Development of a Six-Stage Culture System for Simulating the Gastrointestinal Microbiota of Weaned Infants

References

• Falk PG, Hooper LV, Midtvedt T, Gordon JI. Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol. Mol. Biol. Rev. 1998; 62 (4): 1157–70.
   PubMed Web of Science ®Google Scholar
• Cooperstock MS, Zedd AJ. Intestinal flora of infants. In: Hentges DJ, ed. Human Intestinal Flora in Health and Dis-ease. New York: Academic Press, 1983: 79–99.
   Google Scholar
• Stark PL, Lee A. Microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life. J. Med. Microbiol. 1982; 15: 189–203.
   PubMed Web of Science ®Google Scholar
• Balmer SE, Wharton BA. Diet and faecal flora in the new-born: iron. Arch. Dis. Child. 1991; 66 (12): 1390–4.
   Web of Science ®Google Scholar
• Bullen CL, Tearle PV, Stewart MG. The effect of humanised milks and supplemented breast feeding on the faecal flora of infants. J. Med. Microbiol. 1977; 9: 325–33.
   Google Scholar
• Conway P. Development of intestinal microbiota. In: Mackie RI, White BA, Isaacson RE, eds. Gastrointestinal Microbiol-ogy. New York: Chapman & Hall, 1997: 3–38.
   Google Scholar
• Simon G, Gorbach SL. Normal alimentary tract microflora. In: Blaser MJ, Smith PD, Ravdin JI, Greenberg HB, Guer-rant RL, eds. Infections of the Gastrointestinal Tract. New York: Raven Press, 1995: 53–69.
   Google Scholar
• Holzapfel WH, Haberer P, Snel J, Schillinger U, Huis in't Veld JHJ. Overview of gut flora and probiotics. Int. J. Food Microbiol. 1998; 41: 85–101.
   PubMed Web of Science ®Google Scholar
• Roediger WE, Moore J, Babidge W. Colonic sulfide in patho-genesis and treatment of ulcerative colitis. Digest. Dis. Sci. 1997; 42 (8): 1571–9.
   Google Scholar
• Bartram HP, Kasper K, Dusel G, Liebscher E, Gostner A, Loges C, et al. Effects of calcium and deoxycholic acid on human colonic cell proliferation in vitro. Ann. Nutr. Metabol. 1997; 41: 315–25.
   PubMed Web of Science ®Google Scholar
• Macfarlane GT, Macfarlane S. Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bac-teria. Scand. J. Gastroenterol. 1997; 32 (suppl. 222): 3–9.
   Google Scholar
• Rumney CJ, Rowland IR. In vivo and in vitro models of the human colonic flora. Crit. Rev. Food Sci. Nutr. 1992; 31(4): 299–331.
   PubMed Web of Science ®Google Scholar
• Macfarlane S, Quigley ME, Hopkins MJ, Newton DF, Mac-farlane GT. Polysaccharide degradation by human intestinal bacteria during growth under multi-substrate limiting condi-tions in a three-stage continuous culture system. FEMS Mi-crobiol. Ecol. 1998; 26: 231–43.
   Google Scholar
• Macfarlane GT, Macfarlane S, Gibson GR. Validation of a three-stage compound continuous culture system for investi-gating the effect of retention time on the ecology and metabolism of bacteria in the human colon. Microb. Ecol. 1998; 35: 180–7.
   Google Scholar
• Macfarlane GT, Cummings JH, Macfarlane S, Gibson GR. Influence of retention time on degradation of pancreatic enzymes by human colonic bacteria grown in a 3-stage contin-uous culture system. J. Appl. Bacteriol. 1989; 67 (5): 520–7.
   Google Scholar
• Macfarlane GT, Hay S, Gibson GR. Influence of mucin on glycosidase, protease and arylamidase activities of human gut bacteria grown in a 3-stage continuous culture system. J. Appl. Bacteriol. 1989; 66 (5): 407–17.
   Google Scholar
• Minekus M, Smeets-Peeters M, Bernalier A, Marol-Bonnin S, Havenaar R, Marteau P, et al. A computer-controlled system to simulate conditions of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products. Appl. Microbiol. Biotechnol. 1999; 53: 108–14.
   PubMed Web of Science ®Google Scholar
• Parrett AM, Edwards CA. In vitro fermentation of carbohy-drate by breast fed and formula fed infants. Arch. Dis. Child. 1997; 76: 249–53.
   Web of Science ®Google Scholar
• Lifschitz CH, Wolin MJ, Reed J. Characterisation of carbo-hydrate fermentation in faeces of formula fed and breast fed infants. Pediatr. Res. 1990; 27: 163–9.
   Google Scholar
• Rasmussen HS, Holtug K, Ynggärd K, Mortensen PB. Faecal concentrations and production rates of short chain fatty acids in normal neonates. Acta Pediatr. Scand. 1988; 77: 365–8.
   Google Scholar
• Garland JL, Mills AL. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl. En-viron. Microbiol. 1991; 57: 2351–9.
   PubMed Web of Science ®Google Scholar
• Glimm E, Heuer H, Engelen B, Smalla K, Backhaus H. Statistical comparisons of community catabolic profiles. J. Microbiol. Methods 1997; 30: 71–80.
   Google Scholar
• Verschuere L, Dhont J, Sorgeloos P, Verstraete W. Monitor-ing Biolog patterns and r/K strategists in the intensive culture of Artemiai juveniles. J. Appl. Microbiol. 1997; 83: 603–12.
   Web of Science ®Google Scholar
• Hueur H, Smalla K. Evaluation of community-level catabolic profiling using BIOLOG GN microplates to study microbial community changes in potato phyllosphere. J. Microbiol. Methods 1997; 30: 49–61.
   Web of Science ®Google Scholar
• Boon N, Marie C, Top E, Verstraete W. Comparison of the spatial homogeneity of physico-chemical parameters and bac-terial 16S rRNA genes in sediment samples of a dumping site of dredging sludge. Appl. Microbiol. Biotechnol. 2000; 53: 742–7.
   Web of Science ®Google Scholar
• El Fantroussi S, Verschuere L, Verstraete W, Top EM. Effect of phenylurea herbicides on soil microbial communities esti-mated by analysis of 16S rRNA gene fingerprints and com-munity-level physiological profiles. Appl. Environ. Microbiol. 1999; 65: 982–8.
   PubMed Web of Science ®Google Scholar
• Ovreas L, Forney L, Daae FL, Torsvik V. Distribution of bacterioplankton in meromictic lake Saelevannet, as deter-mined by denaturing gradient gel electrophoresis of PCR-am-plified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 1997; 63: 3367–73.
   PubMed Web of Science ®Google Scholar
• Muyzer G, de Waal EC, Uitterlinden A. Pofiling of complex microbial populations using denaturing gradient gel elec-trophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Microbiol. Biotechnol. 1993; 59: 695–700.
   Web of Science ®Google Scholar
• Muyzer G, Hottenträger S, Teske A, Wawer C. Denaturing gradient gel electrophoresis of PCR amplified 16S rDNA-a new molecular approach to analyse the genetic diversity of mixed microbial communities. Mol. Microb. Ecol. Manual 1996; 3: 1–23.
   Google Scholar
• Norin KE, Carlstedt-Duke B, Höverstad D, Lingaas E, Sax-erholt H, Steinbakk M, et al. Faecal tryptic activity in hu-mans: influence of antibiotics on microbial intestinal degradation. Microb. Ecol. Health Dis. 1988; 1: 65–8.
   Google Scholar
• Nollet L, Demeyer D, Verstraete W. Effect of 2-bromoethane-sulfonic acid and Peptostreptoccus productus ATCC 35244 addition on stimuation of reductive acetogenesis in the rumi-nal ecosystem by selective inhibition of methanogenesis. Appl. Environ. Microbiol. 1997; 63 (1): 194–200.
   Google Scholar
• Bremner JM, Keeney RD. Steam distillation methods for determination of ammonium, nitrate and glycine. Anal. Chem. Acta 1965; 32: 485–95.
   Web of Science ®Google Scholar
• Molly K, Vande Woestyne M, De Smet I, Verstraete W. Validation of the simulator of the human intestinal microbial ecosystem (SHIME) reactor using microorganism-associated activities. Microb. Ecol. Health Dis. 1994; 7: 191–200.
   Web of Science ®Google Scholar
• Molly K, Vande Woestyne M, Verstraete W. Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem. Appl. Microbiol. Biotechnol. 1993; 39 (2): 254–8.
   PubMed Web of Science ®Google Scholar
• Macfarlane GT, Gibson GR, Cummings JH. Comparison of fermentation reactions in different regions of the human colon. J. Appl. Bacteriol. 1992; 72 (1): 57–64.
   Google Scholar
• Guérin-Danan C, Popot AF, Vaissade ACP, Gaudichon C, Pedone C, Bouley C, et al. Pattern of metabolism and compo-sition of the faecal microflora in infants 10 to 18 months old from day care centers. J. Pediatr. Gastroenterol. Nutr. 1997; 25: 281–9.
   Google Scholar
• Weaver LT, Steiner H. The bowel habit of young children. Arch. Dis. Child. 1984; 59: 649–52.
   PubMed Web of Science ®Google Scholar
• Walker AR, Walker BF. Bowel behaviour in young black and white children. Arch. Dis. Child. 1985; 60: 967–70.
   Web of Science ®Google Scholar
• McClure RJ, Newell SJ. Randomised controlled trial of trophic feeding and gut motility. Arch. Dis. Child. Fetal Neonat. Edition 1999; 80: F54–8.
   PubMed Web of Science ®Google Scholar
• Gibson GR, Cummings JH, Macfarlane GT. Use of a three-stage continuous culture system to study the effect of mucin on dissimilatory sulfate reduction and methanogenesis by mixed populations of human gut bacteria. Appl. Environ. Microbiol. 1988; 54 (11): 2750–5.
   Google Scholar
• Cummings JH, Macfarlane GT. The control and conse-quences of bacterial fermentation in the human colon. J. Appl. Microbiol. 1991; 70: 443–59.
   Web of Science ®Google Scholar
• Vonk RJ, Kalivianakis M, Minich DM, Bijleveld CMA, Verkade HJ. The metabolic importance of unabsorbed dietary lipids in the colon. Scand. J. Gastroenterol. 1997; 32 (suppl. 2): 65–7.
   Google Scholar
• Silvester KR, Cummings JH. Does digestibility of meat protein help explain large bowel cancer risk. Nutr. Cancer 1995; 24: 279–88.
   PubMed Web of Science ®Google Scholar
• Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 1999; 69: 1035S–45S.
   Google Scholar
• Shimamura S, Abe F, Ishibashi N, Miyakawa H, Yaeshiwa T, Araya T, et al. Relationship between oxygen sensitivity and oxygen metabolism of Bifidobacterium sp. Journal Dairy Sci. 1992; 75 (12): 3296–306.
   PubMed Web of Science ®Google Scholar
• Zoetendal EG, Akkermans ADL, De Vos WM. Temperature gradient gel electrophoresis analysis of 16S rRNA from hu-man fecal samples reveals stable and host-specific communi-ties of active bacteria. Appl. Environ. Microbiol. 1998; 64 (10): 3854–9.
   Google Scholar
• Walter J, Tannock GW, Tilsala-Timisjarvi A, Rodtong S, Loach DM, Munro K, et al. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gra-dient gel electrophoresis and species-specific PCR primers. Appl. Environ. Microbiol. 2000; 66 (1): 297–303.
   Google Scholar
• Smalla K, Wachtendorf U, Heuer H, Liu W-T, Forney L. Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Appl. Environ. Microbiol. 1998; 64 (4): 1220–5.
   Google Scholar
• Simpson JM, McCracken V.T, White BA, Gaskins HR, Mackie RI. Application of denaturing gradient gel elec-trophoresis for the analysis of the porcine gastrointestinal microbiota. J. Microbiol. Methods 1999; 36: 167–79.
   Google Scholar
• Heavey PM, Rowland IR. The gut microflora of the develop-ing infant: microbiology and metabolism. Scand. J. Gastroen-terol. 1999; 11: 75–83.
   Google Scholar
• Midtvedt AC, Midtvedt T. Production of short chain fatty acids by the intestinal microflora during the first 2 years of human life. J. Pediatr. Gastroenterol. Nutr. 1992; 15: 395–403.
   Web of Science ®Google Scholar
• Miller TL, Wolin MJ. Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora. Appl. Environ. Microbiol. 1992; 62 (5): 1589–92.
   Google Scholar
• Siigur U, NorM KE, Allgoods G, Schlagheck T, Midtvedt T. Concentrations and correlations of faecal short-chain fatty acids and faecal water content in man. Microb. Ecol. Health Dis. 1994; 7: 287–94.
   Google Scholar
• Nollet L, Verstraete W. Gastro-enteric methane versus sul-phate and volatile fatty acid production. Environ. Monit. Asses. 1996; 42: 117–36.
   Web of Science ®Google Scholar
• Demeyer D, Piattoni F, Mbanzamihigo L, Immig I, Nollet L. Alternative hydrogen sink pathways in hindgut fermentation. Reprod. Nutr. Dev. 1997 (suppl. 1): 67–8.
   Google Scholar
• Piveteau P. Metabolism of lactate and sugars by dairy propi-onibacteria: a review. Lait 1999; 79 (1): 23–41.
   Google Scholar
• Rogosa M. Section 8 Anaerobic Gram negative cocci. In: Krieg NR, Holt JG, eds. Bergey's Manual of Systematic Bacteriology. Baltimore: Williams & Wilkins, 1984: 680–5.
   Google Scholar
• Hino T, Shimada K, Maruyama T. Substrate preference in a strain of Megaspaera elsdenii, a ruminal bacterium, and its implication in propionate production and growth competi-tion. Appl. Environ. Microbiol. 1994; 60 (6): 1827–31.
   Google Scholar
• Janssen PH. Isolation of Clostridium prop ionicum strain 19acry3 and further characteristics of the species. Arch. Mi-crobiol. 1991; 155: 566–71.
   Web of Science ®Google Scholar