Chronic wounds represent a large and growing disease burden. Infection and biofilm formation are two of the leading impediments of wound healing, suggesting an important role for the microbiome of these wounds. However, microbial taxa that may impact healing are poorly understood. Debridement is an effective treatment for chronic wounds, but the effect on the microbiome is unknown. Based on prior literature, we hypothesized that anaerobic organisms are exposed to the surface by debridement, contributing to improved healing. We analyzed the bacterial content of the wound surface from 20 outpatients with chronic wounds before and immediately after debridement, as well as healthy skin. Given the large variation observed among different wounds, we introduce a Bayesian statistical method that models patient-to-patient variability and identify several genera that were significantly enriched in wounds vs. healthy skin. Contrary to our expectation, we found no difference between the microbiome of the original wound surface and that exposed by debridement, suggesting that debridement does not directly alter the wound microbiome. However, we found that aerobes and especially facultative anaerobes were significantly associated with wounds that did not heal within 6 months. The facultative anaerobic genus Enterobacter was significantly associated with lack of healing. The results suggest that an abundance of facultative anaerobes is a negative prognostic factor in the chronic wound microbiome, possibly due to the increased robustness of such communities to different metabolic environments.