
19. Larsen N, Vogensen FK, van den Berg FW, et al. Gut microbiota in human adults with type 2 diabetes differs from nondiabetic adults. PLoS One 2010; 5:e9085.
20. Morgan XC, Tickle TL, Sokol H, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012; 13:R79.
21. Gao Z, Tseng CH, Strober BE, et al. Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One 2008; 3:e2719.
22. Schutzer SE, Angel TE, Liu T, et al. Distinct cerebrospinal fluid proteomes differentiate post treatment lymedisease from chronic fatiguesyndrome. PLoS One 2011; 6:e17287.
23. Bassi N, Amital D, Amital H, et al. Chronic fatigue syndrome: characteristics and possible causesfor its pathogenesis. Isr Med Assoc J 2008; 10:79-82.
24. Caporaso JG, Lauber CL, Costello EK, et al. Moving pictures of the human microbiome. Genome Biol 2011; 12:R50.
25. Santiago GL, Cools P, Verstraelen H, et al. Longitudinal studyofthedynamics of vaginal microflora during two consecutive menstrual cycles. PLoS One 2011; 6:e28180.
26. Grice EA, Kong HH, Conlan S, et al. Topographical and temporal diversity of the human skin microbiome. Science 2009; 324:1190-1192.
27. Khan N, Gowthaman U, Pahari S, Agrewala JN. Manipulation ofcostimulatory molecules by intracellular pathogens: veni, vidi, vici!! PLoS Pathog 2012; 8:e1002676.
28. Wang TT, Tavera-Mendoza LE, Laperriere D, et al. Large-scale in silico and microarray-based identification of direct 1, 25-dihydroxyvitamin D3 target genes. Mol Endocrinol 2005; 19:2685-2695.
29. Auvynet C, Rosenstein Y. Multifunctional host defense peptides: antimicrobial peptides, the small yet big players in innate and adaptive immunity. FEBS J 2009; 276:6497-6508.
30. Yenamandra SP, Lundin A, Arulampalam V, et al. Expression profile of nuclear receptors upon Epstein-Barr virus induced B cell transformation. Exp Oncol 2009; 31:92-96.
31. Salazar JC, Duhnam-Ems S, LaVake C, et al. Activation of human monocytes by live Borrelia burgdorferi generates TLR2-dependent and-independent responses which include induction of IFN-beta. PLoS Pathog 2009; 5:e1000444.
32. Chan G, Bivins-Smith ER, Smith MS, et al. Transcriptome analysis reveals human cytomegalovirus reprograms monocyte differentiation toward an M1 macrophage. J Immunol 2008; 181:698-711.
33. Liu PT, Wheelwright M, Teles R, et al. MicroRNA-21 targets the vitamin D-dependent antimicrobial pathway in leprosy. Nat Med 2012; 18:267-273.
34. Coughlan CA, Chotirmall SH, Renwick J, et al. The effect of Aspergillus? fumigatus infection on vitamin D receptor expression in cystic fibrosis. Am J Respir Crit Care Med 2012; 186:999-1007.
35. Albert PJ, Proal AD, Marshall TG. Vitamin D: the alternative hypothesis. Autoimmun Rev 2009; 8:639-644.
36. Proal AD, Albert PJ, Marshall TG. Dysregulation of the vitamin D nuclear receptor may contribute to the higher prevalence of some autoimmune diseases in women. Ann N Y Acad Sci 2009; 1173:252-259.
37. Proal AD, Albert PJ, Marshall TG. Autoimmune disease and the human metagenome. In: Nelson KE, editor. Metagenomics of the human body. New York: Springer; 2010. pp. 231-275.
38. Barna BP, Culver DA, Kanchwala A, et al. Alveolar macrophage cathelicidin deficiency in severe sarcoidosis. J Innate Immun 2012; 4:569-578.
39. Wang TT, Dabbas B, Laperriere D, et al. Directand indirect induction by 1, 25-dihydroxyvitamin D3 of the NOD2/CARD15-defensin beta2 innate immune pathway defective in Crohn disease. J Biol Chem 2010; 285:2227-2231.
40. Vijayendran C, Barsch A, Friehs K, et al. Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene ex-pression profiling. Genome Biol 2008; 9:R72.
41. Fu W, Sanders-Beer BE, Katz KS, et al. Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res 2009; 37:D417-D422.
42. Bouveret E, Brun C. Bacterial interactomes: from interactions to networks. Methods Mol Biol 2012; 804:15-33.
43. Trost B, Lucchese G, Stufano A, et al. No human protein is exempt from bacterial motifs, not even one. Self Nonself 2010; 1:328-334.
44. Kusalik A, Bickis M, Lewis C, et al. Widespread and ample peptide over-lapping between HCV and Homo sapiens proteomes. Peptides 2007; 28:1260-1267.
45. Krishnadev O, Srinivasan N. Prediction of protein-protein interactions be-tween human host and a pathogen and its application to three pathogenic bacteria. Int J Biol Macromol 2011; 48:613-619.
46. Trost B, Pajon R, Jayaprakash T, Kusalik A. Comparing the similarity of different groups of bacteria to the human proteome. PLoS One 2012; 7:e34007.
47. Van Oostrom SH, Picavet HS, van Gelder BM, et al. Multimorbidity and comorbidity in the Dutch population: datafromgeneral practices. BMCPublic Health 2012; 12:715.
48. Lekakh IV, Rott GM, Poverennyi AM. 'Masked' autoantibodies from the serum of healthy blood donors cross-reacting with DNA and bacterial lipopolysac-charides. Biull Eksp Biol Med 1991; 111:516-518.
49. Berlin T, Zandman-Goddard G, Blank M, et al. Autoantibodies in nonau-toimmune individuals during infections. Ann N Y Acad Sci 2007; 1108: 584-593.
50. Anaya JM, Tobon GJ, Vega P, Castiblanco J. Autoimmune disease aggrega-tion in families with primary Sjogren's syndrome. J Rheumatol 2006; 33:2227-2234.
51. Rossman MD, Kreider ME. Lesson learned from ACCESS (A Case Con-trolled Etiologic Study of Sarcoidosis). Proc Am Thorac Soc 2007; 4:453-456.
52. Hemminki K, Li X, Sundquist K, Sundquist J. Shared familial aggregation of susceptibility to autoimmune diseases. Arthritis Rheum 2009; 60:2845-2847.
53. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet 2012; 13:260-270.
54. Weyermann M, Rothenbacher D, Brenner H. Acquisition of Helicobacter pylori infection in early childhood: independent contributions of infected mothers, fathers, and siblings. Am J Gastroenterol 2009; 104:182-189.
55. Maher B. ENCODE: the human encyclopaedia. Nature 2012; 489:46-48.
56. International HapMap Consortium. The International HapMap Project. Nature 2003; 426:789-796.
57. Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. PLoS One 2009; 4:e7767.
58. Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 2011; 6:e17288.
59. Proal AD, Albert PJ, Blaney GP, et al. Immunostimulation in the era of the metagenome. Cell Mol Immunol 2011; 8:213-225.
60. Wang Q, Miller DJ, Bowman ER, et al. MDA5 and TLR3 initiate pro-inflam-matory signaling pathways leading to rhinovirus-induced airways inflammation and hyperresponsiveness. PLoS Pathog 2011; 7:e1002070.