The conjunctival microbiome in health and trachomatous disease: A case control study

Genome Medicine

Volumn 6, Issue , 2014, Pages 1-10

  Zhou, Yanjiao ^a,b   Holland, Martin J ^c   Makalo, Pateh ^d   Joof, Hassan ^d   Roberts, Chrissy h ^c   Mabey, David ^c   Bailey, Robin L ^c   Burton, Matthew J ^c   Weinstock, George M ^a,e   Burr, Sarah E ^c,d  

^a WASHINGTON UNIVERSITY   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^d MEDICAL RESEARCH COUNCIL LABORATORIES   (Gambia)

^e JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

AGE; ARTICLE; BACTERIAL GENE; BACTERIUM DETECTION; CASE CONTROL STUDY; CHILD; CHILDHOOD DISEASE; CHLAMYDIA TRACHOMATIS; COMPARATIVE STUDY; CONJUNCTIVAL MICROBIOME; CONTROLLED STUDY; CORYNEBACTERIUM; DEMOGRAPHY; FEMALE; GAMBIA; GENE SEQUENCE; HUMAN; MALE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; PRIORITY JOURNAL; RETROSPECTIVE STUDY; SEASON; TAXON;

EID: 84925818498     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-014-0099-x     Document Type: Article

References (29)

1. Burton MJ, Hu VH, Massae P, Burr SE, Cheallier C, Afwamba IA, Courtright P, Weiss HA, Mabey DCW, Bailey RL: What is causing active trachoma? The role of nonchlamydial bacterial pathogens in a low prevalence setting. Invest Ophthalmol Vis Sci 2011, 52:6012-6017.
2. Burr SE, Hart JD, Edwards T, Baldeh I, Bojang E, Harding-Esch EM, Holland MJ, Mabey DCW, Sillah A, Bailey RL: Association between ocular bacterial carriage and follicular trachoma following mass azithromycin distribution in The Gambia. PLoS Negl Trop Dis 2013, 7:e2347.
3. Burton MJ, Bowman RJ, Faal H, Aryee EA, Ikumapayi UN, Alexander ND, Adegbola RA, Mabey DC, Foster A, Johnson GJ, Bailey RL: Long term outcome of trichiasis surgery in The Gambia. Br J Ophthalmol 2005, 89:575-579.
4. Burton MJ, Adegbola RA, Kinteh F, Ikumapayi UN, Foster A, Mabey DC, Bailey RL: Bacterial infection and trachoma in The Gambia: a case control study. Invest Ophthalmol Vis Sci 2007, 48:4440-4444.
5. Hu VH, Massae P, Weiss HA, Chevallier C, Onyango JJ, Afwamba IA, Mabey DC, Bailey RL, Burton MJ: Bacterial infection in scarring trachoma. Invest Ophthalmol Vis Sci 2011, 52:2181-2186.
6. Cevallos V, Whitcher JP, Melese M, Alemayehu W, Yi E, Chidambaram JD, Lee S, Reddy H, Gaynor BD, Lietman TM, Keenan JD: Association of conjunctival bacterial infection and female sex in cicatricial trachoma. Invest Ophthalmol Vis Sci 2012, 53:5208-5212.
7. Cox MJ, Cookson WO, Moffat MF: Sequencing the human microbiome in health and disease. Hum Mol Genet 2013, 22:R88-R94.
8. Boyton RJ, Reynolds CJ, Quigley KJ, Altmann DM: Immune mechanisms and the impact of the disrupted lung microbiome in chronic bacterial lung infection and bronchiectasis. Clin Exp Immunol 2013, 171:117-123.
9. Scales BS, Huffnagle GB: The microbiome in wound repair and tissue fibrosis. J Pathol 2013, 229:323-331.
10. Dawson CR, Jones BR, Tarizzo ML: Guide to Trachoma Control. Geneva: World Health Organization; 1981.
11. Holland MJ, Jeffries D, Pattison M, Korr G, Gall A, Joof H, Manjang A, Burton MJ, Mabey DC, Bailey RL: Pathway-focused arrays reveal increased matrix metalloproteinase-7 (matrilysin) transcription in trachomatous trichiasis. Invest Ophthalmol Vis Sci 2010, 51:3893-3902.
12. Human Microbiome Project Consortium: A framework for human microbiome research. Nature 2012, 486:215-221.
13. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW: Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011, 21:494-504.
14. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009, 37:D141-D145.
15. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner M: Vegan: Community Ecology Package. 2011 [ http://cran.r-project.org/web/packages/vegan/index.html ]
16. Venables WN, Ripley BD: Modern Applied Statistics with S. 4th edition. New York: Springer; 2003.
17. Anderson MJ: A new method for non-parametric multivariate analysis of variance. Austral Ecol 2001, 26:32-46.
18. White JR, Nagarajan N, Pop M: Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 2009, 5:e1000352.
19. Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, Revanna KV, Gao X, Antonopoulos DA, Slepak VZ, Shestopalov VI: Diveristy of bacteria at the healthy human conjunctiva. Invest Ophthalmol Vis Sci 2011, 52:5408-5413.
20. Daroy MLG, Lopez JS, Torres BCL, Loy MJ, Tuaño M: Identification of unknown ocular pathogens in clinically suspected eye infections using ribosomal RNA gene sequence analysis. Clin Microbiol Infect 2011, 17:776-779.
21. Willcox MDP: Characterization of the normal microbiota of the ocular surface. Exp Eye Res 2013, 117:99-105.
22. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM: Biogeography of the ecosystems of the healthy human body. Genome Biol 2013, 14:R1.
23. Fierer N, Hamady M, Lauber CL, Knight R: The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 2008, 105:17994-17999.
24. Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA: Bacterial diversity in the oral cavity of ten healthy individuals. ISME J 2010, 4:962-974.
25. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner ACR, Yu W-H, Lakshmanan A, Wade WG: The human oral microbiome. J Bacteriol 2010, 192:5002-5017.
26. Hill PC, Akisanya A, Sankareh K, Cheung YB, Saaka M, Lahai G, Greenwood BM, Adegbola RA: Nasopharyngeal carriage of Streptococcus pneumoniae in Gambian villagers. Clin Infect Dis 2006, 43:673-679.
27. Harding-Esch EM, Edwards T, Sillah A, Sarr I, Roberts C, Snell P, Aryee E, Molina S, Holland MJ, Mabey DC, Bailey RL: Active trachoma and ocular Chlamydia trachomatis infection in two Gambian regions: on course for elimination by 2020? PLoS Negl Trop Dis 2009, 3:e573.
28. Turovskiy Y, Noll KS, Chikindas ML: The etiology of bacterial vaginosis. J Appl Microbiol 2011, 110:1105-1128.
29. Hospodsky D, Pickering AJ, Julian TR, Miller D, Gorthala S, Boehm AB, Peccia J: Hand Bacterial Communities Vary Across Two Different Human Populations. Microbiology 2014, 160:1144-1152.