Post-antibiotic microbiome signatures associated with fiber intake are distinct and specific, with Bifidobacterium and Lachnospira identified as robust genus-level biomarkers enriched in high-fiber intake rather than a uniform enrichment of commensal Clostridia as previously suggested.
Key Findings
Results
High-fiber intake post-antibiotic exposure was not associated with uniform enrichment of commensal Clostridia, contrary to previous models.
Study analyzed 16S rRNA gene sequencing data from the American Gut Project (AGP)
Participants with recent antibiotic exposure were stratified into high-fiber (HF; N = 971) and low-fiber (LF; N = 955) groups
Previous studies suggesting high-fiber diets promote recovery were noted to often rely on small cohorts
The finding directly contradicts prior models predicting Clostridia enrichment under high-fiber post-antibiotic conditions
Results
Bifidobacterium and Lachnospira were identified as genus-level biomarkers significantly enriched in the high-fiber group following antibiotic exposure.
Differential abundance analysis was performed using LEfSe
Key biomarkers were validated using ANCOM-BC and multivariable linear regression adjusting for age, sex, and BMI
Associations were confirmed to be robust by multivariable linear regression (P < 0.001)
These genera are described as 'robust targets for dietary interventions'
Results
Bacteroides and Parabacteroides were enriched in the low-fiber group following antibiotic exposure.
Identified using LEfSe differential abundance analysis
Validated using ANCOM-BC and multivariable linear regression
Associations remained robust after adjusting for age, sex, and BMI (P < 0.001)
Low-fiber group comprised N = 955 participants with recent antibiotic exposure
Results
High-fiber intake was not associated with significantly higher alpha diversity within the one-month post-antibiotic timeframe.
Alpha and beta diversity were assessed as part of the analysis
The timeframe examined was within one month following antibiotic exposure
This finding challenges assumptions that high-fiber diets broadly restore microbiome diversity after antibiotic use
The large sample size (HF N = 971, LF N = 955) provides substantial statistical power for this null finding
Conclusions
Post-antibiotic microbiome signatures associated with fiber intake are genus-specific rather than reflecting broad community-level recovery patterns.
Beta diversity differences between HF and LF groups were assessed
Findings highlight 'the need for precision nutrition strategies to enhance gut resilience'
The authors describe the associations as challenging 'simplistic models of recovery'
Data were drawn from the American Gut Project, a large and diverse adult population
Tang Y, Fu X, Sun Y. (2026). Re-evaluating gut microbiome signatures of post-antibiotic dietary fiber intake in a large adult cohort.. BMC research notes. https://doi.org/10.1186/s13104-026-07708-7