Flaxseed (Linum usitatissimum L.) and chia seed (Salvia hispanica L.) have become increasingly popular in the design of various functional food products. However, information on their functional properties is scarce. The aim of this study is to comparatively evaluate the effects of the dietary fibers (DFs) of flaxseed and chia seed on colonic microbiota composition and metabolic outputs. The neutral and acidic monosaccharide compositions of DFs of flaxseed and chia seed were determined using gas chromatography/mass spectrometry (GC/MS) and spectrophotometer, respectively. Next, in vitro fecal fermentation assays were applied, and samples were collected at different time points for short-chain fatty acids (SCFA) measurements using GC, and fecal microbiota changes before and after fermentation were evaluated through 16S rRNA sequencing. The results revealed that DFs of flaxseed were dominated by xylose and uronic acid moieties, while that of chia seed was dominated by glucose units, indicating that their DFs are structurally different. Higher SCFA generations were observed in the case of flaxseed, suggesting that flaxseed DFs are more readily fermentable by gut microbiota. Flaxseed and chia seed DFs differentially impacted the microbiota compositions at the OTU level; for example, significant increases in the relative abundances of Acidaminococcaceae and Bacteroides stercoris related OTUs, which are known to be propionate producers, were observed in the case of flaxseed, but not chia seed. Interestingly, flaxseed, but not chia seed, DFs suppressed the growth of some pathogenic bacteria. Overall, this study suggests that the functionality of flaxseed and chia seed DFs in relation to colonic microbiota may differ, with flaxseed being more readily fermented and potentially promoting beneficial microbes to a greater extent. Thus, flaxseed could hold promise for developing functional food recipes aimed at supporting colonic health.
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