Functional Pathways of the Gut Microbiome Associated with SCFA Profiles in Preclinical Alzheimer's Disease

Functional activities of the gut microbiome, particularly those contributing to short-chain fatty acid (SCFA) metabolism, play a central role in host-microbe interactions and are linked to neuroinflammatory mechanisms underlying Alzheimer's disease (AD). How microbial metabolic functions relate to SCFA concentrations and cerebral amyloid-β (Aβ) burden during the preclinical stage of AD remains poorly understood. In this study, faecal metagenomes from 87 cognitively unimpaired adults were profiled using HUMAnN3 to generate MetaCyc pathway abundance data, normalised and filtered to retain pathways present in at least 30% of participants. A keyword-based search identified 362 SCFA-related pathways spanning acetate, propionate, butyrate, isobutyrate, valerate and isovalerate metabolism. Associations between microbial functions, SCFA concentrations and Aβ status were evaluated using Spearman correlations, Kruskal-Wallis tests across SCFA quartiles, and multivariable linear regression with false discovery rate correction, supported by canonical correspondence analysis and network modelling. A total of 38 significant SCFA pathway correlations were identified. Acetate, butyrate and total SCFA levels showed positive associations with biosynthetic pathways, including L-arginine biosynthesis II, peptidoglycan biosynthesis and flavin biosynthesis, whereas fermentative pathways such as pyruvate fermentation to acetone and lysine fermentation to butanoate were negatively correlated. Butyrate quartiles demonstrated dose-dependent increases in biosynthetic functions and declines in fermentative routes. Canonical Correspondence Analysis (CCA) confirmed a significant multivariate association, and network analysis revealed enhanced fermentative and methanogenic connectivity among Aβ High participants. These findings indicate that amyloid burden is associated with a shift from anabolic to fermentative microbial metabolism and may inform future studies examining potential mechanistic links in preclinical AD.