Effect of inulin, resistant dextrin, and spermidine on the gut microbiome using Gut3Gel Gradient Colonic as an in vitro substrate

Abstract

The gut microbiome plays an important role in metabolism, immune system regulation, and digestion. Its dysregulation has been implicated to play a role in various diseases both digestive and neurological. The modulation and understanding of our gut microbiome is therefore a highly researched topic. One way to modulate our gut microbiome is through food supplements and ingestion of prebiotics. Prebiotics are host-indigestible compounds that gut bacteria can ferment, breaking them down to short chain fatty acids (SCFAs) which can be absorbed by the host. Research into the effect of these compounds on the gut microbiome is often performed in clinical setting since many bacterial species from our gastrointestinal tract are not culturable in vitro. However, in vivo studies can be limited in their accessibility to the direct site of fermentation and difficulty in performing assays such as SCFA analysis, both essential to elucidating the supplement induced changes in the complex interplay of the gut microbiome. In this study a novel in vitro substrate was used called Gut3Gel Gradient Colonic (G3GC) (Bac3Gel Lda). G3GC is an hydrogel mucus based in vitro substrate that can sustain a wide variety of bacteria by mimicking several key features of human gastrointestinal tract mucus, such as its chemical properties, viscoelastic properties, and gradient structure. Using this substrate the effects of three nutraceuticals, inulin (from chicory root), resistant dextrin (Nutriose FB®), and spermidine (Sprevive®), on the gut microbiome of various donors was studied. Microbiome composition was determined using 16S rRNA gene amplicon sequencing. No statistically significant changes across treatments were found in terms of changes in alpha diversity however beta diversity analysis revealed high variability in pre-treatment microbiome compositions across the donors. Through differential abundance analysis, for both inulin and spermidine treated samples changes in abundance for several bacterial genera were found that are in accordance with previously detected clinical results. For inulin an increased abundance of Bifidobacterium, Lactobacillus, and Pediococcus was detected and a decrease in abundance of Veillonella. For spermidine a decrease in Leuconostoc, which belongs to the Firmicutes phylum, was observed. Resistant dextrin supplementation led to no significant changes in bacterial genera abundance, however this could be due to the effect of using frozen patient samples on the microbial viability. In summary, this study highlights the suitability of G3GC as an in vitro substrate for gut microbiome research and supplementation studies. It also reveals the high intervariability of donors thought to be a likely factor in determining responses to nutraceutical supplementation.