Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments

PLoS Neglected Tropical Diseases

Volumn 8, Issue 12, 2014, Pages

  Whiteson, Katrine L ^a,b   Lazarevic, Vladimir ^a   Tangomo Bento, Manuela ^a   Girard, Myriam ^a   Maughan, Heather ^c   Pittet, Didier ^a   Francois, Patrice ^a   Schrenzel, Jacques ^a  

^a GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c RONIN INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEON; ARTICLE; DNA EXTRACTION; HIGH THROUGHPUT SEQUENCING; MICROARRAY ANALYSIS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MULTIVARIATE ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; STOMATITIS; VINCENT STOMATITIS; BACTERIUM; CHILD; CLASSIFICATION; CROSS-SECTIONAL STUDY; FEMALE; GENETICS; HUMAN; MALE; MICROBIOLOGY; MOUTH; NIGER; NOMA; PRESCHOOL CHILD;

BACTERIAL DNA; RNA 16S;

BACTERIA; CHILD; CHILD, PRESCHOOL; CROSS-SECTIONAL STUDIES; DNA, BACTERIAL; FEMALE; HUMANS; MALE; MOUTH; NIGER; NOMA; RNA, RIBOSOMAL, 16S;

EID: 84928254308     PISSN: 19352727     EISSN: 19352735     Source Type: Journal    
DOI: 10.1371/journal.pntd.0003240     Document Type: Article

References (42)

1. Baratti-Mayer D, Pittet B, Montandon D, Bolivar I, Bornand J-E, et al. (2003) Noma: an "infectious" disease of unknown aetiology. The Lancet infectious diseases 3: 419–431.
2. Bourgeois DM, Diallo B, Frieh C, Leclercq MH, (1999) Epidemiology of the incidence of oro-facial noma: a study of cases in Dakar, Senegal, 1981-1993. The American journal of tropical medicine and hygiene 61: 909–913.
3. Ogbureke KUE, Ogbureke EI, (2010) NOMA: A Preventable "Scourge" of African Children. The open dentistry journal 4: 201–206.
4. Selye H, (1953) Effect of cortisone and somatotrophic hormone upon the development of a noma-like condition in the rat. Oral surgery, oral medicine, and oral pathology 6: 557–561.
5. Falkler WA, JrEnwonwu CO, Idigbe EO, (1999) Isolation of Fusobacterium necrophorum from cancrum oris (noma). The American journal of tropical medicine and hygiene 60: 150–156.
6. Falkler WA, JrEnwonwu CO, Idigbe EO, (1999) Microbiological understandings and mysteries of noma (cancrum oris). Oral diseases 5: 150–155.
7. Falkler WA, Enwonwu CO, Ewell AJ, Idigbe EO, (2000) Isolation of fusobacteria from the oral cavities of malnourished Nigerian children living in agricultural and herding villages. Oral diseases 6: 103–105.
8. Paster BJ, Falkler WA, Jr, JrEnwonwu CO, Idigbe EO, Savage KO, et al. (2002) Prevalent bacterial species and novel phylotypes in advanced noma lesions. Journal of clinical microbiology 40: 2187–2191.
9. Baratti-Mayer D, Gayet-Ageron A, Hugonnet S, François P, Pittet-Cuenod B, et al. (2013) Risk factors for noma disease: a 6-year, prospective, matched case-control study in Niger. The Lancet Global Health 1: e87–e96.
10. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, et al. (2011) Moving pictures of the human microbiome. Genome Biology 12: R50.
11. Friedrich MJ, (2008) Microbiome project seeks to understand human body's microscopic residents. JAMA: The Journal of the American Medical Association 300: 777–778.
12. Mokili JL, Rohwer F, Dutilh BE, (2012) Metagenomics and future perspectives in virus discovery. Current opinion in virology 2: 63–77.
13. Huyghe A, François P, Mombelli A, Tangomo M, Girard M, et al. (2013) Microarray Analysis of Microbiota of Gingival Lesions in Noma Patients. PLoS Negl Trop Dis 7: e2453.
14. Bolivar I, Whiteson K, Stadelmann B, Baratti-Mayer D, Gizard Y, et al. (2012) Bacterial diversity in oral samples of children in niger with acute noma, acute necrotizing gingivitis, and healthy controls. PLoS neglected tropical diseases 6: e1556.
15. Folayan MO, (2004) The epidemiology, etiology, and pathophysiology of acute necrotizing ulcerative gingivitis associated with malnutrition. The journal of contemporary dental practice 5: 28–41.
16. Lazarevic V, Whiteson K, Hernandez D, François P, Schrenzel J, (2010) Study of inter- and intra-individual variations in the salivary microbiota. BMC genomics 11: 523.
17. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335–336.
18. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology 75: 7537–7541.
19. Anderson M, Gorley RN, Clarke RK (2008) Permanova+ for Primer: Guide to Software and Statisticl Methods.
20. Dufrêne M, Legendre P, (1997) SPECIES ASSEMBLAGES AND INDICATOR SPECIES:THE NEED FOR A FLEXIBLE ASYMMETRICAL APPROACH. Ecological Monographs 67: 345–366.
21. Roberts DW, (2007) Labdsv: Ordination and multivariate analysis for ecology. R package version 1: 3–1.
22. R: A language and environment for statistical computing. (2013). Vienna, Austria: R Foundation for Statistical Computing.
23. Anderson MJ, Walsh DCI, (2013) PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing? Ecological Monographs 83: 557–574.
24. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 13: 2498–2504.
25. Elliott D, Kufera JA, Myers RAM, (2000) The microbiology of necrotizing soft tissue infections. The American Journal of Surgery 179: 361–366.
26. Finkelstein R, Oren I, (2011) Soft tissue infections caused by marine bacterial pathogens: epidemiology, diagnosis, and management. Current infectious disease reports 13: 470–477.
27. Reboli AC, Farrar WE, (1989) Erysipelothrix rhusiopathiae: an occupational pathogen. Clinical Microbiology Reviews 2: 354–359.
28. Sinclair M, Hawkins A, Testro A (2013) Something fishy: an unusual Erysipelothrix rhusiopathiae infection in an immunocompromised individual. BMJ case reports 2013. doi: 10.1136/bcr-2013-008873
29. Koren O, Goodrich Julia K, Cullender Tyler C, Spor A, Laitinen K, et al. (2012) Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy. Cell 150: 470–480.
30. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, et al. (2013) Temporal response of the human virome to immunosuppression and antiviral therapy. Cell 155: 1178–1187.
31. Enwonwu CO, Falkler WA, Idigbe EO, (2000) Oro-facial gangrene (noma/cancrum oris): pathogenetic mechanisms. Critical reviews in oral biology and medicine: an official publication of the American Association of Oral Biologists 11: 159–171.
32. Segre JA, (2013) What does it take to satisfy Koch's postulates two centuries later? Microbial genomics and Propionibacteria acnes. The Journal of investigative dermatology 133: 2141–2142.
33. Duran-Pinedo AE, Chen T, Teles R, Starr JR, Wang X, et al. (2014) Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis. The ISME Journal 8: 1659–1672.
34. Kong HH, Oh J, Deming C, Conlan S, Grice EA, et al. (2012) Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome research 22: 850–859.
35. Sibley CD, Parkins MD, Rabin HR, Duan K, Norgaard JC, et al. (2008) A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proceedings of the National Academy of Sciences of the United States of America 105: 15070–15075.
36. Edlund A, Yang Y, Hall AP, Guo L, Lux R, et al. (2013) An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome. Microbiome 1: 25.
37. McLean JS, Fansler SJ, Majors PD, McAteer K, Allen LZ, et al. (2012) Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques. PLoS ONE 7: e32219.
38. Hajishengallis G, Liang S, Payne Mark A, Hashim A, Jotwani R, et al. (2011) Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement. Cell Host & Microbe 10: 497–506.
39. Marsh PD, (1994) Microbial ecology of dental plaque and its significance in health and disease. Advances in dental research 8: 263–271.
40. Madigan MT, Brock TD (2009) Brock biology of microorganisms: Pearson/Benjamin Cummings.
41. Clarke KR, (1993) Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology 18: 117–143.
42. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289–300.