Prebiotic effects of whole plant-based extracts on the human colonic microbiome using a novel in vitro model (MiGut)

The gut microbiome plays an important role in human health, with evidence suggesting that plant-based extracts (PBEs) serve as prebiotics to modulate composition and function of microbiota (1) . This study aimed to investigate the effects of three commercially available water-based extracts—pomegranate (Pomanox®) and lemon (Wellemon®), rich in polyphenolic compounds, and artichoke (Cynamed®), a source of inulin known to enhance the growth and functionality of beneficial microbes (2) . Limited research exists on longer term specific effects of whole food extracts on gut microbiota. Commercial PBEs were digested using the INFOGEST in vitro batch digestion protocol, to simulate digestion from mouth to small intestine (3) . Digested products were used to supplement a previously validated human gut model (MiGut) that simulates different regions of the human colon (4) . Use of INFOGEST coupled with 8 MiGut models, that included two replicates for each PBE and two negative control models (no supplementation), allowed for us to assess the effect of PBEs against one human donor, for comparative analysis with reliability. Post two-week equilibrium period, models were dosed daily with manufacturer recommended amount of in vitro digested PBE for two weeks, before two-week recovery phase. Samples were collected thrice weekly. Quantitative PCR revealed that all three prebiotic treatments induced significant selective alterations in proximal and distal colon, when compared to the end of steady state (before treatment), Wellemon and Cynamed improved growth of beneficial bacteria – Bifidobacterium spp. in both regions (5.28 and 5.26 in proximal and 2.9 and 4.1 log2FC in distal colon respectively, p < 0.05), only Pomanox stimulated growth of Enterobacteriaceae across both regions (proximal 2.8 and distal 5.7 log2FC) whilst only Wellemon induced a significant increase in Prevotella spp. in proximal colon (5.7 log2FC, p < 0.05). Further changes were displayed through a significant decrease in C. leptum in distal colon after treatment with Pomanox and Cynamed (-3.3 and -2.4 log2FC respectively). Total Eubacteria counts were increased in proximal region after supplementation with all three PBEs (1.8-3.7 log2FC). No significant changes occured post steady state in negative control, highlighting reliability of MiGut platform. 16S rRNA sequencing confirmed PBE-dependant alterations. Although diversity was unaffected, each PBE-supplement formed a new and unique bacterial community, forming seperate clusters, with alterations at a species level. We plan to complete full SCFA data analysis. Our study combined the functionality of new models simulating digestion and microbial fermentation to assess PBEs inclusion within the diet to modulate the microbiota. Our observations showcase the functional effect of PBEs to modulate microbiome composition and provide gut health benefits. Increased use of PBEs may also hold implications for environmental sustainability due to use of whole foods, high in waste products, and formulate new supplements that provide select benefits of diets such as MedDiet.