Methods of analyzing gut microbiota

Lactic Acid Bacteria Microbiological and Functional Aspects, Third Edition: Revised and Expanded

Volumn , Issue , 2004, Pages 365-374

  Gueimonde, Miguel ^a   Salminen, Seppo ^a  

^a UNIVERSITY OF TURKU   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 29144501806     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (49)

1. Benno, Y.; Mitsuoka, T. Development of intestinal microflora in humans and animals. Bifidobacteria Microflora. 1986, 5, 13–25.
2. Grönlund, M.M.; Arvilommi, H.; Kero, P.; Lehtonen, O.P.; Isolauri, E. Importance of intestinal colonisation in the maduration of humoral immunity in early infancy: a prospective follow up study of healthy infants aged 0–6 months. Arch. Dis. Child. 2000, 83, F186–F192.
3. Kirjavainen, P.V.; Apostolou, E.; Arvola, T.; Salminen, S.J.; Gibson, G.R.; Isolauri, E. Characterizing the composition of intestinal microflora as a prospective treatment target in infant allegic diseases. FEMS Immunol. Med. Microbiol. 2001, 32, 1–7.
4. Falk, P.G.; Hooper, L.V.; Midvedt, T.; Gordon, J.I. Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol. Mol. Biol. Rev. 1998, 62 (4), 1157–1170.
5. Reuter, G. The Lactobacillus and Bifidobacterium microflora of the human intestina: composition and succession. Curr. Issues Intest. Microbiol. 2001, 2 (2), 43–53.
6. McCartney, A.L.; Wenzhi, W.; Tannock, G.W.: Molecular analysis of the composition of the bifidobacterial and Lactobacillus microflora of humans. Appl. Environ. Microbiol. 1996, 62 (12), 4608–4613.
7. Biavati, B.; Castagnoli, P.; Trovatelli, L.D. Species of the genus Bifidobacterium in the feces of human adults. Microbiologica. 1986, 9 (1), 39–45.
8. Silvi, C.; Verdenelli, M.C.; Orpianesi, C.; Cresci, A. EU project crownalife: functional foods, gut microflora and health ageing. Isolation and identification of Lactobacillus and Bifidobacterium strains from faecal samples of elderly subjects for a possible probiotic use in functional foods. J. Food Eng. 2003, 56, 195–200.
9. Morelli, L.; Cesena, C.; de Haën, C.; Gozzini, L. Taxonomic Lactobacillus composition of feces from human newborns during the first few days. Microb. Ecol. 1998, 35, 205–212.
10. Mevissen-Verhage, E.A.E.; Marcelis, J.H.; de Vos, M.N.; Harmsen-van Amerongen, W.C.M.; Verhoef, J. Bifidobacterium, Bacteroides and Clostridium spp. in fecal samples from breast-fed and bottle-fed infants with and without iron supplement. J. Clin. Microbiol. 1987, 25, 285–289.
11. Corthier, G.; Muller, M.C.; L’Haridon, R.: Selective enumeration of Bacteroides vulgatus and Bacteriodes distasonis organisms in the predominant human fecal flora by using monoclonal antibodies. Appl. Environ. Microbiol. 1996, 62 (2), 735–738.
12. Kaufmann, P.; Pfefferkorn, A.; Teuber, M.; Meile, L. Identification and quantification of bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR. Appl. Environ. Microbiol. 1997, 63 (4), 1268–1273.
13. Dore, J.; Sghir, A.; Hannequart-Gramet, G.; Corthier, G.; Pochart, P. Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst. Appl. Microbiol. 1998, 21 (1), 65–71.
14. Suau, A.; Bonnet, R.; Sutren, M.; Godon, J-J.; Gibson, G.; Collins, M.A.; Dore, J. Direct analysis of genes encoding 16S RNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 1999, 65, 4799–4807.
15. Langendijk, P.S.; Schut, F.; Jansen, G.J.; Raangs, G.C.; Kamphuis, G.R.; Wilkinson, M.H.F.; Welling, G.W.: Quantitative fluorescence in situ hybridization of Bifidobacterium ssp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 1995, 61 (8), 3069–3075.
16. Wilson, K.H.; Blitchington, R.B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 1996, 62 (7), 2273–2278.
17. Harmsen, H.J.M.; Gibson, G.R.; Elfferich, P.; Raangs, G.C.; Wildeboer-Veloo, A.C.M.; Argaiz, A.; Roberfroid, M.B.; Welling, G.W. Comparison of viable cell counts and fluorescence in situ hybridization using specific rRNA-based probes for the quantification of human fecal bacteria. FEMS Microbiol. Lett. 1999, 183, 125–129.
18. Wang, R-F.; Caom W-W.; Campbell, W.L.; Hairston, L.; Franklin, W.; Cerniglia, C.E. The use of PCR to monitor the population abundance of six human intestinal bacterial species in an in vitro semicontinuous culture system. FEMS Microbiol. Lett. 1994, 124, 229–238.
19. Wang, R-F.; Cao, W-W.; Cerniglia, C.E. PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl. Environ. Microbiol. 1996, 62 (4), 1242–1247.
20. Matsuki, T.; Watanabe, K.; Tanaka, R.; Oyaizu, H.: Rapid identification of human intestinal bifidobacteria by 16S rRNA-targeted species- and group-specific primers. FEMS Microbiol. Lett. 1998, 167, 113–121.
21. Matsuki, T.; Watanabe, K.; Tanaka, R.; Fukuda, M.; Oyaizu, H. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene targeted species-specific primers. Appl. Environ. Microbiol. 1999, 65 (10), 4506–4512.
22. Matsuki, T.; Watanabe, K.; Fujimoto, J.; Miyamoto, Y.; Takada, T.; Matsumoto, K.; Oyaizu, H.; Tanaka, R.: Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl. Environ. Microbiol. 2002, 68 (11), 5445–5451.
23. Franks, A.H.; Harmsen, H.J.M.; Raangs, G.C.; Jansen, G.J.; Schut, F.; Welling, G.W.: Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 1998, 64 (9), 3336–3345.
24. Schwiertz, A.; Le Blay, G.; Blaut, M. Quantitation of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 2000, 66 (1), 375–382.
25. Harmsen, H.J.M.; Raangs, G.C.; He T.; Degener, J.E.; Welling, G.W. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl. Environ. Microbiol. 2002, 68 (6), 2982–2990.
26. Sghir, A.; Gramet, G.; Suau, A.; Rochet, V.; Pochart, P.; Dore, J.: Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 2000, 66 (5), 2263–2266.
27. Hopkins, M.J.; Sharp, R.; Macfarlane, G.T. Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles. Gut. 2001, 48, 198–205.
28. Marteau, P.; Pochart, P.; Doré, J.; Béra-Maillet, C.; Bernalier, A.; Corthier, G. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl. Environ. Microbiol. 2001, 67 (10), 4939–4942.
29. Malinen, E.; Matto, J.; Salmitie, M.; Alander, M.; Saarela, M.; Palva, A. PCR-ELISA II: analysis of Bifidobacterium populations in human faecal samples from a consumption trial with Bifidobacterium lactis Bb-12 and a galacto-oligosaccharide preparation. Syst. Appl. Microbiol. 2002, 25 (2), 249–258.
30. Heilig, H.G.H.J.; Zoetendal, E.G.; Vaughan, E.E.; Marteau, P.; Akkermans, A.D.L.; de Vos, W.M. 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. 2002, 68 (1), 114–123.
31. Zoetendal, E.G.; Akkermans, A.D.L.; de Vos, W.M. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 1998, 64 (10), 3854–3859.
32. Satokari, R.M.; Vaughan, E.E.; Akkermans, A.D.L.; Saarela, M.; de Vos, W.M. Bifidobacterial diversity in human feces detected by genus specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 2001, 67 (2), 504–513.
33. Walter, J.; Hertel, C.; Tannock, G.W.; Lis, C.M.; Munro, K.; Hammes, W.P. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 2001, 67 (6), 2578–2585.
34. Kaplan, C.W.; Astaire, J.C.; Sanders, M.E.; Reddy, B.S.; Kitts, C.L. 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM. Appl. Environ. Microbiol. 2001, 67 (4), 1935–1939.
35. Khan, A.A.; Nawaz, M.S.; Robertson, L.; Khan, S.A.; Cerniglia, C.E. Identification of predominant human and animal anaerobic intestinal bacterial species by terminal restriction fragment patterns (TRFP’s): a rapid, PCR-based method. Mol. Cell. Probes. 2001, 15, 349–355.
36. Wang, R-F.; Beggs, M.L.; Robertson, L.H.; Cerniglia, C.E.: Design and evaluation of oligonucleotide- microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 2002a, 213, 175–182.
37. Wang, R-F.; Kim, S.J.; Robertson, L.H.; Cerniglia, C.E. Development of a membrane-array method for the detection of human intestinal bacteria in fecal samples. Mol. Cell. Probes. 2002b, 16, 341–350.
38. Tuohy, K.M.; Finlay, R.K.; Wynne, A.G.; Gibson, G.R. A human volunteer study on the prebiotic effects of HP-Inulin—fecal bacteria enumerated using fluorescent in situ hybridization (FISH). Anaerobe. 2001, 7, 113–118.
39. Kirjavainen PV, Arvola T, Salminen SJ, Isolauri E. Aberrant composition of gut microbiota of allergic infants: a target of bifidobacterial therapy at weaning? Gut. 2002, 51, 51–55.
40. Kalliomäki, M.; Kirjavainen, P.; Eerola, E.; Kero, P.; Salminen, S.; Isolauri, E.: Distinct patterns of neonatal gut microflora in infants in whom atopy was and was not developing. J. Allergy Clin. Immunol. 2001, 107, 129–134.
41. Jansen, G.J.; Wildeboer-Veloo, A.C.M.; Tonk, R.H.J.; Franks, A.H.; Welling, G.W.: Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria. J. Microbiol. Methods 1999, 37, 215–221.
42. Zoetendal, E.G.; Ben-Amor, K.; Harmsen, H.J.; Schut, F.; Akkermans, A.D.; de Vos, W.M. Quantification of uncultured Runinococcus obeum-like bacteria in human fecal samples by fluorescent in situ hybridization and flow cytometry using 16S rRNA-targeted probes. Appl. Environ. Microbiol. 2002, 68 (9), 4225–4232.
43. Requena, T.; Burton, J.; Matsuki, T.; Munro, K.; Simon, M.A.; Tanaka, R.; Watanabe, K.; Tannock, G.W. Identification, detection and enumeration of human Bifidobacterium species by PCR targeting the transaldolase gene. Appl. Environ. Microbiol. 2002, 68 (5), 2420–2427.
44. Huijsdens, X.W.; Linskens, R.K.; Mak, M.; Meuwissen, S.G.M.; Vandenbroucke-Grauls, C.M.J.E.; Savelkoul, P.H.M. Quantification of bacteria adherent to gastrointestinal mucosa by real-time PCR. J. Clin. Microbiol. 2002, 40 (12), 4423–4427.
45. Lyons, S.R.; Griffen, A.L.; Leys, E.J.: Quantitative real-time PCR for Porphyromonas gingivalis and total bacteria. J. Clin. Microbiol. 2000, 38 (6), 2362–2365.
46. Nadkarni, M.A.; Martin, F.E.; Jacques, N.A.; Hunter, N. Determination of bacterial load by real-time PCR using a broad range (universal) probe and primers set. Microbiology 2002, 148, 257–266.
47. Wintzingerode, F.V.; Göbel, U.B.; Stackebrandt, E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 1997, 21, 213–229.
48. Schmalenberger, A.; Schwieger, F.; Tebbe, C.C.: Effect of primers hybridising to different evolutionary conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl. Environ. Microbiol. 2001, 67 (8), 3557–3563.
49. Midtvedt, A.C.; Carlstedt-Duke, B.; Norin, H.; Saxerholt, H.; Midtvedt, T. Development of five metabolic activities associated with the intestinal flora in healthy infants. J. Pediatric. Gastroenterol. Nutr. 1998, 7, 559–567.