Re-evaluating gut microbiome signatures of post-antibiotic dietary fiber intake in a large adult cohort

TL;DR

This study finds that high-fiber diets after antibiotics are linked to specific gut bacteria, not just general gut health, suggesting personalized nutrition could help recovery.

Contribution

The study identifies novel microbial biomarkers (Bifidobacterium and Lachnospira) associated with high-fiber diets post-antibiotics in a large cohort.

Findings

High-fiber intake after antibiotics is linked to increased Bifidobacterium and Lachnospira, not Clostridia.

Bacteroides and Parabacteroides are enriched in low-fiber diets post-antibiotics.

High-fiber diets do not consistently boost gut diversity within one month after antibiotics.

Abstract

Dietary fiber is a key modulator of the gut microbiome, yet its specific role following antibiotic exposure remains under-characterized in large populations. Previous studies suggest high-fiber diets promote recovery, but often rely on small cohorts. We aimed to re-evaluate these microbial signatures and their association with current microbiome states in a large, diverse adult population.

We analyzed 16 S rRNA gene sequencing data from the American Gut Project (AGP). Participants with recent antibiotic exposure were stratified by high-fiber (HF; N = 971) or low-fiber (LF; N = 955) intake. We assessed alpha and beta diversity and identified differentially abundant genera using LEfSe. Key biomarkers were validated using ANCOM-BC and multivariable linear regression adjusting for age, sex, and BMI.

Contrary to previous models, high-fiber intake was not associated with a uniform enrichment of commensal Clostridia. Instead, Bifidobacterium and Lachnospira were identified as genus-level biomarkers significantly enriched in the HF group, while Bacteroides and Parabacteroides were enriched in the LF group. These associations were confirmed to be robust by multivariable linear regression (P < 0.001). High-fiber intake was not associated with significantly higher alpha diversity within the one-month post-antibiotic timeframe.

Post-antibiotic microbiome signatures associated with fiber intake are distinct and specific. We identified Bifidobacterium and Lachnospira as robust targets for dietary interventions, challenging simplistic models of recovery and highlighting the need for precision nutrition strategies to enhance gut resilience.

The online version contains supplementary material available at 10.1186/s13104-026-07708-7.

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