Multi-habitat microbiome profiling identifies habitat-dependent alterations and complementary discriminatory...

Area of Science:

• Microbiome research
• Urology
• Genomics

Background:

• Urolithiasis (kidney stone disease) is associated with microbial shifts in various body sites.
• It remains unclear if these microbial signatures are shared, site-specific, or complementary.
• This study investigates multi-habitat microbiome alterations in urolithiasis.

Purpose of the Study:

• To characterize multi-habitat microbiome alterations in urolithiasis.
• To evaluate if integrated multi-site profiling provides cross-validated disease-associated microbial information.
• To assess the diagnostic potential of multi-habitat microbiome data.

Main Methods:

• Collected salivary, urinary, and fecal samples from 80 stone formers (SF) and 40 healthy controls (HC).
• Utilized 16S rRNA gene sequencing for microbiome profiling.
• Employed random forest models with cross-validation to analyze single- and multi-habitat microbial data.

Main Results:

• Urolithiasis showed modest, habitat-dependent microbial community structure differences.
• SF exhibited significantly reduced fecal microbial richness compared to HC.
• A combined multi-habitat microbiome model achieved higher diagnostic accuracy (AUC 0.865) than a clinical-only model (AUC 0.738).

Conclusions:

• Multi-habitat microbiome profiling reveals habitat-specific alterations in urolithiasis.
• Integrated profiling captures disease-associated microbial information beyond clinical baselines.
• This framework supports future mechanistic and translational studies for urolithiasis.