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Pectins are dietary fibers that are attributed with several beneficial immunomodulatory effects. Depending on the degree of esterification (DE), pectins can be classified as high methoxyl pectin (HMP) or low methoxyl pectin (LMP). The aim of this study was to investigate the effects of pectin methyl-esterification on intestinal microbiota and its immunomodulatory properties in naive mice. Supplementation of the diet with LMP or HMP induced changes in the composition of the intestinal microbiota in mice toward Bacteroides , which was mainly promoted by HMP. Metabolome analysis of stool samples from pectin-fed mice showed a different effect of the two types of pectin on the levels of short-chain fatty acids and bile acids, which was consistent with highly efficient in vivo fermentation of LMP. Analysis of serum antibody levels showed a significant increase in IgG and IgA levels by both pectins, while FACS analysis revealed a decrease of infiltrating inflammatory cells in the intestinal lamina propria by HMP. Our study revealed that the structural properties of the investigated pectins determine fermentability, effects on microbial composition, metabolite production, and modulation of immune responses. Consumption of HMP preferentially altered the gut microbiota and suppressed pro-inflammatory immune responses, suggesting a beneficial role in inflammatory diseases. Two types of pectin with different degree of esterification (DE), a high methoxyl pectin (HMP, 57% DE) from apple and a low methoxyl pectin (LMP, 4.4% DE) from citrus fruits were subjected to healthy mice over 14 days by supplementation of food pellets. Pectin-mediated effect on gastrointestinal microbiota and immune cells, metabolites (bile acids and short chain fatty acid) and total IgA in feces samples, as well as alteration of the humoral immune response (antibodies values of total IgA, IgG and IgE) were analyzed. [Display omitted] [ABSTRACT FROM AUTHOR]