Intermittent fasting-associated microbiome remodeling and functional modulation by Lacticaseibacillus rhamnosus HN001

Objective The gut microbiome is a critical regulator of host metabolism, yet how intermittent fasting (IF) remodels the gut ecosystem independent of dietary composition remains unclear. This study aimed to isolate the effect of feeding rhythm on the gut microbiome and identify specific microbial taxa mediating IF-induced metabolic changes. Methods We employed a family-based ‘shared meal’ model that strictly standardized dietary composition across all participants. Five healthy adults (3 males, 2 females) from a single family participated in a pilot, hypothesis-generating 4-week 16:8 IF intervention with longitudinal fecal sampling for 16S rRNA sequencing and untargeted metabolomics. To functionally test a candidate Lacticaseibacillus-associated mechanism, C57BL/6 J mice were subjected to a 1-week 16:8 IF protocol with or without daily oral supplementation of Lacticaseibacillus rhamnosus HN001. Plasma beta-hydroxybutyrate (betaOHB) and peptide YY (PYY) were measured by ELISA. Results IF was associated with body weight loss in humans (2.1 +/− 0.4 kg, 95% CI: 1.3 to 2.9 kg, p < 0.05) without a significant reduction in caloric intake. In the primary paired genus-level DESeq2 analysis accounting for participant identity, no genus remained significant after false-discovery-rate correction, although Lacticaseibacillus showed a directional decrease after IF, consistent in direction with the original exploratory unpaired analysis. Predicted microbial functional and fecal metabolomic changes were consistent with altered microbial energy metabolism. In mice, IF significantly elevated plasma betaOHB ( p = 0.0046) and reduced body weight, whereas HN001 supplementation reversed these IF-associated effects under the conditions tested. Conclusion In this pilot, hypothesis-generating human cohort, IF was associated with coordinated microbiome and metabolomic remodeling, including a directional Lacticaseibacillus signal that motivated subsequent functional testing. In mice, L. rhamnosus HN001 supplementation reversed IF-associated weight loss and ketosis, supporting the functional plausibility of a Lacticaseibacillus-associated mechanism. The human observations require confirmation in larger, independent cohorts with time-matched non-fasting controls and species-resolved microbiome measurements.