Abstract
The ability of microbial ecologists to analyse the composition of complex bacterial communities has been greatly enhanced by the application of molecular methodologies. The use of these techniques should enable an accurate record of the identity and population dynamics of the inhabitants of the intestinal tract to be obtained, and should promote an improved comprehension of the relationship between the microflora and the human host. This, in turn, will lead to a new concept of the intestinal microflora of humans.
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References
Amann RI, Ludwig W & Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169
Aranki A & Freter R (1972) Use of anaerobic glove boxes for the cultivation of strictly anaerobic bacteria. Am. J. Clin. Nutr. 25: 1329-1334
Ballongue J (1993) Bifidobacteria and probiotic action. In: Salminen S & von Wright A (Eds) Lactic Acid Bacteria (pp 357-428). Marcel Dekker, New York
Barrow PA, Brooker BE, Fuller R & Newport MJ (1980) The attachment of bacteria to the gastric epithelium of the pig and its importance in the microecology of the intestine. J. Appl. Bacteriol. 48: 147-154
Bassam BJ, Allen T, Flood S, Stevens J, Wyatt P & Livak KJ (1996) Nucleic acid sequence detection systems: revolutionary automation for monitoring and reporting PCR products. Australasian Biotechnol. 6: 285-294
Bateup JM, Dobbinson S, McConnell MA, Munro K & Tannock GW (1998) Molecular analysis of the composition of Lactobacillus populations inhabiting the stomach and caecum of pigs. Microbial Ecology in Health and Disease 10: 95-102
Berg RD (1983) Host immune response to antigens of the indigenous intestinal flora. In: Hentges DJ (Ed) Human Intestinal Micro flora in Health and Disease (pp 101-126). Academic Press, New York
Biavati B, Castagnoli P, Crociani F & Trovatelli LD (1984) Species of the genus Bifidobacterium in the feces of infants. Microbiologica 7: 341-345
Biavati B, Castagnoli P & Trovatelli LD (1986) Species of the genus Bifidobacterium in the feces of adults. Microbiologica 9: 39-45
Bry L, Falk PG, Midtvedt T & Gordon JI (1996) A model of host-microbial interactions in an open mammalian ecosystem. Science 273: 1380-1383
Caufield PW (1997) Dental caries — a transmissible and infectious disease revisited: a position paper. Pediatric Dentitstry 19: 491-498
Chadwick VS & Chen W (1999) The intestinal microflora and inflammatory bowel disease. In: Tannock GW (Ed) Medical Importance of the Normal Microflora (pp 177-221). Kluwer Academic Publishers, Dordrecht, The Netherlands
Croucher SC, Houston AP, Bayliss CE & Turner RJ (1983) Bacterial populations associated with different regions of the human colon wall. Appl. Environ. Microbiol. 45: 1025-1033
Cummings JH & Macfarlane GT (1991) The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 70: 443-459
Drasar BS & Barrow PA (1985) Intestinal Microbiology. American Society for Microbiology, Washington DC
Drasar BS & Hill MJ (1974) Human Intestinal Flora. Academic Press, London
Dubos R, Schaedler RW, Costello R & Hoet P (1965) Indigenous, normal, and autochthonous flora of the gastrointestinal tract. J. Exper. Med. 122: 67-76
Felske A, Rheims H, Wolterink A, Stackebrandt E & Akkermans ADL (1997) Ribosome analysis reveals prominent activity of an uncultured member of the class of Actinobacteria in grassland soils. Microbiology 143: 2983-2989
Ferguson WK (1967) The Renaissance. Holt, Rinehart and Winston, New York
Finegold SM (1977) Anaerobic Bacteria in Human Disease. Academic Press, New York
Finegold SM, Attebury R & Sutter VL (1974) Effect of diet on human fecal flora: comparison of Japanese and American diets. Am. J. Clin. Nutr. 27: 1456-1469
Finegold SM, Sutter VL & Mathisen GE (1983) Normal indigenous intestinal flora. In: Hentges DJ (Ed) Human Intestinal Microflora in Health and Disease (pp 3-31). Academic Press, New York
Finegold SM & Sutter VL (1978) Fecal flora in different populations, with special reference lo diet. Am. J. Clin. Nutr. 31: S116-S122
Franks AH, Harmsen HJM, Raangs GC, Jansen GJ, Schut F & Welling GW (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
Fuller R (1989) Probiotics in man and animals. J. Appl. Bacteriol. 66: 365-378
Fuller R (1999) Probiotics for farm animals. In: Tannock GW (Ed) Probiotics: a Critical Review (pp 15-22). Horizon Scientific Press, Wymondham, UK
Fuller R & Brooker BE (1974) Lactobacilli which attach lo the crop epithelium of the fowl. Am. J. Clin. Nutr. 27: 1305-1312
Gastone JSH (1997) Pathogenic role of gut inflammation in the spondyloarthropathies. Current Opinion in Rheumatology 9: 302-307
Goldin BR, Gorbach SL, Saxelin M, Barakat S, Gualtieri L & Salminen S (1992) Survival of Lactobacillus species (strain GG) in human gastroinlestinal tract. Digestive Diseases and Sciences 37: 121-128
Goldin BR, Swenson L, Dwyer J, Sexton M & Gorabch SL1 (980) Effect of diet and Lactobacillus acidophilus supplements on human fecal bacterial enzymes. J. National Cancer Institute 64: 255-261
Goodwin MA, Cooper GL, Brown J, Bickford AA, Waltman WD & Dickson TG (1991) Clinical, pathological, and epizootiological features of the long-segmented filamentous organisms (Bacteria, LSFOs) in the small intestines of chickens, turkeys, and quails. Avian Diseases 35: 872-876
Gordon HA & Pesti L (1971) The gnotobiotic animal as a tool in the study of host-microbial relationships. Bacteriol. Rev. 35: 390-429
Gracey M (1983) The contaminated small bowel syndrome. In: Hentges DJ (Ed) Human Intestinal Microflora in Health and Disease (pp 495-513). Academic Press, New York
Gurtler V & Stanisich VA (1996) New approaches lo typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142: 3-16
Hill JE, Kelley LC & Langheinrich KA (1992) Visceral granulomas in chickens infected with a filamentous bacteria. Avian Diseases 36: 172-176
Holdeman LV & Moore WEC (1972) Roll-lube technique for anaerobic bacteria. Am. J. Clin. Nutr. 25: 1314-1317
Hungate RE (1966) The Rumen and its Microbes. Academic Press, New York
Husni RN, Gordon SM, Washington JA & Longworth DL (1997) Lactobacillus bacteremia and endocarditis: review of 45 cases. Clinical Infectious Diseases 25: 1048-1055
Jepson MA, Clark MA, Simmons NL & Hirst BH (1993) Actin accumulations at sites of attachment of indigenous apathogenic segmented filamentous bacteria to mouse ileal epithelial cells. Infection and Immunity 61: 4001-4004
Kato I, Kobayashi S, Yokokura T & Mutai M (1981) Antitumor activity of Lactobacillus casei in mice. Gann 72: 517-523
Kimura K, McCartney AL, McConnell MA & Tannock GW (1997) Analysis of fecal populations of bifidobacteria and lactobacilli and investigations of the immunological responses of their human hosts to the predominant strains. Appl. Environ. Microbiol. 63: 3394-3398
Klaasen HLBM, Koopman JP, van den Brink ME, van Wezel HPN & Beynen AC (1991) Mono-association of mice with non-cultivable, intestinal, segemented, filamentous bacteria. Archives of Microbiology 156: 148-151
Klaasen HLBM, Koopman JP, Poelma FGJ & Beynen AC (1992) Intestinal, segmented, filamentous bacteria. FEMS Microbiol. Rev. 88: 165-180
Klaasen HLBM, van der Heijden PJ, Stok W, Poelma FGJ, Koopman JP, van den Brink ME, Bakker MH, Eling WMC & Beynen AC (1993) Apathogenic, intestinal, segmented, filamentous bacteria stimulate the mucosal immune system of mice. Infection and Immunity 61: 303-306
Kolenbrander PE (1991) Coaggregation: adherence in the human oral microbial ecosystem. In: Dworkin M (Ed) Microbial Cell-Cell Interactions (pp 303-329). American Society for Microbiology, Washington DC
Lehman TJ, Cremer MA, Walker SM & Dillon AM (1987) The role of humoral immunity in Lactobacillus casei cell wall induced arthritis. J. Rheumatology 14: 415-419
Luckey TD (1963) Germfree Life and Gnotobiology. Academic Press, New York
Macfarlane GT & Macfarlane S (1995) Human intestinal'biofilm' communities. In: Wimpenny J, Handley P, Gilbert P & Lappin-Scott H (Eds) The Life and Death of Biofilm (pp 83-87). BioLine, Cardiff
McCartney AL, Wang W & Tannock GW (1996) Molecular analysis of the composition of the bifidobacterial and lactobacillus micro flora of humans. Appl. Environ. Microbiol. 62: 4608-4613
Mitsuoka T (1992) The human gastrointestinal tract. In: Wood BJB (Ed) The Lactic Acid Bacteria, Volume 1, The Lactic Acid Bacteria in Health and Disease (pp 69-114). Elsevier Applied Science, London
Moore WEC, Cato EP & Holdeman LV (1978) Some current concepts in intestinal bacteriology. Am. J. Clin. Nutr. 31: S33-S42
Moore WEC & Holdeman LV (1974) Special problems associated with the isolation and identification of intestinal bacteria in fecal flora studies. Am. J. Clin. Nutr. 27: 1450-1455
Muyzer G & Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leewenhoek 73: 127-141
O'Sullivan DJ (1999) Methods of analysis of the intestinal microflora. In: Tannock GW (Ed) Probiotics: a Critical Review (pp 23-44). Horizon Scientific Press, Wymondham, UK
Pasteur L (1885) Observations relatives a la note precedente de M. Duclaux. Academies des Sciences, Comptes Rendues (Paris) 100: 68
Perdigon G & Alvarez S (1992) Probiotics and the immune state. In: Fuller R (Ed) Probiotics. The Scientific Basis (pp 146-180). Chapman and Hall, London
Raskin L, Capman WC, Sharp R, Poulsen LK & Stahl DA (1997) Molecular ecology of gastrointestinal ecosystems. In: Mackie RI, White BA & Isaacson RE (Eds) Gastrointestinal Microbiology, Volume 2, Gastrointestinal Microbes and Host Interactions (pp 243-298). Chapman and Hall, New York
Reilly K & Attwood GT (1998) Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR. Appl. Environ. Microbiol. 64: 907-913
Rettger LF, Levy MN, Weinstein L & Weiss JE (1935) Lactobacillus acidophilus and its Therapeutic Application. Yale University Press, New Haven, USA
Reysenbach A-L, Giver LJ, Wickham GS & Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58: 3417-3418
Roberton AM & Corfield AP (1999) Mucin degradation and its significance in inflammatory conditions of the gastrointestinal tract. In: Tannock GW (Ed) Medical Importance of the Normal Microflora (pp 222-261). Kluwer Academic Publishers, Dordrecht, The Netherlands
Salyers AA & Whitt DD (1994) Bacterial Pathogenesis. American Society for Microbiology, Washington DC
Savage DC (1977) Microbial ecology of the gastrointestinal tract. Annual Reviews of Microbiology 31: 107-133
Savage DC (1983) Morphological diversity among members of the gastrointestinal microflora. International Review of Cytology 82: 305-334
Savage DC, Dubos R & Schaedler RW (1968) The gastrointestinal epithelium and its autochthonous bacterial flora. J. Exper. Med. 127: 67-76
Schiffrin EJ, Rochat F, Link-Amster H, Aeschlimann JM & Donnet-Hughes A (1995) Immunomodulation of human blood cells following the ingestion of lactic acid bacteria. J. Dairy Sci. 78: 491-497
Severijnen AJ, van Kleef R, Hazenberg MP & van de Merwe J (1989) Cell wall fragments from major residents of the human intestinal flora induce chronic arthritis in rats. J. Rheumatology 16: 1061-1068
Snel J (1997) Symbiosis between the Mouse and Segmented Filamentous Bacteria: a Gnotobiotic Study. PhD thesis, University of Nijmegen
Stackebrandt E & and Rainey FA (1995) Partial and complete 16S rDNA sequences, their use in generation of 16S phylogenetic trees and their implications in molecular ecological studies. In: Akkermans DL, van Elsas JD & de Bruijn FJ (Eds) Molecular Microbial Ecology Manual (pp 1-17). Kluwer Academic Publishers, Dordrecht, The Netherlands
Summanen P, Baron EJ, Citron DM, Strong C, Wexler HM & Finegold SM (1993) Wadsworth Anaerobic Bacteriology Manual. Star Publishing Company, Belmont, USA
Swaminathan B & Matar GM (1993) Molecular typing methods. In: Persing DH, Smith TF, Tenover FC & White TJ (Eds) Diagnostic Molecular Microbiology. Principles and Applications (pp 26-50). American Society for Microbiology, Washington DC
Szentkuti L, Riedesel H, Enss M-L, Gaertner K & von Engelhardt W (1990) Pre-epithelial mucus layer in the colon of conventional and germfree rats. Histochemistry J. 22: 491-497
Tagg JR, Pybus V, Phillips LV & Fiddes TM (1983) Application of inhibitor typing in a study of the transmission and retention in the human mouth of the bacterium Streptococcus salivarius. Archives of Oral Biology 28: 911-915
Tannock GW (1987) Demonstration of mucosa-associated microbial populations in the colons of mice. Appl. Environ. Microbiol. 53: 1964-1968
Tannock GW (1995a) Normal microflora. An introduction to microbes inhabiting the human body. Chapman and Hall, London
Tannock GW (1995b) Microecology of the gastrointestinal tract in relation to lactic acid bacteria. International Dairy J. 5: 1059-1070
Tannock GW (1997) Influences of the normal microbiota on the animal host. In: Mackie RI, White BA & Isaacson RE (Eds) Gastrointestinal Microbiology, Volume 2, Gastrointestinal Microbes and Host Interactions (pp 466-497). Chapman and Hall, New York
Tannock GW (Ed) (1999) Medical Importance of the Normal Microflora. Kluwer Academic Publishers, Dordrecht, The Netherlands
Tannock GW (Ed) (1999) Probiotics: a Critical Review. Horizon Scientific Press, Wymondham, UK
Tannock GW, Crichton C, Welling GW, Koopman JP & Midtvedt T (1988) Reconstitution of the gastrointestinal microflora of lactobacillus-free mice. Appl. Environ. Microbiol. 54: 2971-2975
Tannock GW, Fuller R, Smith SL & Hall MA (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. 28: 1225-1228
Welling GW, Elfferich P, Raangs GC, Wildeboer-Veloo ACM, Jansen GJ & Degener JE (1997) 16S ribosomal RNA-targeted oligonucleotide probes for monitoring of intestinal tract bacteria. Scandanavian J. Gastroenterology 32 Supplement 222: 17-19
Wilson KH & Blitchington RB (1996) Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62: 2273-2278
Zoetendal E, Akkermans AD & De Vos WM (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
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Tannock, G.W. Analysis of the intestinal microflora: a renaissance. Antonie Van Leeuwenhoek 76, 265–278 (1999). https://doi.org/10.1023/A:1002038308506
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DOI: https://doi.org/10.1023/A:1002038308506