A longitudinal study of the diabetic skin and wound microbiome

Melissa Gardiner, Mauro Vicaretti, Jill Sparks, Sunaina Bansal, Stephen Bush, Michael Liu, Aaron Darling, Elizabeth Harry, Catherine M Burke, Melissa Gardiner, Mauro Vicaretti, Jill Sparks, Sunaina Bansal, Stephen Bush, Michael Liu, Aaron Darling, Elizabeth Harry, Catherine M Burke

Abstract

Background: Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections. The skin microbiome is thought to play important roles in skin defence and immune functioning. Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing. This study examines the skin and wound microbiome in type II diabetes.

Methods: Eight type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, sampling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of eight control subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks. Samples were processed for DNA and subject to 16S rRNA gene PCR and sequencing of the V4 region.

Results: The diabetic skin microbiome was significantly less diverse than control skin. Community composition was also significantly different between diabetic and control skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds tended to be dominated by the most abundant skin Staphylococcus, while other abundant wound taxa differed by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa.

Discussion: The major difference observed in this study of the skin microbiome associated with diabetes was a significant reduction in diversity. The long-term effects of reduced diversity are not yet well understood, but are often associated with disease conditions.

Keywords: 16S rRNA gene sequencing; Diabetes; Diabetic ulcer; Diversity; Skin microbiome.

Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1. Alpha diversity of skin and…
Figure 1. Alpha diversity of skin and wounds.
Box plots of 3 different alpha diversity measures, (A) observed number of OTUs or richness, (B) the Chao I estimator, and (C) the Shannon index, based on OTUs clustered at 97% similarity for control skin, diabetic skin and diabetic wounds. Significant differences are indicated by asterix ∗ = p < 0.05, ∗∗ = p < 0.01 ∗∗∗ = p < 0.001.
Figure 2. Principal coordinates analysis of diabetic…
Figure 2. Principal coordinates analysis of diabetic and control skin samples.
Distances are based on the weighted unifrac metric, calculated using raw counts subjected to a variance stabilising transformation.
Figure 3. The top 10 most abundant…
Figure 3. The top 10 most abundant OTUs in diabetic and control skin per subject.
The top 10 most abundant OTUs in (A) control and (B) diabetic skin per subject. Average abundances per person were calculated from data rarefied to 30,000 sequences per sample. Genus assigned taxonomy is indicated in the legend, individual OTUs of the same genera are indicated with black lines.
Figure 4. Boxplots of intra-individual differences over…
Figure 4. Boxplots of intra-individual differences over time in diabetic and non-diabetic skin microbial communities.
Inter-individual distances are also shown for comparison. The stability of non-diabetic skin was higher (i.e., lower distances over time) than for diabetic skin, however this difference did not reach significance. (Kolmogorov–Smirnov test, p = 0.09).
Figure 5. The top 10 abundant OTUs…
Figure 5. The top 10 abundant OTUs in wounds per subject.
The top 10 abundant OTUs per subject in diabetic (A) wound debridement and (B) wound swab samples. Average abundances per group were calculated from data rarefied to 30,000 sequences per sample. Genus assigned taxonomy is indicated in the legend, or family level where genus was unassigned. Individual OTUs of the same genera are indicated with black lines.
Figure 6. Relative abundance of the top…
Figure 6. Relative abundance of the top 10 OTUs per patient over time.
Patients 1–10 are represented individually in (A–H). Wound area is overlaid as a red line and is represented as a percentage of the largest wound area measured over time. Relative abundances were calculated from data rarefied to 30,000 sequences per sample. Genus assigned taxonomy is indicated in the legend, or family level where genus was unassigned. Individual OTUs of the same genera are indicated with black lines.

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