Phylogenetic Profiling of the Diabetic Foot Ulcer Microbiome of an Afro-Caribbean Population

Diabetic foot ulcers (DFUs) are associated with high morbidity, amputation rates, and healthcare costs in Barbados. This pilot study compares the microbiome diversity of chronic DFUs and paired normal skin (controls) from biopsies in Afro-Caribbean patients with type 2 diabetes using Illumina amplicon sequencing targeting the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer 2 (ITS2) region. Both DFUs and controls harbored diverse bacterial and fungal communities, with differences in taxonomic composition and relative abundance profiles. The dominant bacterial genera were Corynebacterium (18.3% in DFUs, 24.3% in controls) and Staphylococcus (14.9% in DFUs, 14.1% in controls). The dominant bacterial species was Corynebacterium striatum (17.3% in DFUs, 23.8% in controls) followed by Pseudomonas aeruginosa in DFUs (8.9%) and Staphylococcus aureus in controls (13.3%). The dominant fungal genera was Densospora (12% in DFUs, 12.6% in controls). The dominant fungal species was Rhodotorula graminis in DFUs (6.18%) and Paracamarosporium leucadendri in controls (3.85%). Candida duobushaemulonii, with intrinsic resistance to antifungal agents, was detected with higher relative abundance in DFUs than in controls (4.44% vs. 2.36%). Fungal Shannon alpha diversity was significantly reduced in DFUs (p = 0.039), while beta diversity did not differ between groups for bacteria (p = 0.982) or fungi (p = 0.975). The differences in taxonomic composition and relative abundance profiles, and co-occurrence of clinically relevant bacterial and fungal taxa, highlight the potential role of polymicrobial communities in DFU chronicity in the Afro-Caribbean cohort studied, and supports future studies to evaluate implications for antimicrobial stewardship.