Polysaccharide degradation by human intestinal bacteria during growth under multi-substrate limiting conditions in a three-stage continuous culture system

Abstract Human faecal microorganisms were grown on mixtures of chemically diverse polymerised C-sources (starch, pectin, xylan, mucin, arabinogalactan, inulin, guar gum) in a three-stage continuous culture model of the colon. The effects of retention time (R= 27.1 h, R= 66.7 h) on bacterial populations, their expression of hydrolytic enzymes involved in substrate depolymerisation, carbohydrate utilisation and short chain fatty acid formation were investigated. Eleven bacterial marker groups were studied in the fermenters. Strictly anaerobic bacteria predominated including bacteroides, bifidobacteria, clostridia and anaerobic Gram-positive cocci. Changing system retention time from 27.1 to 66.7 h did not significantly affect the predominant bacterial populations in V1, however, enterobacterial cell numbers increased in V3, while saccharolytic anaerobe recoveries declined markedly, reflecting their greater dependence on polymerised carbon sources in the fermentation system. The majority of polysaccharide degrading activity in the colon model was cell-associated, under all culture conditions. Increasing R from 27.1 to 66.7 h did not substantially change overall polysaccharidase (amylase, polygalacturonanase, xylanase, arabinogalactanase, galactomannanase) profiles, however, synthesis of some glycosidases was enhanced (e.g. α-glucosidase, N-acetyl-β-glucosaminidase, neuraminidase), whereas reduced expression of other enzymes such as β-galactosidase, N-acetyl-α-galactosaminidase, α-fucosidase and α-arabinofuranosidase occurred. These observations demonstrate that catabolite regulation is an important control process in the colonic microbiota, with respect to the induction and repression of enzyme synthesis, and that substrate availability plays a major role in regulating bacterial metabolism. Measurements of carbohydrate utilisation demonstrated that while all polysaccharides in the feed medium were digested extensively by bacteria growing in the fermentation system, specific rates of carbohydrate utilisation were maximal at R= 27.1 h. These data also provided evidence of bacterial substrate preferences in the colon model, particularly in relation to xylan and inulin digestion, demonstrating that catabolite regulatory mechanisms were also involved in controlling the assimilation of carbohydrate in the microbiota. Short chain fatty acid measurements showed that fermentation was more efficient at R= 27.1 h compared to R= 66.7 h, with putative conversion of carboh