Defining Host-Microbiome Interactions in Diabetic Wound Healing

At a Glance

In Wisconsin, 750,000 people live with diabetes, and 25 percent of those individuals will develop a diabetic foot ulcer (DFU), a common complication of diabetes, in their lifetime. DFUs can remain open for a long time, and it can be difficult to predict which of these wounds will respond to treatment and heal or require amputation. Wound tissue supports the colonization of a diverse community of microbes referred to as a microbiome. The microbiome in the wound tissue is thought to sustain inflammation which impairs healing and tissue repair. There is a critical, unmet need to develop methods that predict if diabetic wounds will heal in response to treatment, or if they will remain open and healing will be stalled due to a complex microbiome. In this study, researchers hypothesized that the wound microbiome interacts with host healing pathways and genes that control tissue repair. Ultimately, they found that anaerobic bacteria species, which can survive and grow with no oxygen, are more abundant and transcriptionally active in the microbiome of persistent and amputated wounds. Therefore, anaerobic bacteria may serve as a predictive biomarker of wound healing.

The research team has received a $26,000 Wisconsin Alumni Research Foundation (WARF) Technology Accelerator Grant and a $2 million NIH grant to expand their work.

The Challenge

In Wisconsin, 750,000 people live with diabetes, and 25 percent of those individuals will develop a diabetic foot ulcer (DFU) in their lifetime. Because it is difficult to predict if these wounds will respond to treatment and heal, many cases of DFU result in amputation. DFUs can remain open for a long time, and the wound tissue supports the colonization of a diverse community of microbes referred to as a microbiome. The microbiome in the wound tissue does not always cause clinical infection, but it is thought that it might sustain inflammation which impairs healing and tissue repair. There is a critical, unmet need to develop methods that predict if diabetic wounds will heal in response to treatment, or if they will remain open and healing will be stalled due to a complex microbiome.

Project Goals

Researchers hypothesized that the wound microbiome could influence wound healing. The long-term goal of this project was to identify unequivocal biomarkers based on the microbiome for predicting healing outcomes. This goal was approached through two objectives. First, the research team aimed to characterize the associations between host repair pathways and the microbiome after debridement, or the removal of dead tissue and microbes with a scalpel. Second, they sought to identify microbial signatures associated with impaired wound healing in DFU.

Results

Researchers reached their enrollment goal of 100 patients, resulting in the collection of 751 DFU specimens over time. To evaluate the differences in the DFU sample type (pre- or post-debridement), tissue was removed by routine debridement and then a swab of the ulcer bed was collected. Because the samples were composed of both human and microbial cells, researchers identified both human and non-human genetic material. The majority of the non-genetic material corresponded to bacterial species.

All genetic transcripts that were labeled as ‘non-human’ were further classified and quantified. Researchers found that bacterial Staphylococcus species were overrepresented across all healing outcomes and, therefore, are not a good marker of infection or outcome. They found that anaerobic species of bacteria had higher levels of gene expression in persistent and amputated wounds. These results demonstrate the potential for the transcriptional activity of anaerobic bacteria to serve as a predictive biomarker of wound healing.

When examining gene expression of the human cells from wound samples, researchers detected several genes that encode keratins that help form the outer layer of skin, genes that are involved in inflammatory response, and gene transcripts that are known to be involved in the regulation of tissue repair. These findings are consistent with skin and the wound healing process.

Looking to the Future

The data generated by this project was used as preliminary data for a $26,000 Wisconsin Alumni Research Foundation (WARF) Technology Accelerator Grant and a $2 million NIH grant. These awards will support the researchers in developing a simple PCR-based assay to measure biomarkers of diabetic wound healing.