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We have analyzed the prebiotic effect of softwood hemicelluloses on specific bacterial species in vitro and on microbiota diversity and metabolism in healthy mice in vivo. The ethanol-precipitated glycans from the softwood hemicellulose autohydrolysate were able to stimulate in vitro the growth of Bifidobacterium adolescentis, but to a much lesser extent than that of adherent-invasive E. coli. B. adolescentis was the best producer of SCFA. When mice were fed with the ethanol precipitate fraction, the relative abundance of Bacteroidetes increased while that of Proteobacteria diminished, suggesting change towards a less obesogenic microbiome. Following treatment, lipid analysis showed a decrease in cholesterol, bile acids and free fatty acids, indicating a potential cardioprotection role. Furthermore, analysis of fermentation metabolites revealed an increase in metabolites important for immune health and well-being. Our results highlight the value of hemicelluloses as a potential source of prebiotics supporting both a healthy digestive tract and immune system.