Metagenomic Profiling of Gut Microbiota in Response to High-Fiber Dietary Interventions
DOI:
https://doi.org/10.5281/zenodo.22687576Keywords:
gut microbiota, shotgun metagenomics, dietary fiber, short-chain fatty acids, Faecalibacterium prausnitzii, microbiome-diet interactionAbstract
Fiber intake across most industrialised populations sits well below the level associated with a resilient,
fermentation-competent gut microbiota, yet the strain-level and functional consequences of raising fiber intake in
free-living adults are still incompletely mapped. We conducted an 8-week randomised, controlled, parallel-arm
feeding trial in 42 healthy adults comparing a high-fiber diet (35 g fermentable fiber per day, delivered through
whole grains, legumes and inulin-enriched foods) against a habitual-diet control, with stool shotgun metagenomic
sequencing and faecal short-chain fatty acid (SCFA) quantification performed at baseline and week 8. Thirty-nine
participants (19 intervention, 20 control) completed the protocol. Shannon diversity rose from 3.11 to 3.44 in the
intervention arm (paired t-test, P<0.001) with no change in controls (P=0.41), and Bray-Curtis PERMANOVA
showed significant within-arm compositional shift over time in the intervention group only (R2=0.081, P=0.002).
Bifidobacterium, Faecalibacterium prausnitzii, Roseburia spp. and Ruminococcus bromii all increased significantly
in relative abundance (log2 fold changes of 2.29, 1.60, 1.94 and 1.71 respectively, all q<0.01), while the
Bacteroides fragilis group declined modestly. Functional profiling showed coordinated enrichment of glycoside
hydrolase families GH13 and GH43 and of starch and sucrose degradation pathways, and faecal butyrate
concentration increased from 12.4 to 18.7 micromol per gram dry weight (P<0.001), with smaller but significant
increases in propionate. No comparable shifts occurred in the control arm. These results provide strain- and
pathway-resolved evidence that a sustained, moderate increase in dietary fiber reproducibly favours a
saccharolytic, butyrogenic community configuration in adults without pre-existing gastrointestinal disease, and
they identify a compact set of taxa and gene families that could serve as response biomarkers in future
fiber-intervention trials.
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