Autoimmune disease in the era of the metagenome

Autoimmunity Reviews

Volumn 8, Issue 8, 2009, Pages 677-681

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

^a GEORGETOWN UNIVERSITY   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c MURDOCH UNIVERSITY   (Australia)

Author keywords

Autoimmune disease; Metabolome; Metagenome; Microbiota; Vitamin D; Vitamin D receptor (VDR)

Indexed keywords

AUTOANTIBODY;

AUTOIMMUNE DISEASE; BACTERIAL GENOME; DISEASE COURSE; DNA DETERMINATION; EXPERIMENTAL MODEL; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; HUMAN; IMMUNE SYSTEM; METABOLOME; METAGENOME; MICROBIOME; MICROFLORA; MICROORGANISM; NONHUMAN; PATHOGENESIS; REVIEW; RNA TRANSLATION;

ALKANESULFONIC ACIDS; AUTOANTIBODIES; AUTOIMMUNE DISEASES; BACTERIA; DNA, BACTERIAL; GENOMICS; HUMANS; IMMUNITY, INNATE; METABOLOME; METABOLOMICS; MICROBIOME;

EID: 67349263029     PISSN: 15689972     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.autrev.2009.02.016     Document Type: Review

References (40)

1. National Research Council. Committee on metagenomics C, functional A. New science of metagenomics: revealing the secrets of our microbial planet (2007), National Academies Press, Washington, DC
2. Turnbaugh P.J., Ley R.E., Hamady M., Fraser-Liggett C.M., Knight R., and Gordon J.I. The Human Microbiome Project. Nature 449 7164 (2007) 804-810
3. Goodacre R. Metabolomics of a superorganism. J Nutr 137 1 Suppl (2007) 259S-266S
4. Dempsey K.E., Riggio M.P., Lennon A., Hannah V.E., Ramage G., Allan D., et al. Identification of bacteria on the surface of clinically infected and non-infected prosthetic hip joints removed during revision arthroplasties by 16S rRNA gene sequencing and by microbiological culture. Arthritis Res Ther 9 3 (2007) R46
5. Marshall TG. Understanding human disease requires study of a metagenome, not just the human genome. World Gene Congress; 2008 December 5-7; Foshan, China. Available from Available from: http://vimeo.com/2585394
6. Wirostko E., Johnson L., and Wirostko B. Sarcoidosis associated uveitis. Parasitization of vitreous leucocytes by mollicute-like organisms. Acta Ophthalmol (Copenh) 67 4 (1989) 415-424
7. Costerton J.W., Stewart P.S., and Greenberg E.P. Bacterial biofilms: a common cause of persistent infections. Science 284 5418 (1999) 1318-1322
8. Tamames J., and Moya A. Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics 9 (2008) 136
9. Hanage W.P., Fraser C., and Spratt B.G. Fuzzy species among recombinogenic bacteria. BMC Biol 3 (2005) 6
10. Mullard A. Microbiology: the inside story. Nature 453 7195 (2008) 578-580
11. Vijayendran C., Barsch A., Friehs K., Niehaus K., Becker A., and Flaschel E. Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling. Genome Biol 9 4 (2008) R72
12. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., and Barabasi A.L. The human disease network. Proc Natl Acad Sci U S A 104 21 (2007) 8685-8690
13. Ramchandran L., and Shah N.P. Proteolytic profiles and angiotensin-I converting enzyme and alpha-glucosidase inhibitory activities of selected lactic acid bacteria. J Food Sci 73 2 (2008) M75-81
14. Lykouras D., Sampsonas F., Kaparianos A., Karkoulias K., Tsoukalas G., and Spiropoulos K. Human genes in TB infection: their role in immune response. Monaldi Arch Chest Dis 69 1 (2008) 24-31
15. Marshall TG. Bacterial capnine blocks transcription of human antimicrobial peptides. Third International Conference on Metagenomics; 2007 July 11-13; San Diego, CA. Available from http://precedings.nature.com/documents/164/version/1
16. Wang T.T., Tavera-Mendoza L.E., Laperriere D., Libby E., MacLeod N.B., Nagai Y., et al. Large-scale in silico and microarray-based identification of direct 1,25-dihydroxyvitamin D3 target genes. Mol Endocrinol 19 11 (2005) 2685-2695
17. Wang T.T., Nestel F.P., Bourdeau V., Nagai Y., Wang Q., Liao J., et al. Cutting edge: 1,25-dihydroxyvitamin D3 is a direct inducer of antimicrobial peptide gene expression. J Immunol 173 5 (2004) 2909-2912
18. Schauber J., Dorschner R.A., Coda A.B., Buchau A.S., Liu P.T., Kiken D., et al. Injury enhances TLR2 function and antimicrobial peptide expression through a vitamin D-dependent mechanism. J Clin Invest 117 3 (2007) 803-811
19. Waldner H. The role of innate immune responses in autoimmune disease development. Autoimmun Rev 8 5 (2009) 400-404
20. Proal AD, Albert PJ, Marshall TG. Dysregulation of the Vitamin D Nuclear Receptor may contribute to higher prevalence of some autoimmune diseases in women. Ann N Y Acad Sci in press.
21. Waterhouse JC, Perez TH, Albert PJ. Reversing Bacteria-Induced Vitamin D Receptor Dysfunction is Key to Autoimmune Disease. Ann N Y Acad Sci in press.
22. DiGiulio D.B., Romero R., Amogan H.P., Kusanovic J.P., Bik E.M., Gotsch F., et al. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS ONE 3 8 (2008) e3056
23. Pisetsky D.S. The role of innate immunity in the induction of autoimmunity. Autoimmun Rev 8 1 (2008) 69-72
24. Dumas M.E., Maibaum E.C., Teague C., Ueshima H., Zhou B., Lindon J.C., et al. Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study. Anal Chem 78 7 (2006) 2199-2208
25. Hazlett K.R., Caldon S.D., McArthur D.G., Cirillo K.A., Kirimanjeswara G.S., Magguilli M.L., et al. Adaptation of Francisella tularensis to the mammalian environment is governed by cues which can be mimicked in vitro. Infect Immun 76 10 (2008) 4479-4488
26. Kahnert A., Seiler P., Stein M., Bandermann S., Hahnke K., Mollenkopf H., et al. Alternative activation deprives macrophages of a coordinated defense program to Mycobacterium tuberculosis. Eur J Immunol 36 3 (2006) 631-647
27. Blanc G., Ogata H., Robert C., Audic S., Claverie J.M., and Raoult D. Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome. Genome Res 17 11 (2007) 1657-1664
28. Baldwin C.L., and Goenka R. Host immune responses to the intracellular bacteria Brucella: does the bacteria instruct the host to facilitate chronic infection?. Crit Rev Immunol 26 5 (2006) 407-442
29. Birmingham C.L., Canadien V., Gouin E., Troy E.B., Yoshimori T., Cossart P., et al. Listeria monocytogenes evades killing by autophagy during colonization of host cells. Autophagy 3 5 (2007) 442-451
30. Kuijl C., Savage N.D., Marsman M., Tuin A.W., Janssen L., Egan D.A., et al. Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1. Nature 450 7170 (2007) 725-730
31. Wirostko E., Johnson L., and Wirostko W. Juvenile rheumatoid arthritis inflammatory eye disease. Parasitization of ocular leukocytes by mollicute-like organisms. J Rheumatol 16 11 (1989) 1446-1453
32. Wirostko E., Johnson L., and Wirostko B. Crohn's disease. Rifampin treatment of the ocular and gut disease. Hepatogastroenterology 34 2 (1987) 90-93
33. He Y., Reichow S., Ramamoorthy S., Ding X., Lathigra R., Craig J.C., et al. Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondrion-associated gene expression in mouse macrophages. Infect Immun 74 9 (2006) 5035-5046
34. Lutjen-Drecoll E. Morphology of the pars plana region. Dev Ophthalmol 23 (1992) 50-59
35. Shui W., Gilmore S.A., Sheu L., Liu J., Keasling J.D., and Bertozzi C.R. Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J Proteome Res 8 1 (2009) 282-289
36. Hall C.B., Caserta M.T., Schnabel K., Shelley L.M., Marino A.S., Carnahan J.A., et al. Chromosomal integration of human herpesvirus 6 is the major mode of congenital human herpesvirus 6 infection. Pediatrics 122 3 (2008) 513-520
37. Fall S., Mercier A., Bertolla F., Calteau A., Gueguen L., Perriere G., et al. Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms. PLoS ONE 2 10 (2007) e1055
38. Hotopp J.C., Clark M.E., Oliveira D.C., Foster J.M., Fischer P., Torres M.C., et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317 5845 (2007) 1753-1756
39. Goukassian D.A., and Gilchrest B.A. The interdependence of skin aging, skin cancer, and DNA repair capacity: a novel perspective with therapeutic implications. Rejuvenation Res 7 3 (2004) 175-185
40. Marshall T.G., and Marshall F.E. Sarcoidosis succumbs to antibiotics-implications for autoimmune disease. Autoimmun Rev 3 4 (2004) 295-300