Cutaneous Surgical Wounds Have Distinct Microbiomes from Intact Skin

Identification and Analysis of the Ankle Microbiome Using Next-Generation DNA Sequencing: An Observational Analysis

INTRODUCTION

Next-generation DNA sequencing (NGS) technologies have increased the sensitivity for detecting the bacterial presence and have been used in other areas of orthopaedics to better understand the native microbiome of various joints. This study uses NGS to determine whether (1) a unique microbiome exists in human ankle tissues, (2) if components of the ankle microbiome affect patient outcomes, and (3) whether microbes found on the skin are a normal part of the ankle microbiome.

METHODS

A prospective study recruited 32 patients undergoing total ankle arthroplasty (n = 23) or ankle arthrodesis (n = 9) via direct anterior approach between November 2020 and October 2021. During surgery, five layers of the ankle were swabbed: skin (n = 32), retinaculum (n = 31), tibialis anterior tendon (n = 31), joint capsule (n = 31), and distal tibia (n = 32). These swabs (N = 157) were sent to MicroGen Diagnostics (Lubbock) for NGS. Demographics, medical comorbidities, surgical indication, postoperative complications, readmission, and revision surgery rates were collected from patient records.

RESULTS

The mean age was 60.7 (range, 19 to 85) years, and the mean follow-up duration was 10.2 (range, 4.8 to 20.6) months. Of 157 swabs sent for NGS, 19 (12.1%) indicated that bacteria were present (positive), whereas the remaining 138 (87.9%) had no bacteria present (negative). The most common organisms were Cutibacterium acnes in eight ankles (25.0%) and Staphylococcus epidermidis in two ankles (6.25%). Most bacteria were found in the retinaculum (29.6%). Complications, nonunions, infections, 90-day readmission, and revision surgery rates did not differ by NGS profile.

DISCUSSION

This study found that C acnes and S epidermidis were the most common bacteria in the ankle microbiome, with C acnes being present in 25% of ankles. Complication rates did not differ between patients with or without positive bacterial DNA remnants. Thus, we concluded that a unique ankle microbiome is present in some patients, which is unique from that of the skin of the ankle.

LEVEL OF EVIDENCE

Level II, Prospective cohort study.

The wound microbiota: microbial mechanisms of impaired wound healing and infection

The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.

Commensal skin bacteria exacerbate inflammation and delay skin barrier repair

The skin microbiome can both trigger beneficial immune stimulation and pose a potential infection threat. Previous studies have shown that colonization of mouse skin with the model human skin commensal Staphylococcus epidermidis is protective against subsequent excisional wound or pathogen challenge. However, less is known about concurrent skin damage and exposure to commensal microbes, despite growing interest in interventional probiotic therapy. Here, we address this open question by applying commensal skin bacteria at a high dose to abraded skin. While depletion of the skin microbiome via antibiotics delayed repair from damage, probiotic-like application of commensals-- including the mouse commensal Staphylococcus xylosus, three distinct isolates of S. epidermidis, and all other tested human skin commensals-- also significantly delayed barrier repair. Increased inflammation was observed within four hours of S. epidermidis exposure and persisted through day four, at which point the skin displayed a chronic wound-like inflammatory state with increased neutrophil infiltration, increased fibroblast activity, and decreased monocyte differentiation. Transcriptomic analysis suggested that the prolonged upregulation of early canonical proliferative pathways inhibited the progression of barrier repair. These results highlight the nuanced role of members of the skin microbiome in modulating barrier integrity and indicate the need for caution in their development as probiotics.

Genomic characterization of the C. tuberculostearicum species complex, a prominent member of the human skin microbiome

IMPORTANCE

Amplicon sequencing data combined with isolate whole genome sequencing have expanded our understanding of Corynebacterium on the skin. Healthy human skin is colonized by a diverse collection of Corynebacterium species, but Corynebacterium tuberculostearicum predominates on many skin sites. Our work supports the emerging idea that C. tuberculostearicum is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex, including a potentially new species we term Corynebacterium hallux based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomic analysis, and growth in skin-like media. This isolate collection and high-quality genome resource set the stage for developing engineered strains for both basic and translational clinical studies.

Commensal skin bacteria exacerbate inflammation and delay skin healing

The skin microbiome can both trigger beneficial immune stimulation and pose a potential infection threat. Previous studies have shown that colonization of mouse skin with the model human skin commensal Staphylococcus epidermidis is protective against subsequent excisional wound or pathogen challenge. However, less is known about concurrent skin damage and exposure to commensal microbes, despite growing interest in interventional probiotic therapy. Here, we address this open question by applying commensal skin bacteria at a high dose to abraded skin. While depletion of the skin microbiome via antibiotics delayed repair from damage, application of commensals-- including the mouse commensal Staphylococcus xylosus, three distinct isolates of S. epidermidis, and all other tested human skin commensals-- also significantly delayed barrier repair. Increased inflammation was observed within four hours of S. epidermidis exposure and persisted through day four, at which point the skin displayed a chronic-wound-like inflammatory state with increased neutrophil infiltration, increased fibroblast activity, and decreased monocyte differentiation. Transcriptomic analysis suggested that the prolonged upregulation of early canonical proliferative pathways inhibited the progression of barrier repair. These results highlight the nuanced role of members of the skin microbiome in modulating barrier integrity and indicate the need for caution in their development as probiotics.

Topical Application of Skin Biome Care Regimen Containing Live Cultures and Ferments of Cutibacterium acnes defendens strain XYCM42 and the Impact on Clinical Outcomes Following Microneedle-induced Skin Remodeling

Background

The skin, our body's largest organ, hosts a complex microbiome that plays a pivotal role in maintaining health and protecting against pathogens. Even slight disruptions to this delicate balance can influence skin health and disease. Among the diverse microbial community, Cutibacterium acnes (C. acnes) subspecies defendens is known for its positive contribution to skin health. However, the interaction between living microbe probiotics and wound healing after aesthetic procedures, such as microneedling, remains unexplored.

Methods

Our study included 40 participants with acne scars who underwent four microneedling sessions spaced three weeks apart. They were randomly assigned to Group 1, receiving a regimen with live C. acnes defendens strain XYCM42, or Group 2, following a conventional skincare routine with a cleanser, moisturizer, and sunscreen. Our study assessed various endpoints, including the Clinician's Global Aesthetic Improvement Scale (CGAIS), clinical safety, improvement in acne scars using Goodman and Baron's Qualitative and Quantitative Acne Scars Grading Scale and Subject's Global Aesthetic Improvement Scale (SGAIS).

Results

Our analysis of live and photo grading data for CGAIS unveiled a statistically significant difference between the two groups, with Group 1 (XYCM42-based regimen) showing remarkable improvement. A similar positive trend was observed in the photo grading for CGAIS. Additionally, participant diaries indicated that Group 1 experienced a faster decline in posttreatment parameters, including erythema, swelling, burning/tingling, and itching.

Conclusion

Integrating a microbiome-optimized, probiotic XYCM42-based regimen with microneedling demonstrated a high safety profile and enhanced treatment outcomes. These findings mark a milestone in aesthetic dermatology, supporting innovative microbiome-based approaches to improve skin health and aesthetics.

Effects of Factors Influencing Scar Formation on the Scar Microbiome in Patients with Burns

Skin microbiome dysbiosis has deleterious effects, and the factors influencing burn scar formation, which affects the scar microbiome composition, are unknown. Therefore, we investigated the effects of various factors influencing scar formation on the scar microbiome composition in patients with burns. We collected samples from the burn scar center and margin of 40 patients with burns, subgrouped by factors influencing scar formation. Scar microbiome composition-influencing factors were analyzed using univariate and multivariate analyses. Skin graft, hospitalization period, intensive care unit (ICU) admission, burn degree, sex, age, total body surface area burned (TBSA), time post-injury, transepidermal water loss, the erythrocyte sedimentation rate, and C-reactive protein levels were identified as factors influencing burn scar microbiome composition. Only TBSA and ICU admission were associated with significant differences in alpha diversity. Alpha diversity significantly decreased with an increase in TBSA and was significantly lower in patients admitted to the ICU than in those not admitted to the ICU. Furthermore, we identified microorganisms associated with various explanatory variables. Our cross-sectional systems biology study confirmed that various variables influence the scar microbiome composition in patients with burns, each of which is associated with various microorganisms. Therefore, these factors should be considered during the application of skin microbiota for burn scar management.

Emerging Trends and Focus in Human Skin Microbiome Over the Last Decade: A Bibliometric Analysis and Literature Review

Background

Human skin microbiome is the first barrier against exogenous attack and is associated with various skin disease pathogenesis and progression. Advancements in high-throughput sequencing technologies have paved the way for a deeper understanding of this field. Based on the bibliometric analysis, this investigation aimed to identify the hotspots and future research trends associated with human skin microbiomes studied over the past decade.

Methods

The published research on skin microbiome from January 2013 to January 2023 was retrieved from the Web of Science Core Collection. Data cleaning processes to ensure robust data and the bibliometrix packages R, CiteSpace, VOSviewer, Origin, and Scimago Graphica for bibliometric and visual analyses were utilized.

Results

A total of 1629 published documents were analyzed. The overall publication trend steadily increased, with relatively fast growth in 2017 and 2020. The United States of America has the highest number of publications and citations and shows close collaborations with China and Germany. The University of California, San Diego, indicated a higher number of publications than other institutions and the fastest growth rate. The top three most publishing journals on this topic are Microorganisms, Frontiers in Microbiology, and Experimental dermatology. Gallo RL is the most influential author with the highest h- and g-index and most publications in skin microecology, followed by Grice EA and Kong HH. The top 10 most frequently used keywords in recent years included skin microbiome, microbiome, staphylococcus aureus, diversity, atopic dermatitis, skin, bacteria, infections, gut microbiota, and disease.

Conclusion

The skin microbiome is an area of research that requires continuous analysis, and even with much-achieved progress, future research will further be aided as technology develops.

Looking for the Ideal Probiotic Healing Regime

Wound healing is a multi-factorial response to tissue injury, aiming to restore tissue continuity. Numerous recent experimental and clinical studies clearly indicate that probiotics are applied topically to promote the wound-healing process. However, the precise mechanism by which they contribute to healing is not yet clear. Each strain appears to exert a distinctive, even multi-factorial action on different phases of the healing process. Given that a multi-probiotic formula exerts better results than a single strain, the pharmaceutical industry has embarked on a race for the production of a formulation containing a combination of probiotics capable of playing a role in all the phases of the healing process. Hence, the object of this review is to describe what is known to date of the distinctive mechanisms of each of the most studied probiotic strains in order to further facilitate research toward the development of combinations of strains and doses, covering the whole spectrum of healing. Eleven probiotic species have been analyzed, the only criterion of inclusion being a minimum of two published research articles.

Role of Lactiplantibacillus plantarum UBLP-40, Lactobacillus rhamnosus UBLR-58 and Bifidobacterium longum UBBL-64 in the Wound Healing Process of the Excisional Skin

The probiotics Lactiplantibacillus plantarum UBLP-40, Lactobacillus rhamnosus UBLR-58 and Bifidobacterium longum UBBL-64 seem to promote wound healing when applied topically. Our aim was to investigate their effect on the mRNA expression of pro-inflammatory, healing and angiogenetic factors during the healing process of a standardized excisional wound model in rats. Rats subjected to six dorsal skin wounds were allocated to Control; L. plantarum; combined formula of L. rhamnosus plus B. longum; L. rhamnosus; and B. longum treatments, applied every two days, along with tissue collection. The pro-inflammatory, wound-healing, and angiogenetic factors of mRNA expression were assessed by qRT-PCR. We found that L. plantarum exerts a strong anti-inflammatory effect in relation to L. rhamnosus-B. longum, given alone or in combination; the combined regime of L. rhamnosus-B. longum, works better, greatly promoting the expression of healing and angiogenic factors than L. plantarum. When separately tested, L. rhamnosus was found to work better than B. longum in promoting the expression of healing factors, while B. longum seems stronger than L. rhamnosus in the expression of angiogenic factors. We, therefore, suggest that an ideal probiotic treatment should definitively contain more than one probiotic strain to speed up all three healing phases.