Integrated analysis of the diabetic foot ulcer microbiome and host transcriptome supports a microenvironment-microbiota-host repair framework.

BACKGROUND

Diabetic foot ulcers (DFUs) arise from interacting clinical, microbial, and host processes, yet public datasets differ substantially in design, scale, and evidentiary strength.

METHODS

We curated eight public DFU cohorts and defined an evidence hierarchy. PRJNA287759 was reprocessed from raw 16 S reads; outcome tests used one baseline sample per patient (74 healed and 15 non-healed/adverse). GSE134431 compared 13 DFU with 8 diabetic foot skin samples using limma. Host discrimination underwent fold-confined leave-one-sample-out validation, 100 repeated nested five-fold analyses, 200 label permutations, and independent rank-score evaluation in GSE80178.

RESULTS

Baseline diversity and community structure did not differ by outcome (Shannon P = 0.159; Observed ASVs P = 0.669; PERMANOVA R2 = 0.0157, P = 0.142). Rothia was the only nominal genus (P = 0.0307), and none survived FDR correction across prevalence thresholds. GSE134431 yielded 2,873 differentially expressed genes with coherent epidermal repair enrichment. Host leave-one-sample-out AUC was 0.990 (95% CI 0.964-1.000), repeated nested-CV median AUC was 0.981 (95% interval 0.952-1.000), and permutation P was 0.00995. The GSE80178 score separated 6 DFU from 3 diabetic foot skin samples (exact P = 0.0238; AUC = 1.000), although this external comparison was small.

CONCLUSIONS

Host expression provides the strongest evidence, whereas microbiome findings remain exploratory. The repair framework synthesizes parallel evidence without demonstrating causal coupling or a clinically deployable biomarker.