Molecular methods for the analysis of gut microbiota

Microbial Ecology in Health and Disease

Volumn 16, Issue 2-3, 2004, Pages 71-85

  Namsolleck, Pawel ^a   Thiel, Ralph ^a   Lawson, Paul ^b   Holmstrøm, Kim ^c   Rajilic, Mirjana ^d   Vaughan, Elaine E ^d   Rigottier Gois, Lionel ^e   Collins, Matthew D ^b   De Vos, Willem M ^d   Blaut, Michael ^a  

^a GERMAN INSTITUTE OF HUMAN NUTRITION   (Germany)

^b UNIVERSITY OF READING   (United Kingdom)

^c BIONEER A S   (Denmark)

^d WAGENINGEN UNIVERSITY   (Netherlands)

^e CEMAGREF   (France)

Author keywords

DGGE; Dot blot; FISH; Flow cytometry; Gut ecology; In situ gene expression; Micro array; Sequencing; TGGE

Indexed keywords

BACTERIAL GENETICS; CONFERENCE PAPER; FECES; FECES MICROFLORA; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE SEQUENCE; HUMAN; INTESTINE FLORA; MICROSCOPY; MOLECULAR BIOLOGY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW;

BACTERIA (MICROORGANISMS); MICROBIOTA;

EID: 3342952142     PISSN: 0891060X     EISSN: None     Source Type: Journal    
DOI: 10.1080/08910600410032367     Document Type: Conference Paper

References (86)

1. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977; 74: 5088-90.
2. Fox GE, Pechman KR, Woese CR. Comparative cataloguing of 16S ribosomal ribonucleic acid: molecular approach to procaryotic systematics. Int J Syst Bacteriol 1977; 57: 44-57.
3. Moreira D, Philippe H. Molecular phylogeny: pitfalls and progress. Int Microbiol 2000; 3: 9-16.
4. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 1998; 19: 554-68.
5. Palys T, Nakamura LK, Cohan FM. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 1997; 47: 1145-56.
6. Kasai H, Watanabe K, Gasteiger E, Bairoch A, Isono K, Yamamoto S, Harayama S. Construction of the gyr B database for the identification and classification of bacteria. Genome Inform Ser Workshop Genome Inform 1998; 9: 13-21.
7. Hassan AA, Khan IU, Abdulmawjood A, Lammler C. Inter-and intraspecies variations of the 16S-23S rDNA intergenic spacer region of various streptococcal species. Syst Appl Microbiol 2003; 26: 97-103.
8. Anton AI, Martinez-Murcia AJ, Rodriguez-Valera F. Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. J Mol Evol 1998; 47: 62-72.
9. Hedegaard J, Steffensen SA, Norskov-Lauritsen N, Mortensen KK. Sperling-Petersen HU. Identification of Enterobacteriaceae by partial sequencing of the gene encoding translation initiation factor 2. Int J Syst Bacteriol 1999; 49(Pt 4): 1531-8.
10. Amann R, Ludwig W, Schleifer KH. Beta-subunit of ATP-synthase: a useful marker for studying the phylogenetic relationship of eubacteria. J Gen Microbiol 1988; 134(Pt 10): 2815-21.
11. Cousineau B, Cerpa C, Lefebvre J, Cedergren R. The sequence of the gene encoding elongation factor Tu from Chlamydia trachomatis compared with those of other organisms. Gene 1992; 120: 33-41.
12. Moore WE, Holdeman LV. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl Microbiol 1974; 27: 961-79.
13. Bonnet R, Suau A, Doré J, Gibson GR, Collins MD. Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs. Int J Syst Evol Microbiol 2002; 52: 757-63.
14. Hold GL, Pryde SE, Russell VJ, Furrie E, Flint HJ. Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 2002; 39: 33-9.
15. Wilson KH, Blitchington RB. Human colonic biota studied by ribosomal DNA sequence analysis. Appl Environ Microbiol 1996; 62: 2273-8.
16. Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995; 59: 143-69.
17. Harmsen HJM, Elfferich P, Schut F, Welling GW. A 16S rRNA-targeted probe for detection of lactobacilli and enterococci in faecal samples by fluorescent in situ hybridization. Microb Ecol Health Dis 1999; 11: 3-12.
18. Pernthaler J, Pernthaler A, Amann R. Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization. Appl Environ Microbiol 2003; 69: 2631-7.
19. Loy A, Horn M, Wagner M. probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 2003; 31: 514-6.
20. Pernthaler J, Glöckner FO, Schönhuber W. Amann RI. Fluorescence in situ hybridization. In: Paul JH, ed. Marine Microbiology. Methods in Microbiology, vol. 30. San Diego: Academic Press, 2001: 207-26.
21. Hugenholtz P, Tyson GW, Blackall LL. Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods Mol Biol 2002; 179: 29-42.
22. Ashelford KE, Weightman AJ, Fry JC. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 2002; 30: 3481-9.
23. Fuchs BM, Wallner G, Beisker W, Schwippl I, Ludwig W, Amann R. Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 1998; 64: 4973-82.
24. Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F, Welling GW. 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: 3336-45.
25. Vaughan EE, Schut F, Heilig HG, Zoetendal EG, de Vos WM, Akkermans AD. A molecular view of the intestinal ecosystem. Curr Issues Intest Microbiol 2000; 1: 1-12.
26. Langendijk PS, Schut F, Jansen GJ, Raangs GC, Kamphuis GR, Wilkinson MH, Welling GW. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol 1995; 61: 3069-75.
27. Jansen GJ, Wildeboer-Veloo ACM, Tonk RHJ, Franks AH, Welling GW. Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria. J Microbiol Methods 1999; 37: 215-21.
28. Gmur R, Guggenheim B, Giertsen E, Thurnheer T. Automated immunofluorescence for enumeration of selected taxa in supragingival dental plaque. Eur J Oral Sci 2000; 108: 393-402.
29. Singleton S, Cahill JG, Watson GK, Allison C, Cummins D, Thurnheer T, Guggenheim B, Gmur R. A fully automated microscope bacterial enumeration system for studies of oral microbial ecology. J Immunoassay Immunochem 2001; 22: 253-74.
30. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 1990; 56: 1919-25.
31. Rigottier-Gois L, Rochet V, Garrec N, Suau A, Doré J. Enumeration of Bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16S rRNA probes. Syst Appl Microbiol 2003; 26: 110-18.
32. Zoetendal EG, Ben-Amor K, Harmsen HJ, Schut F, Akkermans AD, de Vos WM. 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 2002; 68: 4225-32.
33. Wallner G, Erhart R, Amann RI. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl Environ Microbiol 1995; 61: 1859-66.
34. Rigottier-Gois L, Le Bourhis A-G, Gramet G, Rochet V, Doré J. Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes. FEMS Microbiol Ecol 2003; 43: 237-45.
35. Wallner G, Fuchs B, Spring S, Beisker W, Amann R. Flow sorting of microorganisms for molecular analysis. Appl Environ Microbiol 1997; 63: 4223-31.
36. Porter J, Edwards C, Morgan JA, Pickup RW. Rapid, automated separation of specific bacteria from lake water and sewage by flow cytometry and cell sorting. Appl Environ Microbiol 1993; 59: 3327-33.
37. Suau A, Rochet V, Sghir A, Gramet G, Brewaeys S, Sutren M, Rigottier-Gois L, Doré J. Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst Appl Microbiol 2001; 24: 139-45.
38. Harmsen HJM, Prieur D, Jeanthon C. Group-specific 16S rRNA-targeted oligonucleotide probes to identify thermophilic bacteria in marine hydrothermal vents. Appl Environ Microbiol 1997; 63: 4061-8.
39. Sghir A, Gramet G, Suau A, Rochet V, Pochart P, Doré J. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol 2000; 66: 2263-6.
40. Marteau P, Pochart P, Doré J, Bera-Maillet C, Bernalier A, Corthier G. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl Environ Microbiol 2001; 67: 4939-42.
41. Blaut M, Collins MD, Welling GW, Doré J, van Loo J, de Vos W. Molecular biological methods for studying the gut microbiota: the EU human gut flora project. Br J Nutr 2002; 87(Suppl 2): S203-11.
42. Theron J, Cloete TE. Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 2000; 26: 37-57.
43. Rick WY, Wang T, Bedzyk L, Croker KM. Application of DNA microarrays in microbial systems. J Microbiol Methods 2001; 47: 257-72.
44. Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 2003; 69: 1159-71.
45. Bodrossy L, Stralis-Pavese N, Murrell CL, Radjewski S, Weilharter A, Sessitsch A. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 2003; 5: 566-82.
46. Rudi K, Flateland SL, Hanssen JF, Bengtsson G, Nissen H. Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere. Appl Environ Microbiol 2002; 68: 1146-56.
47. Small J, Call DR, Brockman FJ, Straub TM, Chandler DP. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 2001; 67: 4708-16.
48. El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 2003; 69: 2377-82.
49. Urakawa H, Noble PA, El Fantroussi S, Kelly JJ, Stahl DA. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl Environ Microbiol 2002; 68: 235-44.
50. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 2002; 68: 5064-81.
51. Rudi K, Skulberg OM, Skulberg R, Jakobsen KS. Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl Environ Microbiol 2000; 66: 4004-11.
52. Wang RF, Beggs ML, Robertson LH, Cerniglia CE. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol Lett 2002; 213: 175-82.
53. Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 1997; 63: 2397-402.
54. Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 1993; 59: 695-700.
55. Zoetendal EG, Akkermans AD, de Vos WM. 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: 3854-9.
56. Poulsen LK, Dalton HM, Angles ML, Marshall KC, Molin S, Goodman AE. Simultaneous determination of gene expression and bacterial identity in single cells in defined mixtures of pure cultures. Appl Environ Microbiol 1997; 63: 3698-702.
57. DeLong EF, Wickham GS, Pace NR. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 1989; 243: 1360-3.
58. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985; 230: 1350-4.
59. Hodson RE, Dustman WA, Garg RP, Moran MA. In situ PCR for visualization of microscale distribution of specific genes and gene products in prokaryotic communities. Appl Environ Microbiol 1995; 61: 4074-82.
60. Tani K, Kurokawa K, Nasu M. Development of a direct in situ PCR method for detection of specific bacteria in natural environments. Appl Environ Microbiol 1998; 64: 1536-40.
61. Tolker-Nielsen T, Holmstrom K, Boe L, Molin S. Non-genetic population heterogeneity studied by in situ polymerase chain reaction. Mol Microbiol 1998; 27: 1099-105.
62. Vaid A, Bishop AH. Amplification of fluorescently labelled DNA within Gram-positive and acid-fast bacteria. J Microbiol Methods 1999; 38: 53-62.
63. Lange M, Tolker-Nielsen T, Molin S, Ahring BK. In situ reverse transcription-PCR for monitoring gene expression in individual Methanosarcina mazei S-6 cells. Appl Environ Microbiol 2000; 66: 1796-800.
64. Hoshino T, Noda N, Tsuneda S, Hirata A, Inamori Y. Direct detection by in situ PCR of the amoA gene in biofilm resulting from a nitrogen removal process. Appl Environ Microbiol 2001; 67: 5261-6.
65. Tani K, Muneta M, Nakamura K, Shibuya K, Nasu M. Monitoring of Ralstonia eutropha KT1 in groundwater in an experimental bioaugmentation field by in situ PCR. Appl Environ Microbiol 2002; 68: 412-6.
66. Tolker-Nielsen T, Holmstrom K, Molin S. Visualization of specific gene expression in individual Salmonella typhimurium cells by in situ PCR. Appl Environ Microbiol 1997; 63: 4196-203.
67. Holmstrom K, Tolker-Nielsen T, Molin S. Physiological states of individual Salmonella typhimurium cells monitored by in situ reverse transcription-PCR. J Bacteriol 1999; 181: 1733-8.
68. Lewis PJ, Nwoguh CE, Barer MR, Harwood CR, Errington J. Use of digitized video microscopy with a fluorogenic enzyme substrate to demonstrate cell- and compartment-specific gene expression in Salmonella enteritidis and Bacillus subtilis. Mol Microbiol 1994; 13: 655-62.
69. Heilig HG, Zoetendal EG, Vaughan EE, Marteau P, Akkermans AD, de Vos WM. 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: 114-23.
70. Schwiertz A, Hold GL, Duncan SH, Gruhl B, Collins MD, Lawson PA, Flint HJ, Blaut M. Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces. Syst Appl Microbiol 2002; 25: 46-51.
71. Lawson PA, Song Y, Liu C, Molitoris DR, Väisänen ML, Collins MD, Finegold SM. Anaerotruncus colihominis gen. nov., sp. nov., from human faeces, Int J Syst Evol Microbiol 2004; 54: 413-7.
72. Rautio M, Eerola E, Väisänen-Tunkelrott ML, Molitoris DR, Lawson PA, Collins MD. Reclassification of Bacteroides putridinis (Weinberg et al. 1937) in a new genus Alistipes gen. nov., as Alistipes putridinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources. Syst Appl Microbiol 2003; 26: 182-8.
73. Wolin MJ, Miller TL, Collins MD, Lawson PA. Formate dependent and homoacetic acid fermentation by a bacterium from human feces. Description of Bryantella formatexigens gen. nov., sp. nov. Appl Environ Microbiol 2003; 69: 6321-6.
74. Finegold SM, Väisänen ML, Molitoris DR, Tomzynski TJ, Song Y, Liu C, Collins MD, Lawson PA. Cetobacterium somerae sp. nov. from human feces and emended description of the genus Cetobacterium. Syst Appl Microbiol 2003; 26: 177-81.
75. Song Y, Liu C, Molitoris DR, Tomzynski TJ, Lawson PA, Collins MD. Clostridium bolteae sp. nov., isolated from human sources. Syst Appl Microbiol 2003; 26: 84-9.
76. Steer T, Collins MD, Gibson GR, Hippe H, Lawson PA. Clostridium hathewayi sp. nov., from human faeces. Syst Appl Microbiol 2001; 24: 353-7.
77. Taras D, Simmering R, Collins MD, Lawson PA, Blaut M. Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp nov., isolated from human faeces. Int J Syst Evol Microbiol 2002; 52: 423-8.
78. Simmering R, Taras D, Schwiertz A, Le Blay G, Gruhl B, Lawson PA. Ruminococcus luti sp. nov., isolated from a human faecal sample. Syst Appl Microbiol 2002; 25: 189-93.
79. Hold GL, Schwiertz A, Aminov RI, Blaut M, Flint HJ. Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces. Appl Environ Microbiol 2003; 69: 4320-4.
80. Harmsen HJ, Wildeboer-Veloo AC, Grijpstra J, Knol J, Degener JE, Welling GW. 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 2000; 66: 4523-7.
81. Harmsen HJ, Raangs GC, He T, Degener JE, Welling GW. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 2002; 68: 2982-90.
82. Tannock GW, Munro K, Harmsen HJ, Welling GW, Smart J, Gopal PK. Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 2000; 66: 2578-88.
83. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer KH. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 1996; 142(Pt 5): 1097-106.
84. Schwiertz A, Le Blay G, Blaut M. Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 2000; 66: 375-82.
85. Wallner G, Amann RI, Beisker W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 1993; 14: 136-43.
86. Alm EW, Oerther DB, Larsen N, Stahl DA, Raskin L. The Oligonucleotide Probe Database. Appl Environ Microbiol 1996; 62: 3557-9.