The domain Archaea in human mucosal surfaces

Clinical Microbiology and Infection

Volumn 18, Issue 9, 2012, Pages 834-840

  Matarazzo, F ^a,b   Ribeiro, A C ^a   Faveri, M ^a,c   Taddei, C ^a   Martinez, M B ^a   Mayer, M P A ^b  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b STATE UNIVERSITY OF MARINGÁ   (Brazil)

^c GUARULHOS UNIVERSITY   (Brazil)

Author keywords

Archaea; Intestine; Mouth

Indexed keywords

METHANE;

ARCHAEON; BACTERIAL METABOLISM; INTESTINE FLORA; INTESTINE MUCOSA; METHANOGEN; MICROFLORA; MOUTH FLORA; MOUTH MUCOSA; NONHUMAN; ORGANISMAL INTERACTION; PRIORITY JOURNAL; REVIEW;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 84865278608     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1111/j.1469-0691.2012.03958.x     Document Type: Review

References (78)

1. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977; 74: 5088-5090.
2. Forterre P, Brochier C, Philippe H. Evolution of the archaea. Theor Popul Biol 2002; 61: 409-422.
3. Rother M, Metcalf WW. Genetic technologies for archaea. Curr Opin Microbiol 2005; 8: 745-751.
4. Gribaldo S, Brochier-Armanet C. The origin and evolution of archaea: a state of the art. Phil Trans R Soc Lond B Biol Sci 2006; 361: 1007-1022.
5. Kates M. Archaebacterial lipids: structure, biosynthesis and function. Biochem Soc Symp 1992; 58: 51-72.
6. Albers S-V, Meyer BH. The archaeal cell envelope. Nat Rev Microbiol 2011; 9: 414-426.
7. Koch HG, Moser M, Müller M. Signal recognition particle-dependent protein targeting, universal to all kingdoms of life. Rev Physiol Biochem Pharmacol 2003; 146: 55-94.
8. Ellen AF, Zolghadr B, Driessen AMJ, Albers S-V. Shaping the archaeal cell envelope. Archaea 2010; 608243.
9. Dridi B, Raoult D, Drancourt M. Archaea as emerging organisms in complex human microbiomes. Anaerobe 2011; 17: 56-63.
10. Hulshoff Pol LW, de Castro Lopes SI, Lettinga G, Lens PNL. Anaerobic sludge granulation. Water Res 2004; 38: 1376-1389.
11. Kulik EM, Sandmeier H, Hinni K, Meyer J. Identification of archaeal rDNA from subgingival dental plaque by PCR amplification and sequence analysis. FEMS Microbiol Lett 2001; 196: 129-133.
12. Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, Relman DA. Methanogenic archaea and human periodontal disease. Proc Natl Acad Sci USA 2004; 101: 6176-6181.
13. Scanlan PD, Shanahan F, Marchesi JR. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol 2008; 8: 79.
14. Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS ONE 2009; 4: e7063.
15. Albers S-V, Szabó Z, Driessen AJM. Protein secretion in the archaea: multiple paths towards a unique cell surface. Nat Rev Microbiol 2006; 4: 537-547.
16. Szabó Z, Stahl AO, Albers S-V, Kissinger JC, Driessen AJM, Pohlschröder M. Identification of diverse archaeal proteins with class iii signal peptides cleaved by distinct archaeal prepilin peptidases. J Bacteriol 2007; 189: 772-778.
17. Henche AL, Koerdt A, Ghosh A, Albers SV. Influence of cell surface structures on crenarchaeal biofilm formation using a thermostable green fluorescent protein. Environ Microbiol 2012; 14: 779-793.
18. Ishii Si, Kosaka T, Hori K, Hotta Y, Watanabe K. Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus. Appl Environ Microbiol 2005; 71: 7838-7845.
19. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998; 180: 366-376.
20. DeLong EF. Microbial community genomics in the ocean. Nat Rev Microbiol 2005; 3: 459-469.
21. Horz H-P, Conrads G. Methanogenic archaea and oral infections-ways to unravel the black box. J Oral Microbiol 2011; 3: 11-12.
22. Sakai S, Imachi H, Hanada S, Ohashi A, Harada H, Kamagata Y. Methanocella paludicola gen Nov., sp. Nov., a methane-producing archaeon, the first isolate of the lineage 'rice cluster i', and proposal of the new archaeal order Methanocellales ord. Nov. Int J Syst Evol Microbiol 2008; 58: 929-936.
23. Cavicchioli R. Archaea-timeline of the third domain. Nat Rev Microbiol 2011; 9: 51-61.
24. Miller TL, Wolin MJ, Conway de Macario E, Macario AJ. Isolation of Methanobrevibacter smithii from human feces. Appl Environ Microbiol 1982; 43: 227-232.
25. Belay N, Johnson R, Rajagopal BS, Conway de Macario E, Daniels L. Methanogenic bacteria from human dental plaque. Appl Environ Microbiol 1988; 54: 600-603.
26. Belay N, Mukhopadhyay B, Conway de Macario E, Galask R, Daniels L. Methanogenic bacteria in human vaginal samples. J Clin Microbiol 1990; 28: 1666-1668.
27. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007; 449: 804-810.
28. McKay LF, Brydon WG, Eastwood MA, Housley E. The influence of peripheral vascular disease on methanogenesis in man. Atherosclerosis 1983; 47: 77-81.
29. Piqué JM, Pallarés M, Cusó E, Vilar-Bonet J, Gassull MA. Methane production and colon cancer. Gastroenterology 1984; 87: 601-605.
30. Weaver GA, Krause JA, Miller TL, Wolin MJ. Incidence of methanogenic bacteria in a sigmoidoscopy population: an association of methanogenic bacteria and diverticulosis. Gut 1986; 27: 698-704.
31. Ferrari A, Brusa T, Rutili A, Canzi E, Biavati B. Isolation and characterization of Methanobrevibacter oralis sp. Nov. Curr Microbiol 1994; 29: 7-12.
32. Yamabe K, Maeda H, Kokeguchi S et al. Distribution of archaea in Japanese patients with periodontitis and humoral immune response to the components. FEMS Microbiol Lett 2008; 287: 69-75.
33. Vianna ME, Holtgraewe S, Seyfarth I, Conrads G, Horz HP. Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease. J Bacteriol 2008; 190: 3779-3785.
34. Duncan SH, Louis P, Flint HJ. Cultivable bacterial diversity from the human colon. Lett Appl Microbiol 2007; 44: 343-350.
35. Eckburg PB, Bik EM, Bernstein CN et al. Diversity of the human intestinal microbial flora. Science 2005; 308: 1635-1638.
36. Vianna ME, Conrads G, Gomes BPFA, Horz HP. Identification and quantification of archaea involved in primary endodontic infections. J Clin Microbiol 2006; 44: 1274-1282.
37. Nam Y-D, Chang H-W, Kim K-H et al. Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people. J Microbiol 2008; 46: 491-501.
38. Oxley APA, Lanfranconi MP, Würdemann D et al. Halophilic archaea in the human intestinal mucosa. Environ Microbiol 2010; 12: 2398-2410.
39. Ferry JG. How to make a living by exhaling methane. Annu Rev Microbiol 2010; 64: 453-473.
40. Thauer RK, Shima S. Methane as fuel for anaerobic microorganisms. Ann N Y Acad Sci 2008; 1125: 158-170.
41. Thauer RK, Kaster A-K, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 2008; 6: 579-591.
42. Liu Y, Whitman WB. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 2008; 1125: 171-189.
43. Alves MM, Pereira MA, Sousa DZ et al. Waste lipids to energy: how to optimize methane production from long-chain fatty acids (LCFA). Microb Biotechnol 2009; 2: 538-550.
44. Wolin MJ. Fermentation in the rumen and human large intestine. Science 1981; 213: 1463-1468.
45. Kunkel D, Basseri RJ, Makhani MD, Chong K, Chang C, Pimentel M. Methane on breath testing is associated with constipation: a systematic review and meta-analysis. Dig Dis Sci 2011; 56: 1612-1618.
46. Stams AJM, Plugge CM. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 2009; 7: 568-577.
47. Enoki M, Shinzato N, Sato H, Nakamura K, Kamagata Y. Comparative proteomic analysis of Methanothermobacter themautotrophicusδh in pure culture and in co-culture with a butyrate-oxidizing bacterium. PLoS ONE 2011; 6: e24309.
48. Deppenmeier U. Redox-driven proton translocation in methanogenic archaea. Cell Mol Life Sci 2002; 59: 1513-1533.
49. Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 1997; 61: 262-280.
50. Chassard C, Scott KP, Marquet P et al. Assessment of metabolic diversity within the intestinal microbiota from healthy humans using combined molecular and cultural approaches. FEMS Microbiol Ecol 2008; 66: 496-504.
51. Persson S, Edlund MB, Claesson R, Carlsson J. The formation of hydrogen sulfide and methyl mercaptan by oral bacteria. Oral Microbiol Immunol 1990; 5: 195-201.
52. Conway de Macario E, Macario AJL. Methanogenic archaea in health and disease: a novel paradigm of microbial pathogenesis. Int J Med Microbiol 2009; 299: 99-108.
53. Hooper LV. Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol 2009; 7: 367-374.
54. DiGiulio DB, Romero R, Amogan HP et al. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS ONE 2008; 3: e3056.
55. DiGiulio DB, Romero R, Kusanovic JP et al. Prevalence and diversity of microbes in the amniotic fluid, the fetal inflammatory response, and pregnancy outcome in women with preterm pre-labor rupture of membranes. Am J Reprod Immunol 2010; 64: 38-57.
56. Brandtzaeg P. Update on mucosal immunoglobulin A in gastrointestinal disease. Curr Opin Gastroenterol 2010; 26: 554-563.
57. Vael C, Desager K. The importance of the development of the intestinal microbiota in infancy. Curr Opin Pediatr 2009; 21: 794-800.
58. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol 2007; 5: e177.
59. Stewart JA, Chadwick VS, Murray A. Carriage, quantification, and predominance of methanogens and sulfate-reducing bacteria in faecal samples. Lett Appl Microbiol 2006; 43: 58-63.
60. Hudson MJ, Tomkins AM, Wiggins HS, Drasar BS. Breath methane excretion and intestinal methanogenesis in children and adults in rural Nigeria. Scand J Gastroenterol 1993; 28: 993-998.
61. Samuel BS, Hansen EE, Manchester JK et al. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci USA 2007; 104: 10643-10648.
62. Peled Y, Weinberg D, Hallak A, Gilat T. Factors affecting methane production in humans. Gastrointestinal diseases and alterations of colonic flora. Dig Dis Sci 1987; 32: 267-271.
63. Nakamura N, Lin HC, McSweeney CS, Mackie RI, Gaskins HR. Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease. Ann Rev Food Sci Technol 2010; 1: 363-395.
64. Roccarina D, Lauritano EC, Gabrielli M, Franceschi F, Ojetti V, Gasbarrini A. The role of methane in intestinal diseases. Am J Gastroenterol 2010; 105: 1250-1256.
65. Kleessen B, Kroesen AJ, Buhr HJ, Blaut M. Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls. Scand J Gastroenterol 2002; 37: 1034-1041.
66. Swidsinski A, Weber J, Loening-Baucke V, Hale LP, Lochs H. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol 2005; 43: 3380-3389.
67. Samuel BS, Gordon JI. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci USA 2006; 103: 10011-10016.
68. Marsh PD, Devine DA. How is the development of dental biofilms influenced by the host? J Clin Periodontol 2011; 38 (suppl 11): 28-35.
69. Socransky SS, Haffajee AD. Periodontal microbial ecology. Periodontol 2000 2005; 38: 135-187.
70. Vickerman MM, Brossard KA, Funk DB, Jesionowski AM, Gill SR. Phylogenetic analysis of bacterial and archaeal species in symptomatic and asymptomatic endodontic infections. J Med Microbiol 2007; 56: 110-118.
71. Langendijk-Genevaux PS, Grimm WD, Van der Hoeven JS. Sulfate-reducing bacteria in relation with other potential periodontal pathogens. J Clin Periodontol 2001; 28: 1151-1157.
72. Matarazzo F, Ribeiro AC, Feres M, Faveri M, Mayer MPA. Diversity and quantitative analysis of archaea in aggressive periodontitis and periodontally healthy subjects. J Clin Periodontol 2011; 38: 621-627.
73. Faveri M, Figueiredo LC, Duarte PM, Mestnik MJ, Mayer MPA, Feres M. Microbiological profile of untreated subjects with localized aggressive periodontitis. J Clin Periodontol 2009; 36: 739-749.
74. Vartoukian SR, Palmer RM, Wade WG. The division 'Synergistes'. Anaerobe 2007; 13: 99-106.
75. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 2007; 104: 13780-13785.
76. Sanz JL, Rodríguez N, Amils R. The action of antibiotics on the anaerobic digestion process. Appl Microbiol Biotechnol 1996; 46: 587-592.
77. Silva MP, Feres M, Sirotto TA et al. Clinical and microbiological benefits of metronidazole alone or with amoxicillin as adjuncts in the treatment of chronic periodontitis: a randomized placebo-controlled clinical trial. J Clin Periodontol 2011; 38: 828-837.
78. Michalke K, Schmidt A, Huber B et al. Role of intestinal microbiota in transformation of bismuth and other metals and metalloids into volatile methyl and hydride derivatives in humans and mice. Appl Environ Microbiol 2008; 74: 3069-3075.