Genome-resolved gut metagenomics identifies an Escherichia coli-Collinsella signature associated with gangrenous diabetic foot ulcers
Diabetic foot ulcers (DFU) are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active DFU, comparing Wagner grades 1–3 (n = 30) with Wagner 4 gangrenous disease (n = 13). De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes (MAGs) meeting medium-quality or high-completeness/low-contamination thresholds. Community-level diversity and dominant-taxon composition did not separate Wagner 4 from Wagner 1–3, indicating that advanced disease was not reflected by broad ecological restructuring. Feature-level analysis instead identified a genome-resolved MAG profile. Random forest stability selection yielded 24 informative MAGs, and intersection with covariate-adjusted MaAsLin2 results prioritized three MAGs shared by both approaches: one Escherichia coli MAG enriched in Wagner 4 and two Collinsella MAGs depleted in Wagner 4. This three-MAG model retained much of the discriminatory information of the broader 24-MAG model and captured opposing abundance directions across classifier interpretation, differential-abundance testing and per-MAG abundance distributions. Functional annotation further separated the Wagner 4-enriched Escherichia coli from the Collinsella MAGs. The Escherichia coli MAG carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella MAGs lacked detectable resistance and virulence hits and showed metabolically compact profiles. Exploratory clinical association analysis linked the E. coli–Collinsella abundance score to longer DFU duration, consistent with a gut microbial correlate of chronic or advanced disease burden. These findings support longitudinal gut metagenomic validation to determine whether this signal tracks DFU progression, treatment response or recovery.
Diabetic foot ulcers (DFU) are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active DFU, comparing Wagner grades 1–3 (n = 30) with Wagner 4 gangrenous disease (n = 13). De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes (MAGs) meeting medium-quality or high-completeness/low-contamination thresholds. Community-level diversity and dominant-taxon composition did not separate Wagner 4 from Wagner 1–3, indicating that advanced disease was not reflected by broad ecological restructuring. Feature-level analysis instead identified a genome-resolved MAG profile. Random forest stability selection yielded 24 informative MAGs, and intersection with covariate-adjusted MaAsLin2 results prioritized three MAGs shared by both approaches: one Escherichia coli MAG enriched in Wagner 4 and two Collinsella MAGs depleted in Wagner 4. This three-MAG model retained much of the discriminatory information of the broader 24-MAG model and captured opposing abundance directions across classifier interpretation, differential-abundance testing and per-MAG abundance distributions. Functional annotation further separated the Wagner 4-enriched Escherichia coli from the Collinsella MAGs. The Escherichia coli MAG carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella MAGs lacked detectable resistance and virulence hits and showed metabolically compact profiles. Exploratory clinical association analysis linked the E. coli–Collinsella abundance score to longer DFU duration, consistent with a gut microbial correlate of chronic or advanced disease burden. These findings support longitudinal gut metagenomic validation to determine whether this signal tracks DFU progression, treatment response or recovery.
The Second Affiliated Hospital of Guangxi Medical University