A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity

Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified <i>Pseudomonas</i> to be consistently present across all cohorts, higher abundance of <i>Escherichia</i> and <i>Prevotella</i> in DFU samples across visits while <i>Acinetobacter</i> and <i>Morganella</i> were predominant in non-DFU wounds. Healed DFUs were enriched in <i>Alcaligenes</i> and <i>Corynebacterium</i> while worsened DFUs showed increased abundance of <i>Enterococcus</i> and <i>Serratia</i>. In amputated individuals, <i>Escherichia</i> was found in high abundance, while <i>Staphylococcus</i> was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of <i>Pseudomonas</i> and <i>Acinetobacter</i>, while <i>Prevotella</i> and <i>Escherichia</i> were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.