Dietary changes can modify the gut microbiome, but inter-individual variability in the magnitude and direction of change is common. Baseline microbial composition, host characteristics, and uncontrolled differences in diet, lifestyle, and environment all contribute to this heterogeneity. Shared-living settings, where participants co-reside and consume a standardized diet, reduce environmental and dietary variability and allow clearer examination of determinants of baseline community structure and microbiome response to a controlled dietary regimen.
This study used a 15-day pop-up village design to evaluate determinants of baseline gut microbial composition and the response to a short gut-friendly dietary intervention in a multi-ethnic cohort.
Forty-three adults from North India, South India, and international backgrounds co-lived in a single site for 15 days. The study used a single-arm design in which all participants followed a standardized gut-friendly diet while residing together. Participants were stratified by body mass index (BMI) into two groups: overweight/obese (OW, BMI ≥ 25) and non-overweight (Non-OW, BMI < 25). Stool samples were collected at two timepoints: baseline (pre-intervention) and at the end of the 15-day intervention, yielding 86 total samples.
Stool samples were profiled using Oxford Nanopore shotgun metagenomics. Analyses included taxonomic composition, alpha diversity assessed with per-participant linear mixed-effects models, and differential-abundance testing using a consensus approach across three tools: MaAsLin2, LinDA, and ALDEx2. Additionally, assembly-based functional gene content was evaluated across six major metabolic pathways to assess shifts in functional community composition.
At baseline, two factors significantly structured community composition: geographic region (p = 0.046) and BMI group (p = 0.024). Habitual diet type did not significantly explain baseline variation (p = 0.792). These findings indicate that region of origin and host adiposity were more influential than self-reported habitual diet in shaping the baseline gut microbial community within this multi-ethnic cohort under study conditions.
Overall, the short shared gut-friendly diet produced a small but highly reproducible compositional shift in the cohort. This shift was statistically significant across five distance metrics (p ≤ 0.003). When stratified by BMI group, the response was stronger among overweight (OW) participants, who exhibited a significant community-level shift (p = 0.001). Non-overweight participants did not show a significant change (p = 0.181). The interaction between Timepoint and BMI was significant for Bray–Curtis distance (p = 0.021) and Aitchison distance (p = 0.028), indicating that BMI moderated the effect of the intervention on community composition.
Alpha diversity trends and per-participant mixed-effects results were part of the analytic approach, though specific alpha diversity effect sizes or p-values beyond the reported distance-based metrics were not detailed in the source text.
Consensus differential-abundance analysis across MaAsLin2, LinDA, and ALDEx2 identified several reproducible taxonomic shifts at the species and genus levels. Notable changes at the whole-cohort level included depletion of oral-associated species Streptococcus parasanguinis (q = 0.010) and Gemella sanguinis (q = 0.021). Genus-level results included decreased Actinomyces (q = 0.004) and increased Faecalibacterium (q = 0.016), among six genera that showed differential abundance. These changes are consistent with a coordinated move away from certain oral-associated pathobiont taxa and toward enrichment of fiber-fermenting taxa following the gut-friendly diet.
Assembly-based functional gene content was examined for six major metabolic pathways. At the whole-cohort level, functional community composition remained largely stable despite taxonomic shifts. The source text reports that the six pathways assessed did not show major changes across the cohort, indicating compositional change did not translate into large detectable shifts in the measured pathway-level functional potential within the short intervention window.
In a short, shared-living dietary intervention, a gut-friendly diet elicited a modest but coordinated shift in gut microbiome composition. The shift was characterized by depletion of several oral-associated pathobiont taxa and enrichment of fiber-fermenting taxa such as Faecalibacterium. Importantly, the community-level compositional shift was observed predominantly among overweight participants, suggesting that baseline host adiposity modulates microbiome responsiveness to dietary change. Functional pathway content for six major metabolic routes remained mostly stable over the intervention period.
These results highlight that shared-living, standardized dietary interventions can reveal reproducible microbiome responses and that BMI and geographic origin are important determinants of both baseline composition and responsiveness. The short intervention duration and single-arm design constrain causal inferences about long-term effects and clinical implications.
The authors reported that Centenarians Life Sciences Pvt. Ltd. provided microbiome testing kits and funded analysis of samples. Several authors are employed by Cartema Bio or Thorne Healthtech, and one author is a founder and CSO at Cartema Bio; these affiliations and advisory roles are disclosed as competing interests in the source report.