Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut

Applied and Environmental Microbiology

Volumn 72, Issue 9, 2006, Pages 6204-6211

  Macfarlane, Sandra ^a,b   Macfarlane, George T ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATES; FERMENTATION; METABOLISM; PHYSIOLOGY; WASTES;

BACTERIAL BIOFILMS; FECAL MATERIAL; HOST DIGESTIVE PROCESSES; METABOLIC ACTIVITIES;

BIOFILMS;

ACETIC ACID; BUTYRIC ACID; CARBOHYDRATE; GALACTOSE; GLUCOSE; LACTOSE; MONOSACCHARIDE; OLIGOSACCHARIDE; RAFFINOSE; SUCROSE; SURFACTANT; XYLOSE;

ANALYTICAL METHOD; BACTERIUM; BIOFILM; CARBOHYDRATE; COLONIZATION; EXPERIMENTAL STUDY; FERMENTATION; FOOD CONSUMPTION; METABOLISM; MICROBIAL ACTIVITY; PHENOTYPE; PHYSIOLOGICAL RESPONSE; POLYSACCHARIDE; SCANNING ELECTRON MICROSCOPY;

ACTINOMYCES; ADULT; AEROBIC BACTERIUM; ANAEROBIC BACTERIUM; ARTICLE; BACILLUS SUBTILIS; BACTERIAL COLONIZATION; BACTERIAL METABOLISM; BACTERIUM ADHERENCE; BACTERIUM COLONY; BACTERIUM IDENTIFICATION; BACTEROIDES; BIFIDOBACTERIUM; BIOFILM; CANDIDA ALBICANS; CARBOHYDRATE METABOLISM; CHEMICAL COMPOSITION; CLOSTRIDIUM; COLON FLORA; COLONY FORMING UNIT; CONFOCAL LASER MICROSCOPY; ESCHERICHIA COLI; EUBACTERIUM; FECES ANALYSIS; FEMALE; FERMENTATION; FILTRATION; FLUORESCENCE IN SITU HYBRIDIZATION; HOST PARASITE INTERACTION; HUMAN; KLEBSIELLA PNEUMONIAE; LACTOBACILLUS; MALE; NONHUMAN; PARTICULATE MATTER; PEPTOSTREPTOCOCCUS; PHENOTYPE; SCANNING ELECTRON MICROSCOPY; STAPHYLOCOCCUS AUREUS;

BACTERIA; BASE SEQUENCE; BIOFILMS; CARBOHYDRATE METABOLISM; DIGESTIVE SYSTEM; DNA PROBES; DNA, BACTERIAL; FECES; FERMENTATION; FOOD MICROBIOLOGY; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSCOPY, CONFOCAL; MICROSCOPY, ELECTRON, SCANNING;

BACTERIA (MICROORGANISMS); BACTEROIDES;

EID: 33748793356     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00754-06     Document Type: Article

References (42)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. 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.
3. Anwar, H., M. K. Dasgupta, and J. W. Costerton. 1990. Testing the susceptibility of bacteria in biofilms to antibacterial agents. Antimicrob. Agents Chemother. 34:2043-2046.
4. Beerens, H. 1990. An elective and selective isolation medium for Bifidobacterium spp. Lett. Appl. Bacteriol. 11:155-157.
5. Bradshaw, D. J., and P. D. Marsh. 2003. Novel microscopic methods to study the structure and metabolism of oral biofilms, p. 173-188. In M. Wilson and D. Devine (ed.), Medical implications of biofilms. Cambridge University Press, Cambridge, United Kingdom.
6. Caldwell, D. R., and M. P. Bryant. 1966. Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl. Microbiol. 14:794-801.
7. Child, M. W., A. Kennedy, B. Bahrami, S. Macfarlane, and G. T. Macfarlane. 2006. Studies on the effect of system retention time on bacterial populations colonising a three-stage continuous culture model of the human large gut using fluorescent in situ hybridisation techniques. FEMS Microbiol. Ecol. 55:299-310.
8. Conrad, R., T. J. Phelps, and J. G. Zeikus. 1985. Gas metabolism evidence in support of the juxtaposition of hydrogen-producing and methanogenic bacteria in sewage sludge and lake sediments. Appl. Environ. Microbiol. 50:595-601.
9. Cummings, J. H., E. R. Beatty, S. M. Kingman, and H. N. Englyst. 1996. Digestion and physiological properties of resistant starch in the human large bowel. Br. J. Nutr. 75:733-747.
10. Cummings, J. H., S. A. Bingham, K. W. Heaton, and M. A. Eastwood. 1993. Fecal weight, colon cancer risk and dietary intake of non-starch polysaccharides (dietary fiber). Gastroenterology 103:1783-1789.
11. Cummings, J. H., and G. T. Macfarlane. 1991. The control and consequences of bacterial fermentation in the human colon-a review. J. Appl. Bacteriol. 70:443-459.
12. Degnan, B. A., and G. T. Macfarlane. 1995. Arabinogalactan utilization in continuous cultures of Bifidobacterium longum: effect of co-culture with Bacteroides thetaiotaomicron. Anaerobe 1:103-112.
13. Duncan, S. H., G. L. Hold, H. J. M. Harmsen, C. S. Stewart, and H. J. Flint. 2002. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 52:2141-2146.
14. Duncan, S. H., K. P. Scott, A. G. Ramsey, H. J. M. Harsen, G. W. Welling, C. S. Stewart, and H. J. Flint. 2003. Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system. Appl. Environ. Microbiol. 69:1136-1142.
15. Englyst, H. N., S. Hay, and G. T. Macfarlane. 1987. Breakdown of resistant and readily digestible starch by human gut bacteria. J. Sci. Food Agric. 37:699-706.
16. Fite, A., G. T. Macfarlane, J. H. Cummings, M. J. Hopkins, S. C. Kong, E. Furrie, and S. Macfarlane. 2004. Identification and quantitation of mucosal and faecal desulfovibrios using real time PCR. Gut 53:523-529.
17. 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 quantified by fluorescence in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64:3336-3345.
18. Gibson, G. R., R. A. Rastall, and R. Fuller. 2003. The health benefits of probiotics and prebiotics, p. 52-76. In R. Fuller and G. Perdigon (ed.), Gut flora, nutrition immunity and health. Blackwell Publishing, Oxford, United Kingdom.
19. Hentges, D. J. 1983. Role of the intestinal flora in host defense against infection, p. 311-332. In D. J. Hentges (ed.), Human intestinal microflora in health and disease. Academic Press, London, United Kingdom.
20. Holdeman, L. V., E. P. Cato, and W. E. C. Moore. 1977. Anaerobe laboratory manual, 4th ed. Virginia Polytechnic Institute and State University, Blacksburg, Va.
21. Hopkins, M. J., G. T. Macfarlane, E. Furrie, A. Fite, and S. Macfarlane. 2005. Characterisation of bacteria in infant's stools using real-time PCR and Northern hybridisation analyses. FEMS Microbiol. Ecol. 54:77-85.
22. Huijsdens, X. W., R. K. Linskens, M. Mak, S. G. Meuwissen, C. M. Vandenbroucke-Grauls, and P. H. Savelkoul. 2002. Quantification of bacteria adherent to gastrointestinal mucosa by real-time PCR. J. Clin. Microbiol. 40:4423-4427.
23. Kruh, J., N. Defer, and L. Tichonicky. 1995. Effects of butyrate on cell proliferation and gene expression, p. 275-288. In J. H. Cummings, J. L. Rombeau, and T. Sakata (ed.), Physiological and clinical aspects of short chain fatty acids. Cambridge University Press, Cambridge, United Kingdom.
24. Langendijk, P. S., F. Schut, G. J. Jansen, G. C. Raangs, G. R. Kamphuis, M. H. F. Wilkinson, and G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61:3069-3075.
25. Loge, F. J., R. W. Emerick, D. E. Thompson, D. C. Nelson, and J. L. Darby. 1999. Development of a fluorescent 16S rRNA oligonucleotide probe specific to the family Enterobacteriaceae. Water Environ. Res. 71:75-83.
26. Macfarlane, G. T., and J. H. Cummings. 1991. The colonic flora, fermentation and large bowel digestive function, p. 51-92. In S. F. Phillips, J. H. Pemberton, and R. G. Shorter (ed.), The large intestine: physiology, pathophysiology and disease. Raven Press, New York, N.Y.
27. Macfarlane, G. T., and G. R. Gibson. 1996. Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine, p. 269-318. In R. I. Mackie and B. A. White (ed.), Ecology and physiology of gastrointestinal microbes, vol. 1. Gastrointestinal fermentations and ecosystem. Chapman & Hall, New York, N.Y.
28. Macfarlane, G. T., S. Hay, S. Macfarlane, and G. R. Gibson. 1990. Effect of different carbohydrates on growth, polysaccharidase and glycosidase production by Bacteroides ovatus, in batch and continuous culture. J. Appl. Bacteriol. 68:179-187.
29. Macfarlane, G. T., and S. Macfarlane. 1995. Human intestinal biofilm communities, p. 83-89. In J. Wimpenny, P. Handley, P. Gilbert, and H. Lappin-Scott (ed.), The life and death of biofilms. Bioline, University of Wales College of Cardiff, Cardiff, United Kingdom.
30. Macfarlane, S., E. Furrie, J. H. Cummings, and G. T. Macfarlane. 2004. Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis. Clin. Infect. Dis. 38:1690-1699.
31. Macfarlane, S., M. J. Hopkins, and G. T. Macfarlane. 2000. Bacterial growth and metabolism on surfaces in the large intestine. Microb. Ecol. Health Dis. 2:64-72.
32. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K. H. Schleifer. 1996. 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 142:1097-1106.
33. McBain, A. J., and G. T. Macfarlane. 1998. Ecological and physiological studies on large intestinal bacteria in relation to production of hydrolytic and reductive enzymes involved in formation of genotoxic metabolites. J. Med. Microbiol. 47:407-416.
34. Microbial ID Inc. 1992. Microbial Identification system operational manual. Microbial ID Inc., Newark, Del.
35. Mozes, N., and P. G. Rouxhet. 1992. Influence of surfaces on microbial activity, p. 125-136. In L. Melo, F. T. R. Bott, and B. Capdeville (ed.), Biofilms-science and technology. Kluwer Academic Publishers, Dordrecht, The Netherlands.
36. Nadkarni, M. A., F. E. Martin, N. A. Jacques, and N. Hunter. 2002. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148:257-266.
37. Poxton, I. R., R. Brown, A. Sawyer, and A. Ferguson. 1997. Mucosa-associated bacterial flora of the human colon. J. Med. Microbiol. 46:85-91.
38. Roediger, W. E. W. 1980. The colonic epithelium in ulcerative colitis: an energy-deficiency disease? Lancet ii:712-715.
39. Schiffrin, E. J., D. Brassart, A. L. Servin, F. Rochart, and A. Donnet-Hughes. 1997. Immune modulation of blood leukocytes in humans by lactic acid bacteria: criteria for strain selection. Am. J. Clin. Nutr. 66:515S-520S.
40. Stephen, A. M., and J. H. Cummings. 1980. The microbial contribution to human faecal mass. J. Med. Microbiol. 13:45-56.
41. Swidsinski, A., A. Ladhoff, A. Pernthaler, S. Swidsinski, V. Loening-Baucke, M. Ortner, J. Weber, U. Hoffmann, S. Screiber, M. Dietel, and H. Lochs. 2002. Mucosal flora in inflammatory bowel disease. Gastroenterology 122:44-54.
42. Van Loosdrecht, M. C. M., J. Lyklema, W. Norde, and A. J. B. Zehnder. 1990. Influence of interfaces on microbial activity. Microbiol. Rev. 54:75-87.