Wound Microbiome Research Articles

Innovative Nanocomposites for Drug Delivery: A Novel Approach for Diabetic Foot Ulcer

Abstract: Diabetic Foot Ulcer (DFU) is a chronic wound, and a person with diabetes has an increased lifetime risk of foot ulcers (19%-34%) and high morbidity (65% recurrence in 3-5 years, 20% lifetime amputation). Recent data have shown rising amputation rates, especially in the younger and minority populations. This abstract discusses innovative approaches for addressing this issue. This highlights the use of nanotechnology-based drug nanocomposite systems for natural wound healing therapies, with a focus on nanoparticles, nano-emulsions, and nanogels. This review also emphasizes the potential of hydrogels for drug delivery, highlighting their versatility in various medical applications. Furthermore, it delves into the use of silver nanoparticles (AgNP’s) for treating diabetic wounds while acknowledging the need to address potential toxicity concerns. Finally, the abstract discusses the utilization of traditional herbal medicine and the integration of modern science to advance wound care, particularly focusing on wound microbiome, immune response, and controlled herbal medicine delivery. This study also highlights clinical trials conducted on DFU. Overall, these abstracts highlight the importance of exploring diverse and innovative solutions to chronic wound management.

Biofilms and microbiome profiles in chronic wounds: links to antibiotic use and wound severity in a Sri Lankan cohort.

We have characterized the microbiome of infected chronic diabetic wounds (CDWs), exploring associations with antibiotic use and wound severity in a Sri Lankan cohort. Fifty CDW patients were enrolled, 38 of whom received antibiotics. Tissue biopsies were analysed by microbiome profiling, and wounds were graded using the University of Texas Wound Grading System. Biofilm presence was assessed in 20 wounds. The microbiome was largely dominated by Enterobacteriaceae, Pseudomonadaceae, Streptococcaceae, and Corynebacteriaceae. Proteobacteria levels were significantly higher in antibiotic-treated wounds (P=.019), with increased Pseudomonas abundance. Wounds were categorized as grade 1 (10), grade 2 (29), and grade 3 (11). Alpha diversity varied by wound grade (P=.015), with grade 2 wounds showing the highest diversity and grade 3 the lowest. All 20 tested wounds were biofilm-positive, and community composition varied more in antibiotic-treated wounds (P=.004). CDW microbiomes were dominated by Enterobacteriaceae and Pseudomonadaceae, with elevated Proteobacteria in antibiotic-treated wounds. Alpha diversity correlated with wound severity, peaking in grade 2 wounds. The high prevalence of biofilms in wounds underscores the need for management of CDWs that address microbial complexity.

Unlocking the role of wound microbiome in diabetic, burn, and germ-free wound repair treated by natural and synthetic scaffolds

In current clinical practice, various dermal templates and skin substitutes are used to enhance wound healing. However, the role of wound commensal microbiome in regulating scaffold performance and the healing process remains unclear. In this study, we investigated the influence of both natural and synthetic scaffolds on the wound commensal microbiome and wound repair in three distinct models including diabetic wounds, burn injuries, and germ-free (GF) wounds. Remarkably, synthetic electrospun polycaprolactone (PCL) scaffolds were observed to positively promote microbiome diversity, leading to enhanced diabetic wound healing compared to the natural scaffolds Integra® (INT) and MatriDerm® (MAD). In contrast, both natural and synthetic scaffolds exhibited comparable effects on the diversity of the microbiome and the healing of burn injuries. In GF wounds with no detectable microorganisms, a reversed healing rate was noted showing natural scaffold (MAD) accelerated wound repair compared to the open or the synthetic scaffold (PCL) treatment. Furthermore, the response of the wound commensal microbiome to PCL scaffolds appears pivotal in promoting anti-inflammatory factors during diabetic wound healing. Our results emphasize that the wound commensal microbiome, mediated by different scaffolds plays an important role in the wound healing process.

Understanding and treating diabetic foot ulcers: Insights into the role of cutaneous microbiota and innovative therapies.

Notoriously known as the silent pandemic, chronic, non-healing diabetic foot ulcers (DFUs), pose a significant rate of incidence for amputation and are a major cause of morbidity. Alarmingly, the treatment and management strategies of chronic wounds represent a significant economic and health burden as well as a momentous drain on resources with billions per annum being spent in the US and UK alone. Defective wound healing is a major pathophysiological condition which propagates an acute wound to a chronic wound, further propelled by underlying conditions such as diabetes and vascular complications which are more prevalent amongst the elderly. Chronic wounds are prone to infection, which can exacerbate the condition, occasionally resulting in amputation for the patient, despite the intervention of modern therapies. However, amputation can only yield a 5-year survival rate for 50% of patients, highlighting the need for new treatments for chronic wounds. The dynamic cutaneous microbiota is comprised of diverse microorganisms that often aid wound healing. Conversely, the chronic wound microbiome consists of a combination of common skin commensals such as Staphylococcus aureus and Staphylococcus epidermidis, as well as the opportunistic pathogen Pseudomonas aeruginosa. These bacteria have been identified as the most prevalent bacterial pathogens isolated from chronic wounds and contribute to prolific biofilm formation decreasing the efficiency of antimicrobials and further perpetuating a hyper-inflammatory state. Here, we review recent advances and provide a new perspective on alternative treatments including phage and microbiome transplant therapies and how the definitive role of the cutaneous microbiota impacts the aetiology of DFUs.

P29 Long-read sequencing provides unprecedented insight into the skin and wound microbial landscape

Abstract Introduction and aims It is becoming increasingly evident that the microbial inhabitants of our skin play a key role in cutaneous health and disease. However, our understanding of the contribution of the complex skin microbiome to wound healing outcome remains incomplete. This is, in part, due to the historic challenges around traditional sampling and profiling Methods, which often fail to capture the abundance and diversity of the skin microbiome. Recent advances in microbiome sequencing technologies now enable more comprehensive characterization of skin bacterial composition and host-microbe interactions. Thus, the aim of this study was to utilize a novel long-read sequencing platform to provide species-level microbiome characterization and deliver important insight into the drivers of pathological skin repair. Methods Microbial DNA samples were collected from the skin and wounds of healthy volunteers and patients with chronic wounds (n = 40 per group). Long-read nanopore sequencing was used to profile microbiome samples, while RNA-Seq enabled generation of donor transcriptomic profiles. A multifaceted approach was used to integrate these datasets to investigate the complex interplay between host skin pathology and the microbiome. Results We first identified perturbations in the skin microbiome of patients with chronic wounds, which was significantly less diverse than healthy skin and colonized with key bacteria associated with pathogenicity. These alterations in the skin microbiome also correlated with transcriptomic changes, such as upregulation of genes associated with inflammation, stress and poor healing. Interestingly, long-read sequencing data displayed poor correlation with routine clinical microbiology swabs, while specific clinical characteristics (e.g. glycaemic control and wound duration) were strongly linked to wound microbiome composition. Conclusions Collectively, these data provide crucial new insight into the skin and wound microbial landscape, demonstrating a potential role for specific wound bacteria in modulating pathological skin repair.

The heterogeneous wound microbiome varies with wound care pain, dressing type, and inflammatory gene expression.

Wound dressing changes are essential procedures for wound management. However, ~50% of patients experience severe pain during these procedures despite the availability of analgesic medications, indicating a need for novel therapeutics that address underlying causes of pain. Along with other clinical factors, wound pathogens and inflammatory immune responses have previously been implicated in wound pain. To test whether these factors could contribute to severe pain during wound dressing changes, we conducted an exploratory, cross-sectional analysis of patient-reported pain, inflammatory immune responses, and wound microbiome composition in 445 wounds at the time of a study dressing change. We profiled the bacterial composition of 406 wounds using 16S ribosomal RNA amplicon sequencing and quantified gene expression of 13 inflammatory markers in wound fluid using quantitative real-time polymerase chain reaction (qPCR). Neither inflammatory gene expression nor clinically observed inflammation were associated with severe pain, but Corynebacterium and Streptococcus were of lower relative abundance in wounds of patients reporting severe pain than those reporting little or no pain. Wound microbiome composition differed by wound location, and correlated with six of the inflammatory markers, including complement receptor C5AR1, pro-inflammatory cytokine interleukin (IL)1β, chemokine IL-8, matrix metalloproteinase MMP2, and the antimicrobial peptide encoding cathelicidin antimicrobial peptide. Interestingly, we found a relationship between the wound microbiome and vacuum-assisted wound closure (VAC). These findings identify preliminary, associative relationships between wound microbiota and host factors which motivate future investigation into the directional relationships between wound care pain, wound closure technologies, and the wound microbiome.

Chitogel with deferiprone following endoscopic sinus surgery: improved wound healing and microbiome.

Adhesion formation, sinus ostial narrowing, and presence of pathogenic bacteria are associated with poor outcomes following endoscopic sinus surgery (ESS) for chronic rhinosinusitis. Chitogel has been shown to improve wound healing, restore a healthier microbiome, and reduce post-operative infections post ESS. Deferiprone has antibacterial properties and has been shown to reduce adhesion formation. The aim of the study was to assess whether the addition of low concentration deferiprone to Chitogel further improves surgical outcomes following ESS compared with Chitogel alone. In this double-blinded trial, 45 patients undergoing ESS were prospectively recruited. At the end of the surgery, patients were randomised to receive Chitogel alone, Chitogel with 1 mM of deferiprone, or Chitogel with 5 mM of deferiprone to one side of the sinuses (allowing the other side to serve as control). Patients underwent routine follow-ups with symptom questionnaires and nasoendoscopies performed at 2, 6, and 12 weeks post-operatively. Sinus ostial measurements, microbiology, and microbiome swabs from bilateral middle meatuses were collected intraoperatively and at 12 weeks post-operatively. A significant improvement in the endoscopic appearance of the sinuses and frontal ostial patency was noted at 12 weeks post-operatively (p < 0.05) in all three treatment groups compared with the control. There was no significant difference noted between patients who received Chitogel alone and those who received Chitogel with 1 or 5 mM deferiprone. Chitogel alone, Chitogel with 1 mM deferiprone, and Chitogel with 5 mM deferiprone used following ESS led to a significant improvement in endoscopic appearance of the sinuses and frontal ostial preservation at 12 weeks post-operatively. No significant difference was found with the addition of deferiprone to Chitogel.

Stable closure of acute and chronic wounds and pressure ulcers and control of draining fistulas from osteomyelitis in persons with spinal cord injuries: non-interventional study of MPPT passive immunotherapy delivered via telemedicine in community care.

Micropore particle technology (MPPT) is a topical wound treatment. It is a passive immunotherapy, acting via the skin and wound microbiome without the use of antimicrobial action. In a general patient population, it removed wound infections 60% and initiated tissue regeneration 50% quicker than antibiotics and antiseptics. As MPPT supports the immune system, the aim was to confirm that MPPT is also effective in immunocompromised individuals. People with spinal cord injury (SCI) are immunodeficient due to their injury and not an underlying disease and recruit 50% fewer immune cells to an injury. The study, therefore, determined the efficacy, safety, health economics, and sustainability of MPPT in acute and chronic wounds and pressure ulcers in this patient population. Pressure ulcers in SCI persons are an orphan indication, patient variability is high, and ICH E10 excludes comparators due to ethical concerns. The study design was, therefore, a single-arm, non-interventional, observational, post-market surveillance study of MPPT for treating wounds and pressure ulcers and removing soft tissue infection in connection with draining fistulas in SCI persons. The study was based on telemedicine in community care. The study included 44 wounds. All acute and chronic grade 1-4 wounds and pressure ulcers reached stable closure. In wounds acting as fistulas draining from an underlying, primary focus of infection, e.g., osteomyelitis, MPPT removed the soft tissue infection in approx. 2.5 months and supported regeneration, considerably reducing fistula sizes. Compared to standard care, per-wound cost savings were 51 to 94% depending on wound grade and age, and substantial nursing resources were freed up. The telemedicine approach was well received by participants and supported independence and self-care. The use of antimicrobials, plastics, and synthetic polymers was essentially eliminated. MPPT did not require bed rest. The study confirmed that MPPT is safe and effective in treating acute and chronic wounds in immunocompetent and immunocompromised individuals, including wounds with antimicrobial-resistant infections. MPPT also removes soft tissue infections caused by an underlying primary focus of infection, such as osteomyelitis. Non-healing wounds currently represent an unmet clinical need. The findings suggest that a therapy acting via the microbiome without antimicrobial actions is effective.

Reshaped commensal wound microbiome via topical application of Calvatia gigantea extract contributes to faster diabetic wound healing.

Calvatia gigantea (CG) is widely used as a traditional Chinese medicine for wound treatment. In this study, we aimed to determine the effects of CG extract (CGE) on diabetic wound healing and the commensal wound microbiome. A wound model was established using leptin receptor-deficient db/db mice, with untreated mice as the control group and CGE-treated mice as the treatment group. The wound healing rate, inflammation and histology were analyzed. Additionally, wound microbiome was evaluated via 16S ribosomal RNA (rRNA) gene sequencing. CGE significantly accelerated the healing of diabetic ulcer wounds, facilitated re-epithelialization, and downregulated the transcription levels of the inflammatory cytokines, interleukin-1β and tumor necrosis factor-α. Furthermore, CGE treatment positively affected the wound microbiome, promoting diversity of the microbial community and enrichment of Escherichia-Shigella bacteria in the CGE-treated group. Overall, CGE enhanced diabetic wound healing by modulating the wound microbiome and facilitating macrophage polarization during inflammation. These findings suggest modulation of the commensal wound microbiome using medicinal plants as a potential therapeutic strategy for diabetic wounds.

Wound healing of experimental equine skin wounds and concurrent microbiota in wound dressings following topical propylene glycol gel treatment.

Topical wound treatments rely on carrier formulations with little to no biological impact. The potential for a common vehicle, a propylene glycol (PG) gel, to affect wound healing measures including microbiota is not known. Microbiome characterization, based on next generation sequencing methods is typically performed on tissue or directly obtained wound fluid samples. The utility for primary wound dressings to characterize equine wound microbiota in the context of topical treatments is currently unknown. This investigation reports the topical effect of an 80% PG based gel on wound healing and microbiota in wound dressings. Experiments were performed in six mature horses utilizing a surgical, distal limb wound model, histology of sequential wound biopsies, photographic wound measurements and microbiota profiling via 16s rRNA sequencing of wound dressing samples. Experimental wounds were surveyed for 42 days and either treated (Day 7, 14, 21 and 28; at 0.03 ml/cm2) or unexposed to the PG gel. Wound surface area, relative and absolute microbial abundances, diversity indices and histologic parameters were analyzed in the context of the experimental group (treatment; control) using qualitative or quantitative methods depending on data characteristics. Compared to controls, treatment slowed the wound healing rate (17.17 ± 4.27 vs. 18.56 ± 6.3 mm2/day), delayed the temporal decline of polymorphonucleated cells in wound beds and operational taxonomic units (OTU) in wound dressings and lowered alpha-diversity indices for microbiota in primary wound dressing. Relative abundances of OTUs were in line with those previously reported for equine wounds. Clinical outcomes 42 days post wounding were considered similar irrespective of PG gel exposure. Results highlight the potential for vehicle exposure to alter relevant wound outcome measures, imposing the need for stringent experimental control measures. Primary wound dressings may represent an alternate sample source for characterization of the wound microbiome alleviating the need for additional interventions. Further studies are warranted to contrast the microbiome in wound dressings against that present on wound surfaces to conclude on the validity of this approach.

561. Microbial Analysis and Fungi-Bacteria Correlation in Chronic Wound Infection Patients

Abstract Background Chronic wound infection has become a major healthcare burden globally. The colonized microbiome features and correlation between bacteria and fungi have not been listed. Methods In this study, we enrolled 38 acute wound infection and 28 chronic wound infection patients. The wound swabs sampling at admission were tested by metagenomic next-generation sequencing. Microbial community characteristics in wound infection patients and bacteria-fungi correlations in chronic wound infection patients were analyse after filtering background organisms.Figure 1.Flow chart Results We found that wound microbiome in chronic wound infection patients had higher abundance of Pseudomonas aeruginosa than that in acute wound patients. Meanwhile, microbes with high relative abundant in chronic infection wounds were less significantly association with plasma inflammation factors compared with those in acute infection wounds. Finally, we investigated the association between fungi and bacteria in chronic infection patients and found that relative abundance of Pseudomonas aeruginosa was negatively associated with that of Candida albicans.Figure 2.Comparison of bacteria species relative abundance between groups.Barplot of average relative frequencies of genera. Only genera&amp;gt;1% of relative abundance in wound were represented. C= chronic infection wound group, NC= acute infection wound groupFigure 3.Analysis of Linear Discriminant Analysis (LDA) Effect Size in groups.The bar graph showed pathogens with LDA score log10 &amp;gt;5 in two groups. C= chronic infection wound group, NC= acute infection wound group.Figure 4.Fungi-bacteria network in patients with chronic infection wound.Green dots: bacteria; Blue dots: fungi; red edge: positive correlation; green edge: negative correlation. Relative abundance of Pseudomonas aeruginosa was negatively associated with that of Candida albicans highlighted with red box. Conclusion Our metagenomic sequencing results of wound supported that Pseudomonas aeruginosa may be the biomarker of chronic wound infection and have interaction with candida albicans. Disclosures All Authors: No reported disclosures

Temporal Changes in the Skin Microbiome of Epidermolysis Bullosa Patients following the Application of Wound Dressings.

Epidermolysis bullosa (EB) is a group of rare hereditary skin disorders characterized by the formation of painful blisters, erosions, and ulcers. In addition, the wounds can easily become infected with different pathogens. Therefore, the dynamics in the microbial populations across the various stages of EB can shed light on pathophysiology, the effect of treatment, and the factors involved in its recovery, but they are understudied. We thus sought to characterize the skin microbiome among patients with EB over time. A prospective study conducted in the pediatric dermatology clinic at Soroka Medical Center, Beer-Sheva, Israel. Children (0-18) with simplex and recessive dystrophic EB were sampled at two different time points: before a therapeutic regimen and 90 days (±14 days) later. Samples were obtained from lesional skin (wound), healthy, non-lesional skin, and seborrheic skin (forehead). Samples were subject to 16S rRNA amplicon sequencing. Analyses performed included comparisons of relative abundance at the phyla and genera taxonomic levels, alpha and beta diversity comparisons, and differential abundance. 32 children with EB were enrolled, for whom 192 skin microbiome samples were obtained. Lesional skin samples harbored significantly less Bacteroidota and Fusobacteriota before the initiation of treatment. Following topical dressing, we observed more Firmicutes and less Proteobacteria in lesional skin samples than healthy and seborrheic skin samples. In addition, Staphylococcus was significantly more abundant in lesional samples than in non-lesional and seborrheic samples following treatment. Our study recaptured the reduced bacterial diversity and increased staphylococcal carriage in EB patients, showing a potential effect of topical dressing either directly on the wound microbiome or indirectly through the contribution towards skin healing. The detection of Firmicutes in general, and S. aureus specifically, commensurate with the application of a wound dressing may warrant the use of additional treatment methods to facilitate wound healing. Future studies in these patients should prospectively correlate the temporal changes in the microbiome associated with various treatment modalities in order to optimize the care of EB patients.

Lecithin and Chitosan as Building Blocks in Anti-Candida Clotrimazole Nanoparticles.

The main focus when considering treatment of non-healing and infected wounds is tied to the microbial, particularly bacterial, burden within the wound bed. However, as fungal contributions in these microbial communities become more recognized, the focus needs to be broadened, and the remaining participants in the complex wound microbiome need to be addressed in the development of new treatment strategies. In this study, lecithin/chitosan nanoparticles loaded with clotrimazole were tailored to eradicate one of the most abundant fungi in the wound environment, namely C. albicans. Moreover, this investigation was extended to the building blocks and their organization within the delivery system. In the evaluation of the novel nanoparticles, their compatibility with keratinocytes was confirmed. Furthermore, these biocompatible, biodegradable, and non-toxic carriers comprising clotrimazole (~189 nm, 24 mV) were evaluated for their antifungal activity through both disk diffusion and microdilution methods. It was found that the activity of clotrimazole was fully preserved upon its incorporation into this smart delivery system. These results indicate both that the novel carriers for clotrimazole could serve as a therapeutic alternative in the treatment of fungi-infected wounds and that the building blocks and their organization affect the performance of nanoparticles.

Wound healing and microbiome, an unexpected relationship.

Skin wounds are common and represent a major public health and economical problem, with risks of complications and a significant negative impact on the quality of life of patients. Cutaneous wound healing is a tightly regulated process resulting in the restoration of tissue integrity. Wound healing involves the interaction of several skin, immune and vascular cells, growth factors and cytokines. However, external actors can play an important role in wound healing, such as the skin microbiome, which is the microbial commensal collection of bacteria, fungi and viruses inhabiting the skin. Indeed, recent advances have featured the interactions, within the wound environment, between different microbial species and between microbial species and the host immune system. This article reviews the relationship between the skin microbiome and the wound healing process. Although cutaneous wounds are a potential entry site for infection, the wound microbiome can have either a detrimental or a beneficial role on wound healing. Thus, targeting the skin microbiome could represent an essential part of wound healing management.

Cutaneous Surgical Wounds Have Distinct Microbiomes from Intact Skin.

Infections are relatively rare following cutaneous surgical procedures, despite the potential for wound exposure to pathogens both during surgery and throughout the healing process. Although gut commensals are believed to reduce the risk of intestinal infections, an analogous role for skin commensals has not been described. In fact, the microbiome of normally healing surgical skin wounds has not yet been profiled using culture-independent techniques. We characterized the wound microbiome in 53 patients who underwent skin cancer surgery and healed without signs or symptoms of infection. A week after surgery, several bacterial species displayed significant differences in relative abundance when compared to control, nonoperated skin from the same patient. The relative abundance of the most common bacterium found on intact skin, Cutibacterium acnes, was reduced in wounds 5-fold. Staphylococcus aureus, a frequent cause of postoperative skin infections, was enriched 6.4-fold in clinically noninfected wounds, suggesting active suppression of pathogenicity. Finally, members of the Corynebacterium genus were the dominant organism in postoperative wounds, making up 37% of the average wound microbiome. The enrichment of these bacteria in normally healing wounds suggests that they might be capable of providing colonization resistance. Future studies focused on the biological and clinical significance of the wound microbiome may shed light on normal wound healing and potential therapeutic opportunities to mitigate infection risk. IMPORTANCE Commensal bacteria on skin may limit the ability of pathogenic bacteria to cause clinically significant infections. The bacteria on healing acute wounds, which might provide such a protective effect, have not been described using culture-independent approaches in the absence of antibiotics. We compare the microbiome of wounds a week after skin cancer removal surgery with intact skin from the same patient. We find that the potentially pathogenic species S. aureus is common on these healing wounds despite the absence of symptoms or signs of infection. We report that bacteria often considered as potential skin probiotics, including Staphylococcus epidermidis, do not reach high relative abundance in wound microbiomes. In contrast, specific members of the Corynebacterium genus, rarely associated with infections, were significantly enriched in healing wounds compared to intact skin. Future work is needed to see if Corynebacterium species or derivatives thereof could be employed to lower the risk of wound infection.

A fucoidan-gelatin wound dressing accelerates wound healing by enhancing antibacterial and anti-inflammatory activities

Microbial infections and the slow regression of inflammation are major impediments to wound healing. Herein, a tilapia fish skin gelatin-fucose gum-tannic acid (Gel&Fuc-TA) hydrogel wound dressing (Gel&Fuc-TA) was designed to promote wound healing by mixing and reacting tannic acid (TA) with tilapia fish skin gelatin (Gel) and fucoidan (Fuc). Gel&Fuc-TA hydrogel has a good network structure as well as swelling and release properties, and shows excellent antibacterial, antioxidant, cell compatibility, and hemostatic properties. Gel&Fuc-TA hydrogel can promote the expression of vascular endothelial growth factor (VEGF), platelet endothelial cell adhesion molecule-1 (CD-31), and alpha-smooth muscle actin (α-SMA), enhance collagen deposition, and accelerate wound repair. Gel&Fuc-TA hydrogel can change the wound microbiome, reduce wound microbiome colonization, and decrease the expression of microbiome-related proinflammatory factors, such as lipopolysaccharide (LPS), Toll-like receptor 2 (TLR2), and Toll-like receptor 4 (TLR4). Gel&Fuc-TA hydrogel effectively regulates the conversion of wound macrophages to the M2 (anti-inflammatory phenotype) phenotype, decreases the expression of interleukin-6 (IL-6), interleukin-1β (IL-1β) and tumor necrosis factor-alpha (TNF-α), and increases the expression of arginase-1 (Arg-1), interleukin-10 (IL-10) and transforming growth factor-beta (TGF-β), thereby reducing the inflammatory response. In summary, Gel&Fuc-TA hydrogel prepared using a rational green cross-linking reaction can effectively accelerate wound healing.

The Wound Microbiome.

Breach of the skin barrier and subsequent wound healing occur in the context of microbial communities of bacteria, fungi, and viruses. These polymicrobial communities are dynamic and important components of the wound environment and are associated with differential healing outcomes. Here, we highlight both culture-dependent and -independent methods that have furthered our understanding of the wound microbiome. We discuss common themes that have developed from such studies about the microbial inhabitants of diverse wound types. We additionally explore the wide range of microbial mechanisms that influence healing, from invading pathogens to beneficial commensals. These insights can be leveraged to better predict healing outcomes and derive novel microbial-based therapies for chronic wounds.

Revealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systems.

The human gut microbiome is composed of a diverse consortium of microorganisms. Relatively little is known about the diversity of the bacteriophage population and their interactions with microbial organisms in the human microbiome. Due to the persistent rivalry between microbial organisms (hosts) and phages (invaders), genetic traces of phages are found in the hosts’ CRISPR-Cas adaptive immune system. Mobile genetic elements (MGEs) found in bacteria include genetic material from phage and plasmids, often resultant from invasion events. We developed a computational pipeline (BacMGEnet), which can be used for inference and exploratory analysis of putative interactions between microbial organisms and MGEs (phages and plasmids) and their interaction network. Given a collection of genomes as the input, BacMGEnet utilizes computational tools we have previously developed to characterize CRISPR-Cas systems in the genomes, which are then used to identify putative invaders from publicly available collections of phage/prophage sequences. In addition, BacMGEnet uses a greedy algorithm to summarize identified putative interactions to produce a bacteria-MGE network in a standard network format. Inferred networks can be utilized to assist further examination of the putative interactions and for discovery of interaction patterns. Here we apply the BacMGEnet pipeline to a few collections of genomic/metagenomic datasets to demonstrate its utilities. BacMGEnet revealed a complex interaction network of the Phocaeicola vulgatus pangenome with its phage invaders, and the modularity analysis of the resulted network suggested differential activities of the different P. vulgatus’ CRISPR-Cas systems (Type I-C and Type II-C) against some phages. Analysis of the phage-bacteria interaction network of human gut microbiome revealed a mixture of phages with a broad host range (resulting in large modules with many bacteria and phages), and phages with narrow host range. We also showed that BacMGEnet can be used to infer phages that invade bacteria and their interactions in wound microbiome. We anticipate that BacMGEnet will become an important tool for studying the interactions between bacteria and their invaders for microbiome research.

Metagenomics of diabetic foot ulcer undergoing treatment with total contact casting: a case study.

Diabetic foot ulcers (DFUs) are characterised by the presence of many microbes, some of which may not be identified by traditional culture techniques. Total contact casting (TCC) remains the gold-standard for offloading, yet little is known about the microbiome of wounds that progress from hard-to-heal to closed within a TCC. A patient with a DFU underwent weekly treatment with TCC to closure. Samples for next-generation sequencing (NGS) and bioinformatics analysis of tissue samples were collected during each visit. Detection, identification, characterisation of the microbial community and abundance of microbes in each sample were compared. Abundance of microbes, identified by species and strain, changed with each treatment visit. By the final week of treatment, species diversity of the wound microbiome had decreased significantly, highlighted by an observed decrease in the number of total microorganisms present. Resistance genes for tetracyclines were detected in the first sample, but not in subsequent samples. The results of this study suggest dynamic microbiological changes associated with DFUs as they progress to healing within a TCC. As NGS becomes more readily available, further studies will be helpful to gain an improved understanding of the significance of the wound microbiome in patients with DFUs.

555 A novel inhabitant of the wound microbiome promotes wound healing through IL-6-mediated re-epithelialization

The skin microbiome exists at the interface of all cutaneous wounds, but microbial community constituents with the potential to confer a beneficial wound healing response are virtually unexplored. We previously performed a metagenomic analysis of diabetic foot ulcer samples and unearthed one such candidate microbe, Alcaligenes faecalis, which was the fourth most abundant species in the cohort but has scarcely been studied in the context of wounds. We found that treating murine diabetic wounds with A.