A Small In Vitro Fermentation Model for Screening the Gut Microbiota Effects of Different Fiber Preparations

Abstract

The development of prebiotic fibers requires fast high-throughput screening of their effects on the gut microbiota. We demonstrated the applicability of a mictotiter plate in the in vitro fermentation models for the screening of potentially-prebiotic dietary fibers. The effects of seven rye bran-, oat- and linseed-derived fiber preparations on the human fecal microbiota composition and short-chain fatty acid production were studied. The model was also used to study whether fibers can alleviate the harmful effects of amoxicillin-clavulanate on the microbiota. The antibiotic induced a shift in the bacterial community in the absence of fibers by decreasing the relative amounts of Bifidobacteriaceae, Bacteroidaceae, Prevotellaceae, Lachnospiraceae and Ruminococcaceae, and increasing proteobacterial Sutterilaceae levels from 1% to 11% of the total microbiota. The fermentation of rye bran, enzymatically treated rye bran, its insoluble fraction, soluble oat fiber and a mixture of rye fiber:soluble oat fiber:linseed resulted in a significant increase in butyrate production and a bifidogenic effect in the absence of the antibiotic. These fibers were also able to counteract the negative effects of the antibiotic and prevent the decrease in the relative amount of bifidobacteria. Insoluble and soluble rye bran fractions and soluble oat fiber were the best for controlling the level of proteobacteria at the level below 2%.

Keywords: fecal fermentation; fiber preparation; in vitro colon model; inulin; linseed; resistant starch; rye bran.

Figure 1

The bacterial population changes and SCFA accumulation after 48 h fecal fermentation of commercial dietary fiber preparations. (A) The number of main microbial groups as defined by qPCR; (B) the concentration of SCFAs at the end on the fermentation; (C) bacterial community profile at family level. LAC—Lactobacillus group, Bifido—Bifidobacterium spp., BCoAT—butyryl-CoA:acetate CoA-transferase gene; MCC—microcrystalline cellulose, RS—resistant starch, XOS—xylo-oligosaccharide. Values with different letters showed significant differences among the groups (p < 0.05). The samples with inulin were not included in analysis of variance (ANOVA) since only duplicates were available for the analysis.

Figure 2

The bacterial population changes and SCFA accumulation after 48 h fermentation of in-house dietary fiber preparations. (A) The number of main microbial groups as defined by qPCR; (B) the concentration of SCFAs at the end on the fermentation; (C) the bacterial community profile at the family level. LAC—Lactobacillus group, Bifido—Bifidobacterium spp., BCoAT—butyryl-CoA:acetate CoA-transferase gene; MCC—microcrystalline cellulose, LS—linseed, RB—rye bran, EnzRB—enzymatically treated rye bran, Sol EnzRB—soluble fraction of enzymatically treated rye bran, Insol EnzRB—insoluble fraction of enzymatically treated rye bran, SolBG—soluble oat fiber preparation, RF:BG:LS—a mixture of rye fiber:soluble oat fiber preparation:linseed as the ratio of 40:40:20. Values with different letters showed significant differences among the groups (p < 0.05).

Figure 3

The bacterial community profile at family level in the control samples (baseline, no fibers, microcrystalline cellulose) without and with amoxicillin-clavulanate (Ab) after 48 h of incubation. MCC—microcrystalline cellulose; Ab—amoxicillin-clavulanate.

Figure 4

The relative abundance of selected families in the samples with (+AMX, green) and without (−AMX, red) amoxicillin-clavulanate after 48 h of fermentation of RS and experimental fiber preparations. (A) Porphyromonadaceae (p_Bacteroidetes), (B) Peptostreptococcaceae (p_Firmicutes), (C) Sutterellaceae (p_Proteobacteria).