Human Colonic Microbiota: Ecology, Physiology and Metabolic Potential of Intestinal Bacteria

REFERENCES

• Savage DC. Microbial ecology of the gastrointestinal tract. Ann Rev Microbiol 1977;31: 107–33.
   PubMed Web of Science ®Google Scholar
• Cummings JH, Bingham SA, Heaton KW, Eastwood MA. Fecal weight, colon cancer risk and dietary intake of non-starch polysaccharides (dietary fiber). Gastroenterology 1993;103: 1783–9.
   Web of Science ®Google Scholar
• Cummings JH. Diet and transit through the gut. J Plant Foods 1978;3: 83–95.
   Google Scholar
• Banwell JG, Branch WJ, Cummings JH. The microbial mass in the human large intestine. Gastroenterology 1981;80: 1104.
   Web of Science ®Google Scholar
• Cummings JH, Banwell JG, Englyst HN, Coleman N, Segal I, Bersohn D. The amount and composition of large bowel contents. Gastroenterology 1990;98: A408.
   Google Scholar
• Stephen AM, Cummings JH. The microbial contribution to human faecal mass. J Med Microbiol 1980;13: 45–56.
   PubMed Web of Science ®Google Scholar
• Croucher SC, Houston AP, Bayliss CE, Turner RJ. Bacterial populations associated with different regions of the human colon wall. Appi Environ Microbiol 1983;45: 1025–33.
   PubMed Web of Science ®Google Scholar
• Macfarlane S, McBain AJ, Macfarlane GT. Consequences of biofilm and sessile growth in the large intestine. Adv Dent Res. In press.
   Google Scholar
• Freter R. Mechanisms that control the microflora. In: Hentges DJ, editor. Human intestinal microflora in health and disease. London: Academic Press 1983: 35–54.
   Google Scholar
• Macfarlane GT, Cummings JH. The colonic flora, fermentation, and large bowel function. In: Phillips SF, Pemberton JH, Shorter RG, editors. The large intestine, physiology, pathophysiology and disease. New York: Raven Press 1991: 51–92.
   Google Scholar
• Macfarlane GT, Gibson GR. Co-utilization of polymerized carbon sources by Bacteroides ovatus grown in a two-stage continuous culture system. Appl Environ Microbiol 1991;57: 1–6.
   PubMed Web of Science ®Google Scholar
• Degnan BA, Macfarlane GT. Carbohydrate utilization patterns and substrate preferences in Bacteroides thetaiotaomicron. Anaerobe 1995;1: 25–33.
   PubMed Web of Science ®Google Scholar
• Macfarlane GT, Degnan BA. Catabolite regulatory mechanisms in relation to polysaccharide breakdown and carbohydrate utilization. In: Malkki Y, editor. Dietary fibre and the human colon. COST 92. In press.
   Google Scholar
• Macfarlane GT. Fermentation reactions in the large intestine. In: Cummings JH, Rombeau JL, Sakata T, editors. Short chain fatty acids: metabolism and clinical importance. Columbus: Ross Laboratories Press 1991: 5–10.
   Google Scholar
• Macfarlane GT, Gibson GR, Cummings JH. Comparison of fermentation reactions in different regions of the colon. J Appl Bacteriol 1992;72: 57–64.
   PubMedGoogle Scholar
• Cummings JH, Pomare EW, Branch WJ, Naylor CPE, Macfarlane GT. Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut 1987;28: 1221–7.
   PubMed Web of Science ®Google Scholar
• Macfarlane GT, Gibson GR, Macfarlane S. Short chain fatty acid and lactate production by human intestinal bacteria grown in batch and continuous culture. In: Binder HJ, Cummings JH, Soergel KH, editors. Short chain fatty acids. London: Kluwer 1994: 44–60.
   Google Scholar
• Cummings JH, Gibson GR, Macfarlane GT. Quantitative estimates of fermentation in the hind gut of man. Acta Vet Scand 1989;86: 76–82.
   Google Scholar
• Macfarlane GT, Gibson GR, Drasar BS, Cummings JH. Metabolic significance of the colonic microflora. In: Whitehead R, editor. Gastrointestinal and oesophageal physiology. Edinburgh: Churchill Livingstone 1995: 249–74.
   Google Scholar
• Cummings JH. Short chain fatty acids. In: Gibson GR, Macfarlane GT, editors. Human colonic bacteria: role in nutrition, physiology and pathology. Boca Raton: CRC Press 1995: 101–30.
   Google Scholar
• Macfarlane GT, Englyst HN. Starch utilization by the human large intestinal microflora. J Appl Bacteriol 1986;60: 195–201.
   PubMedGoogle Scholar
• Etterlin C, McKeown A, Bingham SA, Elia M, Macfarlane GT, Cummings JH. D-Lactate and acetate as markers of fermentation in man. Gastroenterology 1992;102: A551.
   Google Scholar
• Macfarlane GT, Gibson GR. Metabolic activities of the normal colonic flora. In: Gibson SAW, editor. Human health: the contribution of microorganisms. London: Springer Verlag 1994: 17–52.
   Google Scholar
• Gibson GR, Macfarlane GT, Cummings JH. Occurrence of sulphate-reducing bacteria in human faeces and the relationship of dissimilatory sulphate reduction to methanogenesis in the large gut. J Appl Bacteriol 1988;65: 103–11.
   PubMedGoogle Scholar
• Gibson GR, Cummings JH, Macfarlane GT. Competition for hydrogen between sulphate-reducing bacteria and methanogenic bacteria from the human large intestine. J Appl Bacteriol 1988; 65: 241–7.
   PubMedGoogle Scholar
• Lajoie SF, Bank S, Miller TL, Wolin MJ. Acetate production from hydrogen and [13C] carbon dioxide by the microflora of human feces. Appl Environ Microbiol 1988;54: 2723–7.
   PubMed Web of Science ®Google Scholar
• Nagase M, Matsuo T. Interactions between amino acid degrading bacteria and methanogenic bacteria in anaerobic digestion. Biotechnol Bioeng 1982;24: 2227–39.
   PubMed Web of Science ®Google Scholar
• Allison C, Macfarlane GT. Dissimilatory nitrate reduction by Propionibacterium acnes. Appl Environ Microbiol 1989;55: 2889–903.
   Web of Science ®Google Scholar
• Macfarlane GT, Cummings JH, Allison C. Protein degradation by human intestinal bacteria. J Gen Microbiol 1986;132: 1647–56.
   PubMedGoogle Scholar
• Macfarlane GT, Macfarlane S. Utilization of pancreatic trypsin and chymotrypsin by proteolytic and non-proteolytic Bacteroides fragilis type bacteria. Curr Microbiol 1991;23: 143–8.
   Web of Science ®Google Scholar
• Macfarlane S, Macfarlane GT. Proteolysis and amino acid fermentation. In: Gibson GR, Macfarlane GT, editors. Human colonic bacteria: role in nutrition, physiology and pathology. Boca Raton: CRC Press 1991;1995: 75–100.
   Google Scholar
• Macfarlane GT, Allison C, Gibson SAW, Cummings JH. Contribution of the microflora to proteolysis in the human large intestine. J Appl Bacteriol 1988;64: 37–6.
   PubMedGoogle Scholar
• Holdeman LV, Cato EP, Moore WEC, editors. Anaerobic laboratory manual, 4th ed. Blacksburg: Virginia Polytechnic Institute Anaerobe Laboratory 1977.
   Google Scholar
• Barker HA. Amino acid degradation by anaerobic bacteria. Ann Rev Biochem 1981;50: 23–40.
   PubMed Web of Science ®Google Scholar
• Nisman B. The Stickland reaction. Bacteriol Rev 1954;1: 16–42.
   Google Scholar
• Stams AJM, Hansen TA. Fermentation of glutamate and other compounds by Acidaminobacter hydrogenoformans gen. nov., sp. nov., an obligate anaerobe isolated from black mud. Studies with pure cultures and mixed cultures with sulfate-reducing and methanogenic bacteria. Arch Microbiol 1984;137: 329–37.
   Google Scholar
• Macfarlane GT, Allison C. Utilization of protein by human gut bacteria. FEMS Microbiol Ecol 1986;38: 19–24.
   Web of Science ®Google Scholar
• Macfarlane GT, Gibson GR, Beatty E, Cummings JH. Estimation of short chain fatty acid production from protein by human intestinal bacteria, based on branched chain fatty acid measurements. FEMS Microbiol Ecol 1992;101: 81–8.
   Web of Science ®Google Scholar
• Wilson DR, Ing TS, Metcalfe-Gibson A, Wrong OM. In vivo dialysis of faeces as a method of stool analysis. III. The effect of intestinal antibiotics. Clin Sci 1968;24: 211–21.
   Google Scholar
• Wrong OM, Vince AJ, Waterlow JC. The contribution of endogenous urea to faecal ammonia in man, determined by 15N-labelling of plasma urea. Clin Sci 1985;68: 193–9.
   PubMed Web of Science ®Google Scholar
• Visek WJ. Effects of urea hydrolysis on cell life-span and metabolism. Fed Proc 1972;31: 1760–5.
   Google Scholar
• Visek WJ. Diet and cell growth modulation by ammonia. Am J Clin Nutr 1978;31: S216–S220.
   PubMed Web of Science ®Google Scholar
• Weber FL, Banwell JG, Fresard KM, Cummings JH. Nitrogen in fecal bacteria, fiber and soluble fractions of patients with cirrhosis: effects of lactulose and lactulose plus neomycin. J Lab Clin Med 1987;110: 259–63.
   PubMed Web of Science ®Google Scholar
• Smith EA, Macfarlane GT. Enumeration of human colonic bacteria producing phenolic and indolic compounds: effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism. J Appl Bacteriol 1996;81: 288–302.
   PubMedGoogle Scholar
• Ramakrishna BS, Gee D, Weiss A, Pannall P, Robert-Thomas IC, Roediger WEW. Estimation of phenolic conjugation by colonic mucosa. J Clin Pathol 1989;42: 620–3.
   PubMed Web of Science ®Google Scholar
• Schmidt EG. Urinary phenols. Simultaneous determination of phenol and p-cresol in urine. J Biol Chem 1949;179: 211–5.
   PubMed Web of Science ®Google Scholar
• Cummings JH, Hill MJ, Bone ES, Branch WJ, Jenkins DJA. The effect of meat protein and dietary fiber on colonic function and metabolism. Part II. Bacterial metabolites in faces and urine. Am J Clin Nutr 1979;32: 2094–101.
   PubMed Web of Science ®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 continuous culture system. J Appl Bacteriol 1989;67: 521–7.
   Google Scholar
• Horning EC, Dalgleish DE. The association of skatole forming bacteria in the small intestine with the malabsorption syndrome and certain anaemias. Biochem J 1958;70: 13–14P.
   Web of Science ®Google Scholar
• Dalgliesh CE, Kelley W, Horning EC. Excretion of a sulphatoxyl derivative of skatole in pathological states in man. Biochem J 1958;70: 13 p.
   Web of Science ®Google Scholar
• Carlson JR, Yokohama MT, Dickenson EO. Induction of pulmonary edema and emphysema in cattle and goats with 3- methylindole. Science 1972;176: 298–9.
   PubMed Web of Science ®Google Scholar
• Yokohama MT, Tabori C, Miller ER, Hogberg MG. The effects of antibiotics in the weanling pig diet on growth and excretions of volatile phenolic and aromatic bacterial metabolites. Am J Clin Nutr 1982;35: 1417–24.
   PubMed Web of Science ®Google Scholar
• Gale EF. The bacterial amino acid decarboxylases. Adv Enzymol 1946;6: 1–32.
   Google Scholar
• Johnson KA. The production of secondary amines by human gut bacteria and its possible relevance to carcinogenesis. Med Lab Sci 1977;34: 131–43.
   PubMedGoogle Scholar
• White Tabor C, Tabor H. Polyamines in microorganisms. Microbiol Rev 1985;49: 81–99.
   PubMedGoogle Scholar
• Drasar BS, Hill MJ. Human intestinal microflora. London: Academic Press 1974.
   Google Scholar
• Phear EA, Ruebner B. The in vitro production of ammonium and amines by intestinal bacteria in relation to nitrogen toxicity as a factor in hepatic coma. Br J Exp Path 1956;37: 253–62.
   PubMedGoogle Scholar
• Shephard SE, Schlatter C, Lutz WK. N-Nitrosocompounds: relevance to human cancer. In: Battels H, O'Neill IK, Herman RS, editors. IARC Scientific Publications No, 57. Lyons: International Agency for Research on Cancer Scientific Publications 1987: 328–32.
   Google Scholar
• Calmels S, Ohshima H, Vincent P, Gounot AM, Bartsch H. Screening of microorganisms for nitrosation catalysis at pH 7 and kinetic studies on nitrosamine formation from secondary amines by E. coli strains. Carcinogenesis 1985;6: 911–5.
   PubMed Web of Science ®Google Scholar
• Fine DH, Ross R, Roonbehler DP, Silvergleid A, Song L. Formation in vivo of volatile nitrosamines in man after ingestion of cooked bacon and spinach. Nature 1977;265: 753–5.
   PubMed Web of Science ®Google Scholar
• McNeil NI, Cummings JH, James WPT. Short chain fatty acid absorption by the human large intestine. Gut 1978;19: 819–22.
   PubMed Web of Science ®Google Scholar
• Anon. Headache, tyramine, serotonin and migraine. Nutr Rev 1968;26: 40–4.
   Google Scholar
• Boulton AA, Cookson B, Paulton R. Hypertensive crisis in a patient on MAOI antidepressants following a meal of beef liver. CMAJ 1970;102: 1395.
   Google Scholar
• Murray KE, Shaw KJ, Adams RF, Conway PL. Presence of N- acyl and acetoxy derivatives of putrescine and cadaverine in the human gut. Gut 1993;34: 489–93.
   PubMed Web of Science ®Google Scholar
• Allison C, Macfarlane GT. Influence of pH, nutrient availability, and growth rate on amine production by Bacteroides fragilis and Clostridium perfringens. Appl Environ Microbiol 1989;55: 2894–8.
   PubMed Web of Science ®Google Scholar
• Brookes JB, Moore WEC. Gas chromatographic analysis of amines and other compounds produced by several species of Clostridium. Can J Microbiol 1969;15: 1433–7.
   PubMed Web of Science ®Google Scholar