신생아 장내 미생물의 형성과 이의 분석을 위한 분자 생태학적 기술

Development of Intestinal Microorganisms and Molecular Ecological Methods for Analysis of Intestinal Ecosystem in the Neonate

  • 박자령 (한국생명공학연구원 생물자원센터, 연세대학교 생명공학과) ;
  • 배진우 (한국생명공학연구원 생물자원센터) ;
  • 이성근 (충북대학교 미생물학과) ;
  • 남영도 (한국생명공학연구원 생물자원센터) ;
  • 오종원 (연세대학교 생명공학과) ;
  • 박용하 (한국생명공학연구원 생물자원센터)
  • Park Ja Ryeong (Biological Resources Center, Korea Research Institute of Bioscience and Biotechology(KRIBB), Department of Biotechnology, Yonsei University) ;
  • Bae Jin-Woo (Biological Resources Center, Korea Research Institute of Bioscience and Biotechology(KRIBB)) ;
  • Rhee Sung-Keun (Department of Microbiology, Chungbuk National University) ;
  • Nam Young-Do (Biological Resources Center, Korea Research Institute of Bioscience and Biotechology(KRIBB)) ;
  • Oh Jong-Won (Department of Biotechnology, Yonsei University) ;
  • Park Yong-Ha (Biological Resources Center, Korea Research Institute of Bioscience and Biotechology(KRIBB))
  • 발행 : 2005.09.01

초록

인간의 장(腸)은 태어날 때만 해도 무균 상태이지만 태어나면서 산모나 주위 환경에 의해 미생물이 형성되기 시작한다. 미생물은 숙주 안에서 면역, 영양학적, 생리학적, 보호과정 등의 특징을 유발시키며, 밀접한 상호작용을 한다[6,24, 35]. 많은 연구를 통해 장내 미생물이 우리에게 주는 이로운 점들이 밝혀 지긴 했지만, 우리가 목표로 하는 장내 미생물이 숙주의 장내, 건강 상태를 조절하는 메커니즘은 아직 뚜렷하게 밝혀 지지 않고 있다. 즉, 숙주(인간)의 건강의 상태를 결정지어 주는 장내미생물 biomarker의 확립이 아직 불분명한 상태이다. 장내미생물의 방대한 다양성으로 인하여, 이를 연구하기 위한 분자 생태학 기술의 올바른 접목과 더 나은 방향으로의 기술 발전이 필요하다. 앞으로 더 나은 기술 개발을 통해, 신생아 장내의 초기에 형성되는 미생물을 검출하고, 여러 외부 요인에 따라 어떻게 연속되어 가면서 어떠한 역할을 하는지를 밝힐 수 있다면, 질병 치료뿐 아니라 예방도 가능해 질 것이다.

Up to date, a number of review papers were reported on intestinal microorganisms that influence the health and disease of human being and diet that directly influence the establishment of intestinal microbial populations. Importance of studying intestinal microorganisms in the neonate arises from the easy approach to studying initial acquisition and settlement of intestinal microorganisms. Despite of the importance, few studies of neonatal intestinal microorganisms have been carried out and there is no paper focusing the factors to influence the development of intestinal microorganisms and molecular ecological methods for the analysis of intestinal ecosystem in the neonate. In this review, we summarized the status of our current knowledge of basic initial acquisition and settlement of intestinal microorganisms. And recent development of molecular ecological methods in studying the intestinal microbiology was also discussed.

키워드

참고문헌

  1. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56: 1919-1925
  2. Amann, R. I., W. Ludwig. and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169
  3. Bartosch, S., A. Fite, G. T. Macfarlane, and M. E. McMurdo. 2004. Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. Appl. Environ. Microbiol. 70: 3575-3581 https://doi.org/10.1128/AEM.70.6.3575-3581.2004
  4. Bennet, R., M. Eriksson, C. E. Nord, and R. Zetterstrom 1982. Suppression of aerobic and anaerobic faecal flora in newborns receiving parenteral gentamicin and ampicillin. Acta Paediatr Scand. 71: 559-562 https://doi.org/10.1111/j.1651-2227.1982.tb09474.x
  5. Benno, Y., K. Sawada, and T. Mitsuoka. 1984. The intestinal microflora of infants: composition of fecal flora in breast-fed and bottle-fed infants. Microbiol. Immunol. 28: 975-986 https://doi.org/10.1111/j.1348-0421.1984.tb00754.x
  6. Berg, R. 1996. The indigenous gastrointestinal microflora. Trends Microbiol. 4: 430-435 https://doi.org/10.1016/0966-842X(96)10057-3
  7. Bezirtzoglou, E. 1997. The intestinal microflora during the first weeks of life. Anaerobe 3: 173-177 https://doi.org/10.1006/anae.1997.0102
  8. Bullen, C. L., P. V. Tearle, and M. G Stewart. 1977. The effect of 'hurnanised' milks and supplemented breast feeding on the faecal flora of infants. J. Med. Microbiol. 10: 403-413 https://doi.org/10.1099/00222615-10-4-403
  9. Kunz, C., S. Rudloff, W. Baier, N. Klein, and S. Strobel. 2000. Oligosaccharides in human milk: structural, functional and metabolic aspects. Annu. Rev. Nutr. 20: 699-722 https://doi.org/10.1146/annurev.nutr.20.1.699
  10. Chizhikov, V., A. Rasooly, K. Chumakov, and D. D. Levy. 2001. Microarray analysis of microbial virulence factors. Appl. Environ. Microbiol. 67: 3258-3263 https://doi.org/10.1128/AEM.67.7.3258-3263.2001
  11. Favier, C. F., W. M. de Vos., and A. D. Akkermans 2003. Development of bacterial and bifidobacterial communities in feces of newborn babies. Anaerobe 9: 219-229 https://doi.org/10.1016/j.anaerobe.2003.07.001
  12. Favier, C. F., E. E. Vaughan, W. M. de Vos, and A. D. Akkermans 2002. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68: 219-226 https://doi.org/10.1128/AEM.68.1.219-226.2002
  13. Franks, A. H., H. J. Harmsen, G. C. Raangs, G. J. Jansen, F. Schut, and G. W Welling. 1998. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64: 3336-3345
  14. Haarman, M., and J. Knol. 2005. Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula. Appl. Environ. Microbiol. 71: 2318-2324 https://doi.org/10.1128/AEM.71.5.2318-2324.2005
  15. Harmsen, H. J., A. C. M. Wildeboer-Veloo, J. Grijpstra, J. Knol, J. E. Degener, and G. W. Welling. 2000. Development of 16S rRNA-based probes for the Coriobacterium group and the Atopobium cluster and their application for enumeration of Coriobacteriaceae in human feces from volunteers of different age groups. Appl. Environ. Microbiol. 66: 4523-4527 https://doi.org/10.1128/AEM.66.10.4523-4527.2000
  16. Heilig, H. G., E. G. Zoetendal, E. E. Vaughan, P. Marteau, A. D. Akkermans, and W. M. de Vos. 2002. Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl. Environ. Microbiol. 68: 114-123 https://doi.org/10.1128/AEM.68.1.114-123.2002
  17. Harmsen, H. J., G. C. Raangs, A. H. Franks, A. C. M. Wildeboer-Veloo, and G. W. Welling. 2002. The Effect of the Probiotic Inulin and the Probiotic Bifidobacterium longum on the Fecal Microflora of Healthy Volunteers Measured by FISH and DGGE. Microb. Ecol. Health Dis. 14: 211-219
  18. Holzapfel, W H., P. Haberer, J. Snel, U. Schillinger, and Huis in't Veld. 1998. Overview of gut flora and probiotics. Int. J. Food Microbiol. 41: 85-101 https://doi.org/10.1016/S0168-1605(98)00044-0
  19. Lay, C., M. Sutren, V. Rochet, K. Saunier, J. Dore, and L. Rigottier-Gois. 2005. Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota. Environ. Microbiol. 7: 933-946 https://doi.org/10.1111/j.1462-2920.2005.00763.x
  20. Ludwig, W., S. Dorn, N. Springer, G. Kirchhof, and K.H. Schleifer. 1994. PCR-based preparation of 23S rRNAtargeted group-specific polynucleotide probes. Appl. Environ. Microbiol. 60: 3236-3244
  21. Lundequist, B., C. E. Nord, and J. Winberg. 1985. The composition of the faecal microflora in breastfed and bottle fed infants from birth to eight weeks. Acta Paediatr Scand. 74: 45-51 https://doi.org/10.1111/j.1651-2227.1985.tb10919.x
  22. Matto. J., E. Malinen., M.-L. Suihko, M. Alander, A. Paiva, and M. Saarela. 2004. Genetic heterogeneity and functional properties of intestinal Bifidobacteria. J. Appl. Microbiol. 97: 459-470 https://doi.org/10.1111/j.1365-2672.2004.02340.x
  23. MacGregor, R. R. 3rd, and W.W. Jr. Tunnessen. 1973. The incidence of pathogenic organisms in the normal flora of the neonate's external ear and nasopharynx. Clin. Pediatr. (Phila) 12: 697-700 https://doi.org/10.1177/000992287301201214
  24. Mackie, R. I., S. Alune, and H. R. Gaskins. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69: 1035S-1045S https://doi.org/10.1093/ajcn/69.5.1035s
  25. Muyzer, G., E. C. de Waal, and A.G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700
  26. Torun, M. M., H. Bahar, E. GUr, Y. Tatan, M. Alikaifolu, and A. Arvas. 2002. Anaerobic fecal tlora in healthy beast-fed Turkish babies born by different methods. Anaerobe 8: 63-67 https://doi.org/10.1006/anae.2002.0415
  27. Niewold, T. A., H. H. Kerstens, J. van der Meulen, M. A. Smits, and M. M. Hulst. 2005. Development of a porcine small intestinal cDNA micro-array: characterization and functional analysis of the response to enterotoxigenic E. coli. Vet. Immunol. Immunopathol. 105: 317-329 https://doi.org/10.1016/j.vetimm.2005.02.010
  28. Brigidi, P., B. Vitali, E. Swennen, G. Bazzocchi, and D. Matteuzzi. 2001. Effects of probiotic administration upon the composition and enzymatic activity of human fecal microbiota in patients with irritable bowel syndrome or functional diarrhea. Res. Microbial. 152: 735-741 https://doi.org/10.1016/S0923-2508(01)01254-2
  29. Eckburg, P. B., E. M. Bike, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson, D. A. Reiman. 2005. Diversity of the human intestinal microbial tlora. Science 308(5728): 1635-1638 https://doi.org/10.1126/science.1110591
  30. Namsolleck, P., R. Thiel, P. A. Lawson, K. Holmstrom, M. Rajilic, E. E. Vaughan, L. Rigottier-Gois, M. D. Collins, W. M. de Vos, and M. Blaut. 2004. Molecular methods for the analysis of gut microbiota. Microb. Ecol. Health Dis. 16: 71-85 https://doi.org/10.1080/08910600410032367
  31. Reid, G., J. Jass, M. T. Sebulsky, and J. K. McCormick. 2003. Potential uses of probiotics in clinical practice. Clin. Microbiol. Rev. 16: 658-672 https://doi.org/10.1128/CMR.16.4.658-672.2003
  32. Reiman, D. A and S. Falkow. 2001. The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 9: 206-208 https://doi.org/10.1016/S0966-842X(01)02041-8
  33. Rigottier-Gois, L., V. Rochet, N. Garrec, A Suau, and J. Dore. 2003. Enumeration of Bacteroides species in human faeces by tluorescent in situ hybridisation combined with tlow cytometry using 16S rRNA probes. Syst. Appl. Microbiol. 26: 110-118 https://doi.org/10.1078/072320203322337399
  34. Roc'o Mart'na, S. L., M. A. Carlota Reviriegoa, E. Jime' neza, M. N. O. L. Mar' na, J. S. J. N. Julio Bozab, L. Ferna' ndeza, J. X. A. Juan, and M. Rodr'gueza. 2004. The commensal microtlora of human milk: new perspectives for food bacteriotherapy and probiotics. Trends Food Sci. Technol. 15: 121-127 https://doi.org/10.1016/j.tifs.2003.09.010
  35. Mackie, R. I., S. Alune, and H. R. Gaskins. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69: 1035S-1045S https://doi.org/10.1093/ajcn/69.5.1035s
  36. Sakata, S., T. Tonooka, S. lshizeki, M, Takada, M. Sakamoto, M. Fukuyama, and Y. Benno. 2005. Culture-independent analysis of fecal microbiota in infants, with special reference to Bifidobacterium species. FEMS Microbiol. Lett. 243: 417-423 https://doi.org/10.1016/j.femsle.2005.01.002
  37. Meance, S., C. Cayuela, A. Raimondi, P. Turchet, C. Lucas, and J. M. Antoine. 2003. Recent advances in the use of functional foods: effects of the commercial fermented milk with Bifidobacterium animalis strain DN-173 010 and yoghurt strains on gut transit time in the elderly. Microb. Ecol. Health Dis. 15: 15-22 https://doi.org/10.1080/08910600310015565
  38. Simhon, A., J. R. Douglas, B. S. Drasar, and J. F. Soothill. 1982. Effect of feeding on infant's faecal flora. Arch. Disease in Childhood 57: 54-58
  39. Songjinda, P., J. Nakayama, Y. Kuroki, S. Tanaka, S. Fukuda, C. Kiyohara, T. Yamamoto, K. lzuchi, T. Shirakawa, and K. Sonomoto. 2005. Molecular monitoring ofthe developmental bacterial community in the gastrointestinal tract of Japanese infants. Biosci. Biotechnol. Biochem. 69: 638-641 https://doi.org/10.1271/bbb.69.638
  40. Sprunt, K. and G. Leidy. 1988. The use of bacterial interference to prevent infection. Can. J. Microbiol. 34: 332-338 https://doi.org/10.1139/m88-061
  41. Matsuki, T., K.Watanabe, J. Fujimoto, Y. Miyamoto, T. Takada, K. Matsumoto, H. Oyaizu, and R. Tanaka. 2002. Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl. Environ. Microbiol. 68: 5445-5451 https://doi.org/10.1128/AEM.68.11.5445-5451.2002
  42. Tannock, G. W. 1997. Probiotic properties of lactic-acid bacteria: plenty of scope for fundamental R&D. Trends Biotechnol. 15: 270-274 https://doi.org/10.1016/S0167-7799(97)01056-1
  43. Tannock, G. W., R. Fuller, S. L. Smith, and M. A. Hall. 1990. Plasmid profiling of members of the family Enterobacteriaceae, Lactobacilli, and Bifidobacteria to study the transmission of bacteria from mother to infant. J. Clin. Microbiol. 284: 1225-1228
  44. Wang, R. F., M. L. Beggs, B. D. Erickson, and C. E. Cemiglia. 2004. DNA microarray analysis of predominant human intestinal bacteria in fecal samples. Mol. Cell Probes 18: 223-234 https://doi.org/10.1016/j.mcp.2004.03.002
  45. Wang, R. F., M. L. Beggs, L. H. Robertson, and C. E. Cerniglia. 2002. Design and evaluation of oligonucleotidemicroarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213: 175-182 https://doi.org/10.1111/j.1574-6968.2002.tb11302.x
  46. Wang, R. F., S. J. Kim, L. H. Robertson, and C. E. Cemiglia. 2002. Development of a membrane-array method for the detection of human intestinal bacteria in fecal samples. Mol. Cell Probes 16: 341-350 https://doi.org/10.1006/mcpr.2002.0432
  47. Weisburg, W. G, S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697-703 https://doi.org/10.1128/jb.173.2.697-703.1991
  48. Wu, L., D. K. Thompson, G Li, R. A. Hurt, J. M. Tiedje, and J. Zhou. 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67: 5780-5790 https://doi.org/10.1128/AEM.67.12.5780-5790.2001
  49. X. W. Huijsdens, R. K. Linskens, J. Koppes, Y. L. Tang, S. G. Meuwissen, C. M. Vandenbroucke-Grauls, and P. H. Savelkoul. 2004. Detection of Helicobacter species DNA by quantitative PCR in the gastrointestinal tract of healthy individuals and of patients with inflammatory bowel disease. FEMS Immunol. Med. Microbiol. 41: 79-84 https://doi.org/10.1016/j.femsim.2004.01.007
  50. Yoshioka, H., K. Iseki, and K. Fujita. 1983. Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants. Pediatrics 72: 317-321
  51. Hingoh, Y, M. Ohkuma, and T. Kudo. 2003. Molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidate). FEMS Microbiol Ecol. 44: 231-242 https://doi.org/10.1016/S0168-6496(03)00026-6
  52. Zoetendal, E. G, A. D. Akkermans, and W. M. De Vos. 1998. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64: 3854-3859
  53. Zoetendal, E. G, K. Ben-Amor, H. J. Harmsen, F. Schut, A. D. Akkermans, and W. M. de Vos. 2002. Quantification of uncultured Ruminococcus obeum-like bacteria in human fecal samples by fluorescent in situ hybridization and flow cytometry using 16S rRNA-targeted probes. Appl. Environ. Microbiol. 68: 4225-4232 https://doi.org/10.1128/AEM.68.9.4225-4232.2002