Shotgun Metagenomic Characterization of Skin Microbiome Shifts in Human Scabies Before and After Scabicidal Treatment
Scabicidal treatment with permethrin was associated with increased alpha diversity and reduced microbial burden at moist sites, but no taxonomic or functional difference survived correction for multiple testing.
| Population | Patients with clinically confirmed active scabies |
|---|---|
| Exposure | Shotgun metagenomic sequencing before and after scabicidal treatment (permethrin) |
| Comparator | Same-site (moist) pre- vs. post-treatment samples; dry vs. moist sites pre-treatment |
| Outcome | Alpha diversity (Shannon/Simpson) at moist sites post- vs. pre-treatment; Beta-diversity community composition (PERMANOVA) moist sites post- vs. pre-treatment; Total microbial burden (non-host/non-mite read fraction) post- vs. pre-treatment; Bacterial burden (bacterial reads) post- vs. pre-treatment; Genus/species-level taxonomic differences (post- vs. pre-treatment, FDR-corrected); Predicted functional pathway abundance (post- vs. pre-treatment, FDR-corrected); Fungal/archaeal burden post- vs. pre-treatment |
Summary of findings
| Outcome | Effect | 95% CI | Certainty | Clinical relevance | Notes |
|---|---|---|---|---|---|
| Alpha diversity (Shannon/Simpson) at moist sites post- vs. pre-treatment | Shannon p=0.0297; Simpson p=0.0177; in the effect size or 95% CI reported | — | Very low | — | 1 studies |
| Beta-diversity community composition (PERMANOVA) moist sites post- vs. pre-treatment | PERMANOVA p=0.029; in the effect size or 95% CI reported | — | Very low | — | 1 studies |
| Total microbial burden (non-host/non-mite read fraction) post- vs. pre-treatment | p=0.0124; in the effect size or 95% CI reported | — | Very low | — | 1 studies |
| Bacterial burden (bacterial reads) post- vs. pre-treatment | p<0.05; in the effect size or 95% CI reported | — | Very low | — | 1 studies |
| Genus/species-level taxonomic differences (post- vs. pre-treatment, FDR-corrected) | minimum BH-FDR adjusted p=0.594 (genus), 0.557 (species); in the taxon met FDR threshold | — | Very low | — | 1 studies |
| Predicted functional pathway abundance (post- vs. pre-treatment, FDR-corrected) | minimum BH-FDR adjusted p=0.116; in the pathway met FDR threshold | — | Very low | — | 1 studies |
| Fungal/archaeal burden post- vs. pre-treatment | p>0.1; in the effect size or 95% CI reported | — | Very low | — | 1 studies |
Context
Scabies affects hundreds of millions globally and is associated with cutaneous dysbiosis, Staphylococcus predominance, and secondary infection risk. The molecular basis of microbiome changes during and after treatment was previously unknown. Shotgun metagenomic sequencing enables simultaneous characterization of bacteria, fungi, viruses, and archaea from clinical samples.
What the study showed
Alpha diversity was higher in post-treatment moist-site samples vs. pre-treatment (Shannon p=0.0297; Simpson p=0.0177), with a difference in community composition (PERMANOVA p=0.029). Total microbial burden was significantly lower post-treatment (p=0.0124), driven by reductions in bacterial and viral reads (p<0.05 for both). No genus- or species-level taxonomic difference, and no functional pathway, survived BH-FDR correction (minimum adjusted p: 0.594 at genus; 0.557 at species; 0.116 for pathways). Staphylococcus was the dominant pre-treatment genus, with a relative decrease of 33.58% post-treatment, but without corrected statistical significance.
How it was done
Longitudinal observational study using shotgun metagenomic sequencing of skin samples from scabies patients, collected at dry (Pre-DR) and moist (Pre-MO) sites before treatment and at moist sites after treatment (Post-MO). Analysis included cross-domain taxonomic profiling and functional pathway prediction (HUMAnN). Benjamini-Hochberg FDR correction was applied for multiple comparisons.
Effect magnitude
No effect sizes with 95% CI were reported for taxonomic or functional comparisons; diversity and microbial burden differences were expressed as p-values only, without standardized effect measures or confidence intervals.
Risk of bias
Extremely small sample size (n not clearly specified in the provided text, suggesting fewer than 20 participants), no healthy skin control group, no post-treatment dry-site samples, absence of negative controls to distinguish environmental contamination from true colonization (e.g., Botrytis cinerea). No formal risk-of-bias tool applied; observational design without randomization precludes causal inference. Exploratory taxonomic comparisons based on unadjusted p-values lack inferential validity.
What this study does NOT prove
This study does not prove that scabicidal treatment restores the skin microbiome to a healthy state, nor that the observed taxonomic changes are causally linked to scabies pathophysiology or treatment mechanism of action. Results are not generalizable without replication in larger, adequately controlled samples.
In clinical practice
The data do not support modification of current clinical practice. The finding of Staphylococcus aureus as the dominant pre-treatment taxon is consistent with the clinically recognized secondary infection risk, but without adjusted risk quantification. Monitoring for secondary bacterial infection remains indicated by existing practice, not by this study.
Limitations
Extremely small sample size (n not clearly specified in the provided text, suggesting fewer than 20 participants), no healthy skin control group, no post-treatment dry-site samples, absence of negative controls to distinguish environmental contamination from true colonization (e.g., Botrytis cinerea). No formal risk-of-bias tool applied; observational design without randomization precludes causal inference. Exploratory taxonomic comparisons based on unadjusted p-values lack inferential validity.
What is still missing
Studies with a healthy skin control group, adequately powered samples, paired pre- and post-treatment samples at both anatomical sites, collection negative controls, and functional analyses linked to clinical outcomes.
Technical appendix
Version history
- 1.0 · 2026-11-04 — Auto-generated under Evidence Standard v1.0