Longitudinal Evaluation of the Skin Microbiome and Association with Microenvironment and Treatment in Canine Atopic Dermatitis

Longitudinal evaluation of the cutaneous and rectal microbiota of German shepherd dogs with perianal fistulas undergoing therapy with ciclosporin and ketoconazole

BACKGROUND

Perianal fistulas are painful ulcers or sinus tracts that disproportionately affect German shepherd dogs and are proposed as a spontaneous animal model of fistulising Crohn's disease.

OBJECTIVES

To characterise the rectal and cutaneous microbiota in German shepherd dogs with perianal fistulas and to investigate longitudinal shifts with lesion resolution during immunomodulatory therapy.

ANIMALS

Eleven German shepherd dogs with perianal fistulas and 15 healthy German shepherd dogs.

MATERIALS AND METHODS

Affected dogs were evaluated and swabbed at three visits, 30 days apart, while undergoing treatment with ciclosporin and ketoconazole. Healthy German shepherd dogs were contemporaneously sampled. Sites included the rectum, perianal skin and axilla. The microbiome was evaluated following sequencing of the V4 hypervariable region of the 16S ribosomal RNA (rRNA) gene.

RESULTS

Alpha diversity was not significantly different between healthy and affected dogs at each of the three body sites (p > 0.5), yet rectal and perianal beta diversities from affected dogs differed significantly from those of healthy dogs at Day 0 (p = 0.004). Rectal and perianal relative abundance of Prevotella spp. increased and perianal Staphylococcus spp. relative abundance decreased in affected dogs over time, coincident with lesion resolution.

CONCLUSIONS AND CLINICAL RELEVANCE

Changes in lesional cutaneous and rectal microbiota occur in German shepherd dogs with perianal fistulas and shift over time with lesion resolution during immunomodulatory therapy. Further investigations of the role of cutaneous and enteric microbiota in the pathogenesis of perianal fistulas, and whether manipulation of microbial populations may ameliorate disease, are needed.

Considerations for performing companion animal skin microbiome studies

The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.

Bacterial microbiota and proinflammatory cytokines in the anal sacs of treated and untreated atopic dogs: Comparison with a healthy control group

The pathogenesis of anal sacculitis has not been extensively investigated, although atopic dogs seem to be predisposed to the disease. The aim of this study was therefore to characterize and compare the bacterial microbiota and pro-inflammatory cytokines in the anal sacs of dogs from three groups (healthy dogs, untreated atopic dogs and atopic dogs receiving antipruritic treatment or allergen-specific immunotherapy) in order to determine whether changes could be at the origin of anal sacculitis in atopic dogs. Bacterial populations of anal sac secretions from fifteen healthy dogs, fourteen untreated and six treated atopic dogs were characterized by sequencing the V4 region of the 16S rRNA gene using Illumina technology. Proinflammatory cytokines were analyzed with the Luminex multiplex test. Community membership and structure were significantly different between the anal sacs of healthy and untreated atopic dogs (P = 0.002 and P = 0.003, respectively) and between those of untreated and treated atopic dogs (P = 0.012 and P = 0.017, respectively). However, the community structure was similar in healthy and treated atopic dogs (P = 0.332). Among the proinflammatory cytokines assessed, there was no significant difference between groups, except for interleukin 8 which was higher in the anal sacs of untreated atopic dogs compared to treated atopic dogs (P = 0.02), and tumor necrosis factor-alpha which was lower in the anal sacs of healthy dogs compared to treated atopic dogs (P = 0.04). These results reveal a dysbiosis in the anal sacs of atopic dogs, which may partially explain the predisposition of atopic dogs to develop bacterial anal sacculitis. Treatments received by atopic dogs (oclacitinib, desloratadine and allergen-specific immunotherapy) shift the microbiota of the anal sacs towards that of healthy dogs. Further studies are required to identify significant cytokines contributing to anal sacculitis in atopic dogs.

Efficacy of Chlorhexidine Impregnated Wipes for the Local Dysbiosis in Atopic Dogs: A Multicentric Prospective Study

(1) Background: Dysbiosis is frequently observed in Canine Atopic Dermatitis (CAD). Antimicrobial treatment may be necessary to treat flare ups and the use of topical treatments is beneficial to prevent the development of bacterial resistance. Wipes are an easy way to apply antiseptic agents on the skin. The aim of this study was to evaluate the benefits of 3% chlorhexidine impregnated wipes (Pyoskin® wipes, MP Labo, France) on local areas of dysbiosis in dogs with CAD. (2) Methods: A total of 20 dogs suffering from CAD presented with localised areas of dysbiosis were included in this study. Affected areas were cleansed with the daily application of chlorhexidine wipes once a day for 14 days. Follow-up visits were scheduled after one and two weeks. Clinical signs (lesions and pruritus), dysbiosis scored by cytological counts (cocci and Malassezia) and investigator and owner global appreciation were evaluated. (3) Results: A statistically significant decrease in clinical scores and cytological counts were observed as soon as D7 and until D14. Both owner and investigator appreciation were considered high (4) Conclusions: The use of chlorhexidine impregnated wipes is a useful and easy way to manage localised dysbiosis in atopic dogs and allows limiting of systemic medication to prevent bacterial resistance.

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs

Human cutaneous squamous cell carcinomas (SCCs) and actinic keratoses (AK) display microbial dysbiosis with an enrichment of staphylococcal species, which have been implicated in AK and SCC progression. SCCs are common in both felines and canines and are often diagnosed at late stages leading to high disease morbidity and mortality rates. Although recent studies support the involvement of the skin microbiome in AK and SCC progression in humans, there is no knowledge of this in companion animals. Here, we provide microbiome data for SCC in cats and dogs using culture-independent molecular profiling and show a significant decrease in microbial alpha diversity on SCC lesions compared to normal skin (P ≤ 0.05). Similar to human skin cancer, SCC samples had an elevated abundance of staphylococci relative to normal skin-50% (6/12) had >50% staphylococci, as did 16% (4/25) of perilesional samples. Analysis of Staphylococcus at the species level revealed an enrichment of the pathogenic species Staphylococcus felis in cat SCC samples, a higher prevalence of Staphylococcus pseudintermedius in dogs, and a higher abundance of Staphylococcus aureus compared to normal skin in both companion animals. Additionally, a comparison of previously published human SCC and perilesional samples against the present pet samples revealed that Staphylococcus was the most prevalent genera across human and companion animals for both sample types. Similarities between the microbial profile of human and cat/dog SCC lesions should facilitate future skin cancer research.

IMPORTANCE

The progression of precancerous actinic keratosis lesions (AK) to cutaneous squamous cell carcinoma (SCC) is poorly understood in humans and companion animals, despite causing a significant burden of disease. Recent studies have revealed that the microbiota may play a significant role in disease progression. Staphylococcus aureus has been found in high abundance on AK and SCC lesions, where it secretes DNA-damaging toxins, which could potentiate tumorigenesis. Currently, a suitable animal model to investigate this relationship is lacking. Thus, we examined the microbiome of cutaneous SCC in pets, revealing similarities to humans, with increased staphylococci and reduced commensals on SCC lesions and peri-lesional skin compared to normal skin. Two genera that were in abundance in SCC samples have also been found in human oral SCC lesions. These findings suggest the potential suitability of pets as a model for studying microbiome-related skin cancer progression.

Canine Atopic Dermatitis: Prevalence, Impact, and Management Strategies

Atopic dermatitis (AD) is a common inflammatory and pruritic allergic skin disease in humans and dogs worldwide. The pathogenesis of AD is multifactorial, immunologically complex, and may involve genetic factors, epidermal barrier dysfunction, microbiome changes, immune dysregulation, and allergic sensitization. Across species, prevalence of AD is on the rise. At present, there is no cure for canine AD (CAD). The treatment for CAD is multifaceted and aimed at controlling the pruritus, associated inflammation, and infections, repairing the skin barrier function, and dietary management. This review presents data on prevalence, impact, and complex immunological interactions in AD with a focus on subsequent management of the disease in the canine population. A multimodal approach for management of CAD to address varying clinical signs and responses to therapies is discussed.

Update on the skin barrier, cutaneous microbiome and host defence peptides in canine atopic dermatitis

BACKGROUND

Canine atopic dermatitis (AD) is a complex inflammatory skin disease associated with cutaneous microbiome, immunological and skin barrier alterations. This review summarises the current evidence on skin barrier defects and on cutaneous microbiome dysfunction in canine AD.

OBJECTIVE

To this aim, online citation databases, abstracts and proceedings from international meetings on skin barrier and cutaneous microbiome published between 2015 and 2023 were reviewed.

RESULTS

Since the last update on the pathogenesis of canine AD, published by the International Committee on Allergic Diseases of Animals in 2015, 49 articles have been published on skin barrier function, cutaneous/aural innate immunity and the cutaneous/aural microbiome in atopic dogs. Skin barrier dysfunction and cutaneous microbial dysbiosis are essential players in the pathogenesis of canine AD. It is still unclear if such alterations are primary or secondary to cutaneous inflammation, although some evidence supports their primary involvement in the pathogenesis of canine AD.

CONCLUSION AND CLINICAL RELEVANCE

Although many studies have been published since 2015, the understanding of the cutaneous host-microbe interaction is still unclear, as is the role that cutaneous dysbiosis plays in the development and/or worsening of canine AD. More studies are needed aiming to design new therapeutic approaches to restore the skin barrier, to increase and optimise the cutaneous natural defences, and to rebalance the cutaneous microbiome.

A Randomized Controlled Trial to Evaluate the Impact of a Novel Probiotic and Nutraceutical Supplement on Pruritic Dermatitis and the Gut Microbiota in Privately Owned Dogs

Pruritic dermatitis (PD) is a common presentation of canine allergic skin diseases, with diversity in severity and treatment response due to complex etiopathogenesis. Evidence suggests the gut microbiota (GM) may contribute to the development of canine allergies. A 10-week double-blind randomized controlled trial evaluated a novel probiotic and nutraceutical blend (PNB) on clinical signs of skin allergy, health measures, and the GM of privately owned self-reported pruritic dogs. A total of 105 dogs were enrolled, with 62 included in pruritus and health analysis and 50 in microbiome analysis. The PNB supported greater improvement of owner-assessed clinical signs of PD at week 2 than the placebo (PBO). More dogs that received the PNB shifted to normal pruritus (digital PVAS10-N: <2) by week 4, compared to week 7 for the PBO. While a placebo effect was identified, clinical differences were supported by changes in the GM. The PNB enriched three probiotic bacteria and reduced abundances of species associated with negative effects. The PBO group demonstrated increased abundances of pathogenic species and reduced abundances of several beneficial species. This trial supports the potential of the PNB as a supplemental intervention in the treatment of PD; however, further investigation is warranted, with stricter diagnostic criteria, disease biomarkers and direct veterinary examination.

A review of cutaneous hypersensitivity reactions in dogs: A diagnostician's guide to allergy

Allergic dermatoses are common in people and domestic animals. Resultant lesions are routinely biopsied and submitted for histological examination to confirm a diagnosis or rule out diseases with overlapping or atypical clinical features. Diagnostic pathologists and clinicians are often faced with the difficult task of determining whether an allergic reaction pattern is present on both the microscopic and macroscopic levels and correlating histopathologic findings with clinical and historical data to achieve a precise clinical diagnosis. The bulk of the current veterinary literature on allergic dermatoses focuses on atopic dermatitis in dogs, distantly followed by cats, horses, and other animals. The objectives of this review are to demonstrate the key histopathologic and clinical diagnostic features of the various allergy-mediated reaction patterns, and to provide diagnosticians with a practical guide for clinicopathological correlations. Current concepts in the pathophysiology of immediate hypersensitivity reactions, with a focus on atopic dermatitis, are discussed. Points of potential histopathologic overlap between the "classic" allergic reaction pattern and less common inflammatory, predominately eosinophilic, conditions that may mimic this pattern will be discussed with the goal of highlighting the critical need for collaboration between pathologists and clinicians in furthering patient care.

Common superficial and deep cutaneous bacterial infections in domestic animals: A review

The skin covers the external surface of animals, and it is constantly exposed to and inhabited by different microorganisms, including bacteria. Alterations in the skin barrier allow commensal and/or pathogenic bacteria to proliferate and penetrate deep into the lower layers of the skin. Being the first barrier to the external environment, the skin is prone to injuries, allowing the penetration of microorganisms that may lead to severe deep infections. Companion animals, especially dogs, are prone to bacterial infections, often secondary to allergic dermatitis. When environmental conditions are unfavorable, horses, cattle, sheep, and goats can develop superficial infections, such as those caused by Dermatophilus congolensis. Deep inflammation is commonly caused by Mycobacterium spp., which results in granulomatous to pyogranulomatous dermatitis and panniculitis. Likewise, bacteria such as Nocardia spp. and Actinomyces spp. can cause deep pyogranulomatous inflammation. Bacteria that lead to deep necrotizing lesions (eg, necrotizing fasciitis/flesh-eating bacteria) can be severe and even result in death. This review includes an overview of the most common cutaneous bacterial infections of domestic animals, highlighting the main features and histologic morphology of the bacteria, cutaneous structures involved, and the type of inflammatory infiltrates.

A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs

BACKGROUND

Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential intervention is modulation of the composition of gut microbiota, and in fact, probiotic treatment has been proposed and tried in human atopic dermatitis (AD) patients. Since dogs are currently receiving intensive medical care, this will be the same option for dogs, while evidence of gut dysbiosis in cAD is still missing, although skin microbial profiling in cAD has been conducted in several studies. Therefore, we conducted a comprehensive analysis of both gut and skin microbiota in cAD in one specific cAD-predisposed breed, Shiba Inu. Additionally, we evaluated the impact of commonly used medical management on cAD (Janus kinase; JAK inhibitor, oclacitinib) on the gut and skin microbiota. Furthermore, we genotyped the Shiba Inu dogs according to the mitochondrial DNA haplogroup and assessed its association with the composition of the gut microbiota.

RESULTS

Staphylococcus was the most predominant bacterial genus observed in the skin; Escherichia/Shigella and Clostridium sensu stricto were highly abundant in the gut of cAD-affected dogs. In the gut microbiota, Fusobacteria and Megamonas were highly abundant in healthy dogs but significantly reduced in cAD-affected dogs. The abundance of these bacterial taxa was positively correlated with the effect of the treatment and state of the disease. Oclacitinib treatment on cAD-affected dogs shifted the composition of microbiota towards that in healthy dogs, and the latter brought it much closer to healthy microbiota, particularly in the gut. Additionally, even within the same dog breed, the mtDNA haplogroup varied, and there was an association between the mtDNA haplogroup and microbial composition in the gut and skin.

CONCLUSIONS

Dysbiosis of both the skin and the gut was observed in cAD in Shiba Inu dogs. Our findings provide a basis for the potential treatment of cAD by manipulating the gut microbiota as well as the skin microbiota. Video Abstract.

The role of bacterial colonisation in severity, symptoms and aetiology of hand eczema: The importance of Staphylococcus aureus and presence of commensal skin flora

BACKGROUND

The role and causality of the microbial ecosystem on the skin in relation to the development of hand eczema (HE) is still unknown.

OBJECTIVES

To investigate the prevalence of different bacterial colonisations in HE patients and their association with the severity, symptoms and aetiology of the disease.

METHODS

In a retrospective cohort study of 167 HE patients, bacterial swabs from lesional skin were collected for culturing. Patients were categorised according to bacterial colonisation, HE severity, HE symptoms and HE aetiology.

RESULTS

The majority of the patients were tested positive for Staphylococcus aureus (S. aureus) (n = 131, 78.4%) and/or commensal skin flora (CSF; n = 130, 77.8%), while other bacteria species were found only sporadically. Severe HE was significantly more prevalent in skin with S. aureus (odds ratio [OR]: 5.13, 95% confidence interval [CI]: 2.21-11.94) and less common in skin with CSF (OR: 0.20, 95% CI: 0.05-0.88). S. aureus colonisation was also associated with atopic HE aetiology (p < 0.001) and acute HE symptoms such as blisters, erosions and crusts (p = 0.003).

CONCLUSIONS

The main colonisation of HE patients is with S. aureus and is associated with disease severity, acute HE symptoms and atopic HE aetiology. CSF is associated with mild HE, which could result in new therapeutic approaches.

Impacts to canine dermal microbiota associated with repeated bathing

Introduction

Working dogs routinely operate in environmental conditions which may necessitate daily bathing to remove contaminants or soilage. The impacts of frequent or repeated bathing on the canine dermal microbiota are unknown. The objective of this study was to characterize changes in canine dermal microbial populations following repeated daily bathing.

Methods

Labrador retrievers (n = 16) were bathed daily using a dilute dish detergent solution (1.6% detergent solution) over the course of 14 days. Dermal microbial DNA was collected via sterile swabs (n = 142) taken at days 0, 7, 14, 16, 21, 28, 35, 42, and 49 and analyzed for alpha diversity, beta diversity and relative abundance to assess changes in the dermal microbiota via 16 s sequencing.

Results

Results indicate that daily bathing significantly increased Shannon diversity, Chao1, and several rare amplicon sequence variants. Although typically reported in highest abundance, relative abundance was decreased in the phyla Actinobacteria, Firmicutes, and Proteobacteria (p < 0.05).

Conclusion

Repeated daily bathing with dilute dish detergent significantly reduced normal healthy dermal microbial taxa and created significant changes in the dermal microbiota of canines. Disruption to the canine dermal microbiota may cause negative impacts to canine dermal health and require further investigation.

The feline skin microbiome: interrelationship between health and disease

PRACTICAL RELEVANCE

As with other species, the skin microbiome of cats has been assessed over the past few years utilizing modern technologies. This has resulted in the identification of many more bacterial and fungal organisms compared with what had been recorded historically on the skin in various states of health and disease using culture-based studies. This information is expanding the knowledge of how microbial communities are impacted by various changes in the skin health of cats. More specifically, how these microbial communities change in the face of health and disease, and how various therapeutic interventions affect the cutaneous microbiome, lends a greater understanding of disease pathogenesis and provides a growing area of research for correcting dysbiosis and improving feline skin health.

EVIDENCE BASE

Most studies on the feline skin microbiome thus far have been descriptive in nature. These provide a framework for the next level of investigations on how various states of health and disease impact the products produced by the cutaneous microbiome (ie, the cutaneous metabolome), as well as how targeted interventions may promote the restoration of balance.

AIMS

This review aims to summarize what is currently known about the feline cutaneous microbiome and its clinical implications. The role of the skin microbiome in health and disease, the current state of research in this area and the potential for future studies to produce targeted interventions for cats are a particular focus.

Nasal microbiota profiles in shelter dogs with dermatological conditions carrying methicillin-resistant and methicillin-sensitive Staphylococcus species

Dermatological conditions may be complicated by Staphylococcus spp. infections influencing skin and nasal microbiota. We investigated the associations between the resident nasal microbiota of shelter dogs with and without dermatological conditions carrying methicillin-resistant and -sensitive Staphylococcus spp. Nasal sampling of 16 dogs with and 52 without dermatological conditions were performed upon shelter admission (baseline), and then bi-weekly until discharge (follow-up). All samples were cultured for Staphylococcus spp., while 52 samples underwent microbiota analysis. Two elastic net logistic regression (ENR) models (Model 1-baseline samples; Model 2-follow-up samples) were developed to identify predictive associations between dermatological conditions and the variables: signalment, antimicrobial treatment, and nasal microbial genera. Follow-up nasal samples of dogs with dermatological conditions had decreased microbiota diversity and abundance compared to dogs without dermatological conditions. Our ENR models identified predictive differences in signalment and nasal microbial genera between baseline and follow-up samples. Co-occurrence networks showed nasal microbial genera were more dissimilar when comparing dogs with and without dermatological conditions at follow-up. Overall, this study is the first to investigate Staphylococcus spp. carriage effects on nasal microbial genera in a canine animal shelter population, and ultimately reveals the importance of investigating decolonisation and probiotic therapies for restoring nasal microbiota.

Is Vitamin D3 a Worthy Supplement Protecting against Secondary Infections in Dogs with Atopic Dermatitis?

Canine atopic dermatitis (CAD) is a common, chronic, inflammatory skin disease in dogs worldwide. This disease often predisposes for secondary organisms overgrowth and skin infections with pathogens, such as Staphylococcus pseudintermedius and Malassezia pachydermatis. Unfortunately, the causes of this disease in both humans and animals are not fully understood; therefore, the only possible option is a lifelong, symptomatic treatment. The management of CAD is mainly based on limiting contact with allergens and antipruritic therapy, most often with glucocorticoids and antihistamines. A serious problem in this situation is the fact, that long-term administration of glucocorticoids leads to side effects like polyuria, alopecia, increased susceptibility to infection, muscle atrophy, and many others. For this reason, great emphasis is placed on the development of replacement and supportive therapies. It is a well-documented fact that reduced concentrations of serum vitamin D3 contribute to the severity of atopic dermatitis symptoms in humans. Moreover, unlike the most commonly used therapeutic methods, of which the main goal is to ameliorate inflammation and pruritus, namely the symptoms of AD, vitamin D3 supplementation affects some underlying factors of this disease. Therefore, in this review, we summarize the current state of knowledge regarding the role of vitamin D3 in CAD, its protective effect against secondary bacterial and fungal infections, and the potential of its supplementation in dogs.

Establishing an experimental model for canine atopic dermatitis through epicutaneous application of Dermatophagoides farinae

There is no established protocol for the development of an experimental canine atopic dermatitis model in laboratory beagles. This study aimed to establish an experimental model that mimics spontaneous canine atopic dermatitis (CAD) clinically, immunologically, and microbiologically, by repeated epicutaneous applications of mite antigens and to describe the entire process including sensitization and provocation in detail for reproducibility. Six intact male laboratory beagle dogs aged 14 months were included in this study. During the sensitization and provocation phase, the house dust mite (HDM) paste consisted of Dermatophagoides farinae (Der f ) and mineral oil, which was applied focally to the 10 × 10 cm area of the right groin as evenly as possible. Further, 120 mg of Der f was applied to each dog twice a week for 12 weeks during the sensitization phase and 25 mg and 120 mg was applied to each dog for the first 2 weeks and subsequent 2 weeks, respectively, during the provocation phase. Thereafter, the applied area was covered with a dressing. Skin lesions including erythema, hyperpigmentation, excoriation, and lichenification were induced and exacerbated gradually through the experimental time course in all six dogs. The canine atopic dermatitis extent and severity index (CADESI) score and transepidermal water loss (TEWL) significantly increased after sensitization and provocation. IL-13 and IL-31 levels increased significantly after provocation as a result of the activation of the T helper-2 (Th2) response. On the contrary, the IL-10 levels decreased significantly after sensitization, which suggested a suppression of Tregs activity. After the completion of provocation, skin microbiome analysis showed that Firmicutes was the most abundant phylum, which indicated bacterial dysbiosis. This study demonstrated that epicutaneous application of HDM in beagle dogs resulted in the elevation of serum HDM-specific IgE levels and clinical atopic scores, a high TEWL, and microbiome dysbiosis resembling spontaneous CAD. These results suggest that this tailored protocol of epicutaneous exposure to Der f may provide support for the development of the experimental CAD model in laboratory beagles.

Comparison of the Gut Microbiome between Atopic and Healthy Dogs—Preliminary Data

Simple Summary

Atopic dermatitis is a common inflammatory and itchy skin disease, constituting a global issue that affects up to 15% of the general human and dog population. The pathogenesis of this disease is known to be multifactorial and not only consisting of skin barrier dysfunction, but also with immunological dysregulation and skin microbiota changes having a central role. In humans, establishment of the gut microbiota in early life influences the development of allergies, among others also atopic dermatitis in children. To the author’s knowledge, there is currently no study comparing the gut microbiome between allergic and healthy dogs. We now present results demonstrating that allergic dogs have a significantly different gut microbiota when compared to healthy control dogs. Further investigations including a larger number of dogs are now required to confirm these results, in addition to studies utilizing novel interventions targeting the gut microbiota.

Abstract

Human studies show that in addition to skin barrier and immune cell dysfunction, both the cutaneous and the gut microbiota can influence the pathogenesis of atopic diseases. There is currently no data on the gut-skin axis in allergic canines. Therefore, the aim of this study was to assess the bacterial diversity and composition of the gut microbiome in dogs with atopic dermatitis (AD). Stool samples from adult beagle dogs (n = 3) with spontaneous AD and a healthy control group (n = 4) were collected at Days 0 and 30. After the first sampling, allergic dogs were orally dosed on a daily basis with oclacitinib for 30 days, and then re-sampled. Sequencing of the V3–V4 region of the 16S rRNA gene was performed on the Illumina MiSeq platform and the data were analyzed using QIIME2. The atopic dogs had a significantly lower gut microbiota alpha-diversity than healthy dogs (p = 0.033). In healthy dogs, a higher abundance of the families Lachnospiraceae (p = 0.0006), Anaerovoracaceae (p = 0.006) and Oscillospiraceae (p = 0.021) and genera Lachnospira (p = 0.022), Ruminococcustorques group (p = 0.0001), Fusobacterium (p = 0.022) and Fecalibacterium (p = 0.045) was seen, when compared to allergic dogs. The abundance of Conchiformibius (p = 0.01), Catenibacterium spp. (p = 0.007), Ruminococcus gnavus group (p = 0.0574) and Megamonas (p = 0.0102) were higher in allergic dogs. The differences in alpha-diversity and on the compositional level remained the same after 1 month, adding to the robustness of the data. Additionally, we could also show that a 4-week treatment course with oclacitinib was not associated with changes in the gut microbiota diversity and composition in atopic dogs. This study suggests that alterations in the gut microbiota diversity and composition may be associated with canine AD. Large-scale studies preferably associated to a multi-omics approach and interventions targeting the gut microbiota are needed to confirm these results.

Characterization of the oral and fecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony

Atopic dermatitis (AD) is a chronic and relapsing multifactorial inflammatory skin disease that also affects dogs. The oral and gut microbiota are associated with many disorders, including allergy. Few studies have addressed the oral and gut microbiota in dogs, although the skin microbiota has been studied relatively well in these animals. Here, we studied the AD-associated oral and gut microbiota in 16 healthy and nine AD dogs from a purebred Shiba Inu colony. We found that the diversity of the oral microbiota was significantly different among the dogs, whereas no significant difference was observed in the gut microbiota. Moreover, a differential abundance analysis detected the Family_XIII_AD3011_group (Anaerovoracaceae) in the gut microbiota of AD dogs; however, no bacterial taxa were detected in the oral microbiota. Third, the comparison of the microbial co-occurrence patterns between AD and healthy dogs identified differential networks in which the bacteria in the oral microbiota that were most strongly associated with AD were related with human periodontitis, whereas those in the gut microbiota were related with dysbiosis and gut inflammation. These results suggest that AD can alter the oral and gut microbiota in dogs.

A comparison of canine decontamination cleansers: Implications for water use, dermal pH, and contaminant reduction

Environmental contamination is commonly experienced by working canines deployed in the field. Unfortunately, data regarding safety and efficacy of cleansers recommended for decontamination is lacking. Client-owned canines recruited from the community (n = 43) were randomly assigned to one of four treatment groups: povidone-iodine scrub [60mL Betadine® 7.5% povidone-iodine surgical scrub (Avrio Health L.P, Stamford, CT)], chlorhexidine scrub [60 mL Nolvasan® 2% chlorohexidine surgical scrub (Zoetis, Kalamazoo, MI)], dish detergent [60mL Dawn® dish detergent (Proctor & Gamble, Cincinnati, OH)], or water alone (control). A visual score assessing removal of a fluorescent marker (GloGerm, Moab, UT) applied between the shoulder blades was used to rate effectiveness of decontamination. Cleanser effect on canine dermal barrier function was determined by measuring pre- and post-decontamination dermal pH and trans-epidermal water loss (TEWL). Analysis of visual scores was performed using PROC FREQ and Chi Square. Significance was set a priori at 0.05 for all tests. Efficacy of fluorescent marker removal was significantly affected by cleanser (P<0.0001). Dermal pH was also highly affected by cleanser (P < 0.0001). In contrast, TEWL was unchanged across cleansers (P = 0.2686). Common veterinary cleansers utilized for canine decontamination demonstrate similarity in effectiveness for removal of a simulated contaminant and negative impact on dermal barrier function.

Efficacy of Antimicrobial Treatment in Dogs with Atopic Dermatitis: An Observational Study

There is a shortage of studies reporting the efficacy of antimicrobial treatment of dogs with atopic dermatitis (AD) and skin infections (SIs). The aim of this study was to evaluate the change in the severity of skin lesions and pruritus, and the overall efficacy of antimicrobial treatment, in dogs with AD and bacterial overgrowth/infection and/or Malassezia dermatitis. A total of 20 dogs with AD and SIs were prospectively enrolled (group A) and they were examined before and after the administration of systemic antimicrobials that resulted in the resolution of SIs. In addition, 19 dogs fulfilling the same inclusion criteria and treated with systemic, with or without topical antimicrobials, were included retrospectively (group B). Since there were no major differences between the groups, their results were combined. The severity of skin lesions decreased significantly, by 30% based on Canine Atopic Dermatitis Extent and Severity Index-4 (CADESI-4), by 28.1% based on the erythema domain of CADESI-4 and based on owner’s global assessment of the severity of skin lesions. Pruritus decreased significantly, by 34.7% based on the Pruritus Visual Analogue Scale (PVAS). The efficacy of antimicrobial treatment was assessed as good to excellent by the investigator and the owner in 55% and 60% of the dogs, respectively. Despite the significant improvement, there was high variability in the response to treatment among dogs. Further studies are needed to find factors that determine the response to antimicrobial treatment in dogs with AD and SIs.

Fresh Food Consumption Increases Microbiome Diversity and Promotes Changes in Bacteria Composition on the Skin of Pet Dogs Compared to Dry Foods

The skin is the first barrier the body has to protect itself from the environment. There are several bacteria that populate the skin, and their composition may change throughout the dog’s life due to several factors, such as environmental changes and diseases. The objective of this research was to determine the skin microbiome changes due to a change in diet on healthy pet dogs. Healthy client-owned dogs (8) were fed a fresh diet for 30 days then dry foods for another 30 days after a 4-day transition period. Skin bacterial population samples were collected after each 30-day feeding period and compared to determine microbiome diversity. Alpha diversity was higher when dogs were fed the fresh diet compared to the dry foods. Additionally, feeding fresh food to dogs increased the proportion of Staphylococcus and decreased Porphyromonas and Corynebacterium. In conclusion, changing from fresh diet to dry foods promoted a relative decrease in skin microbiome in healthy pet dogs.

Malassezia: Zoonotic Implications, Parallels and Differences in Colonization and Disease in Humans and Animals

Malassezia spp. are commensals of the skin, oral/sinonasal cavity, lower respiratory and gastrointestinal tract. Eighteen species have been recovered from humans, other mammals and birds. They can also be isolated from diverse environments, suggesting an evolutionary trajectory of adaption from an ecological niche in plants and soil to the mucocutaneous ecosystem of warm-blooded vertebrates. In humans, dogs and cats, Malassezia-associated dermatological conditions share some commonalities. Otomycosis is common in companion animals but is rare in humans. Systemic infections, which are increasingly reported in humans, have yet to be recognized in animals. Malassezia species have also been identified as pathogenetic contributors to some chronic human diseases. While Malassezia species are host-adapted, some species are zoophilic and can cause fungemia, with outbreaks in neonatal intensive care wards associated with temporary colonization of healthcare worker’s hands from contact with their pets. Although standardization is lacking, susceptibility testing is usually performed using a modified broth microdilution method. Antifungal susceptibility can vary depending on Malassezia species, body location, infection type, disease duration, presence of co-morbidities and immunosuppression. Antifungal resistance mechanisms include biofilm formation, mutations or overexpression of ERG11, overexpression of efflux pumps and gene rearrangements or overexpression in chromosome 4.

Symbiotic microorganisms: prospects for treating atopic dermatitis

INTRODUCTION

Atopic dermatitis (AD) is a common chronic recurrent inflammatory skin disease. The pathogenesis is unclear but may be related to genetic, immune, and environmental factors and abnormal skin barrier function. Symbiotic microorganisms in the gut and on the skin are associated with AD occurrence.

AREAS COVERED

We discuss the metabolism and distribution of intestinal and skin flora and review their relationship with AD, summarizing the recent applications of intestinal and skin flora in AD treatment, and discussing the prospect of research on these two human microbiota systems and their influence on AD treatment. The PubMed database was searched to identify relevant publications from 1949 to 2020 for the bibliometric analysis of atopic dermatitis and symbiotic microorganisms.

EXPERT OPINION

Many studies have suggested a potential contribution of microbes in the intestine and on the skin to AD. Bacteria living on the skin can aggravate AD by secreting numerous virulence factors. Moreover, the metabolism of intestinal flora can influence AD occurrence and development via the circulatory system. Current evidence suggests that by regulating intestinal and skin flora, AD can be treated and prevented.

Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths

Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. Furthermore, we isolated nine strains of Brevibacterium and Rothia capable of producing substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales that inhabit sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem. This article is protected by copyright. All rights reserved.

Skin Microbiota Was Altered in Crocodile Lizards (Shinisaurus crocodilurus) With Skin Ulcer

Skin diseases commonly affect reptiles, but their relationships to the closely related skin microbiome are not well-understood. In recent years, both the wild and captive populations of the crocodile lizard, a Class I protected endangered animal in China, have suffered serious skin diseases that hamper the rescue and release projects for their conservation. This study conducted a detailed prevalence investigation of a major dermatosis characterized by foot skin ulcer in crocodile lizards. It should be noticed that skin ulcer has been prevalent in both captive and wild populations. There was positive correlation between skin ulcer and temperature, while no significant relationship between skin ulcer and humidity, sex, and age. We further studied the relationship between skin ulcer and the skin microbiota using meta-taxonomics. Results showed that the skin microbiota of crocodile lizards was significantly different from those of the environmental microbial communities, and that skin microbiota had a significant relationship with skin ulcer despite the impact of environment. Both bacterial and fungal communities on the ulcerated skin were significantly changed, which was characterized by lower community diversity and different dominant microbes. Our findings provide an insight into the relationship between skin microbiota and skin disease in reptile, serving as a reference for dermatological etiology in wildlife conservation.

Investigation on the Effect of Dose, Frequency and Duration of Allergen Exposure on Development of Staphylococcal Infections in a Chronic Model of Canine Atopic Dermatitis

Canine atopic dermatitis (CAD) is chronic and frequently complicated by Staphylococcal infections. Understanding the role of allergen dose, frequency and duration of exposure in triggering infections requires a model. Most models elicit acute inflammation and do not mimic real-life disease. Here we describe the effects of allergen exposures on development of infections in a model of chronic CAD. Diagnosis of pyoderma was based on clinical signs and consistent cytology. Study 1 evaluated the role of duration of exposure keeping the daily dose constant (25 mg/day). The one-week protocol involved three exposures, 3 days in a row. The one-month protocol involved twice-weekly challenges for 4 weeks. The three-month protocol involved twice-weekly challenges for 12 weeks. Study 2 evaluated different daily doses while keeping constant the total weekly dose (25 mg) and duration (3 weeks). Low-dose used 5 mg/day for 5 days, each week. High-dose used 12.5 mg/day twice-weekly. In Study 1, the longer the exposure, the more dogs developed pyoderma (6/9 in the three-month study, 2/9 in the one-month and 0 in the one-week). In Study 2, low-dose daily exposure caused more infections (5/8) than high-dose infrequent exposure (0/8). It is concluded that low-grade, daily exposure for a long time is most relevant for development of staphylococcal infections.

Efficacy of Phototherapy With 308-nm Excimer Light for Skin Microbiome Dysbiosis and Skin Barrier Dysfunction in Canine Atopic Dermatitis

The management of canine atopic dermatitis, an allergic skin disorder, is challenging. To investigate the effect of phototherapy using a 308-nm excimer light as a topical treatment for canine atopic dermatitis, 10 dogs with canine atopic dermatitis and 10 with non-allergic skin were enrolled in this study. Phototherapy was applied every 7 days for a total of 2 months. The skin microbiome, skin barrier function, and clinical outcomes were evaluated after phototherapy. Phototherapy significantly changed the composition of the skin microbiome of dogs with atopic dermatitis and significantly increased the relative abundance of the phyla Actinobacteria and Cyanobacteria. It significantly alleviated the clinical signs of canine atopic dermatitis without serious adverse effects. Transepidermal water loss, as a measure of skin barrier function, significantly decreased after phototherapy. In addition, phototherapy increased microbial diversity and decreased the relative abundance of Staphylococcus pseudintermedius associated with the severity of canine atopic dermatitis. These results suggest that the excimer light therapy is a suitable and safe therapeutic option for canine atopic dermatitis, which is also a spontaneous animal model of atopic dermatitis.

Recombinant human interferon-α14 for the treatment of canine allergic pruritic disease in eight dogs

BACKGROUND

Allergic pruritic diseases are increasingly common in dogs. This group of conditions hampers life quality as pruritus progressively interferes with normal behaviours. Therefore, new treatment modalities for canine allergic pruritic diseases are necessary. While novel drugs have recently reached the market, there is still the need for other therapeutic approaches. Some dogs are refractory even to the newer compounds, and cost is also an important issue for these. Older therapeutic modalities are only moderately successful or have considerable secondary effects, as is the case with glucocorticoids.

OBJECTIVES

Report on the use of recombinant human interferon-α14 (rhIFN-α14) for the treatment of canine allergic pruritus. Following the experience with a similar compound in the Japanese market, it was expected that rhIFN-α14 could alter the Th1/Th2 disbalance that drives these diseases.

METHODS

Here, we present an uncontrolled trial in which eight dogs with clinical diagnosis of allergic pruritus were treated with rhIFN-α14, either orally or via subcutaneous injections. Skin condition, microbiota and anti-interferon antibody levels were assessed.

RESULTS

The parenteral use of interferon induced hypersensitivity in two of the three dogs in which it was used. The oral administration was consistently safe and could reduce signs of the allergic condition in three of the five treated animals. Treatment also altered the skin microbiota, as verified by next-generation sequencing.

CONCLUSION

The present results indicate that rhIFN-α14 is a viable candidate for the treatment of canine allergic pruritus. Future controlled studies are needed, and the oral route is indicated for further trials.

Ichthyosis and hereditary cornification disorders in dogs

The stratum corneum (SC), the outermost layer of the epidermis, serves a crucial role in maintaining body hydration and protection from environmental insults. When the stratum corneum is injured or when the genetic blueprints are flawed, the body is at risk of dehydration, secondary infections and allergen sensitization. Advancements in veterinary dermatology have revealed a wide gamut of disease from relatively benign to lethal that specifically arise from flawed structural proteins, enzymes or lipids needed to create the corneocytes and lipid bilayers of the SC. Some conditions closely mimic their human counterparts while others are unique to the dog. This review will focus on forms of ichthyosis in the dog.

Experimental test of microbiome protection across pathogen doses reveals importance of resident microbiome composition

The commensal microbes inhabiting a host tissue can interact with invading pathogens and host physiology in ways that alter pathogen growth and disease manifestation. Prior work in house finches (Haemorhous mexicanus) found that resident ocular microbiomes were protective against conjunctival infection and disease caused by a relatively high dose of Mycoplasma gallisepticum. Here, we used wild-caught house finches to experimentally examine whether protective effects of the resident ocular microbiome vary with the dose of invading pathogen. We hypothesized that commensal protection would be strongest at low M. gallisepticum inoculation doses because the resident microbiome would be less disrupted by invading pathogen. Our five M. gallisepticum dose treatments were fully factorial with an antibiotic treatment to perturb resident microbes just prior to M. gallisepticum inoculation. Unexpectedly, we found no indication of protective effects of the resident microbiome at any pathogen inoculation dose, which was inconsistent with the prior work. The ocular bacterial communities at the beginning of our experiment differed significantly from those previously reported in local wild-caught house finches, likely causing this discrepancy. These variable results underscore that microbiome-based protection in natural systems can be context dependent, and natural variation in community composition may alter the function of resident microbiomes in free-living animals.

Effect of topical medication on the nasomaxillary skin-fold microbiome in French bulldogs

BACKGROUND

Host-microbe interactions may influence dermatitis pathogenesis in the nasomaxillary folds of French bulldogs, which is often complicated by secondary bacterial and fungal infections.

OBJECTIVE

To assess the skin-fold microbiome in systemically healthy French bulldogs and to determine the influence of topical medications on this microbiome.

ANIMALS

Nineteen healthy French bulldogs.

METHODS AND MATERIALS

Next-generation DNA sequencing was applied to characterise the microbiome composition in the nasomaxillary folds of systemically healthy French bulldogs. Subsequently, the effect of two topical products on the fold microbiome was assessed. Seven dogs were treated with a protease product (Kalzyme; enzyme) that inhibits biofilm formation without biocidal activity, six dogs were treated with a 2% chlorhexidine diacetate solution (Nolvasan; CHX) with biocidal activity, and six dogs were untreated. Dogs were randomly assigned to each group, and the investigator was blinded.

RESULTS

The primary skin bacterial phyla inhabiting the folds at inclusion were Firmicutes, Actinobacteria and Proteobacteria. The primary skin fungal phyla were Ascomycota and Basidiomycota. Topical treatment increased the diversity of bacterial and fungal compositions over time (increase in microbial diversity score: enzyme 38%, chlorhexidine 11%, control <5%) and the relative abundance of pathogens reduced significantly (enzyme, P = 0.028; CHX, P = 0.048). A clear correlation (r²  = 0.83) was observed between the abundance of clinically relevant pathogens and microbial diversity.

CONCLUSIONS

The nasomaxillary skin-fold microbiome of healthy French bulldogs contained a high abundance of clinically relevant pathogens (mean 36.4%). Topical therapy with enzyme increased microbial diversity of skin folds and reduced the relative abundance of pathogens.

Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important emerging zoonotic pathogen that causes severe skin infections. To combat infections from drug-resistant bacteria, the transplantation of commensal antimicrobial bacteria as a therapeutic has shown clinical promise. We screened a collection of diverse staphylococcus species from domestic dogs and cats for antimicrobial activity against MRSP. A unique strain (S. felis C4) was isolated from feline skin that inhibited MRSP and multiple gram-positive pathogens. Whole genome sequencing and mass spectrometry revealed several secreted antimicrobials including a thiopeptide bacteriocin micrococcin P1 and phenol-soluble modulin beta (PSMβ) peptides that exhibited antimicrobial and anti-inflammatory activity. Fluorescence and electron microscopy revealed that S. felis antimicrobials inhibited translation and disrupted bacterial but not eukaryotic cell membranes. Competition experiments in mice showed that S. felis significantly reduced MRSP skin colonization and an antimicrobial extract from S. felis significantly reduced necrotic skin injury from MRSP infection. These findings indicate a feline commensal bacterium that could be utilized in bacteriotherapy against difficult-to-treat animal and human skin infections.

Dogs' Microbiome From Tip to Toe

Microbiota and microbiome, which refers, respectively, to the microorganisms and conjoint of microorganisms and genes are known to live in symbiosis with hosts, being implicated in health and disease. The advancements and cost reduction associated with high-throughput sequencing techniques have allowed expanding the knowledge of microbial communities in several species, including dogs. Throughout their body, dogs harbor distinct microbial communities according to the location (e.g., skin, ear canal, conjunctiva, respiratory tract, genitourinary tract, gut), which have been a target of study mostly in the last couple of years. Although there might be a core microbiota for different body sites, shared by dogs, it is likely influenced by intrinsic factors such as age, breed, and sex, but also by extrinsic factors such as the environment (e.g., lifestyle, urban vs rural), and diet. It starts to become clear that some medical conditions are mediated by alterations in microbiota namely dysbiosis. Moreover, understanding microbial colonization and function can be used to prevent medical conditions, for instance, modulation of gut microbiota of puppies is more effective to ensure a healthy gut than interventions in adults. This paper gathers current knowledge of dogs' microbial communities, exploring their function, implications in the development of diseases, and potential interactions among communities while providing hints for further research.

Wolves, dogs and humans in regular contact can mutually impact each other's skin microbiota

In contrast to humans and dogs, the skin microbiota of wolves is yet to be described. Here, we investigated the skin microbiota of dogs and wolves kept in outdoor packs at the Wolf Science Center (WSC) via 16S rRNA gene amplicon sequencing. Skin swab samples were also collected from human care takers and their pet dogs. When comparing the three canine groups, representing different degrees of human contact to the care takers and each other, the pet dogs showed the highest level of diversity. Additionally, while human skin was dominated by a few abundant phylotypes, the skin microbiota of the care takers who had particularly close contact with the WSC animals was more similar to the microbiota of dogs and wolves compared to the humans who had less contact with these animals. Our results suggest that domestication may have an impact on the diversity of the skin microbiota, and that the canine skin microbiota can be shared with humans, depending on the level of interaction.

Epithelial-immune crosstalk with the skin microbiota in homeostasis and atopic dermatitis - a mini review

The skin is a complex and dynamic ecosystem, wherein epithelial cells, immune cells and the skin microbiota actively interact and maintain barrier integrity and functional immunity. Skin microbes actively tune the functions of the resident immune cells. Dysbiosis - alterations in the resident microbiota - leads to the dysregulation of host immunity. Microbiome analyses in humans and dogs with atopic dermatitis (AD) have shown shifts in microbial diversity, and in particular, an increased proportion of staphylococci. Monogenic diseases that manifest AD-like symptoms provide insights into the pathogenesis of AD and the mechanisms of dysbiosis, from both the epithelial and immunological perspectives. The symbiotic relationships between the host and microbiota must be maintained constitutively. Detailed mechanisms of how host immunity regulates commensal bacteria in the steady state have been reported. The skin harbours multiple tissue-resident immune cells, including both innate and adaptive immune cells. Recent studies have highlighted the fundamental role of innate lymphoid cells (ILCs) in the maintenance of barrier functions and tissue homeostasis. ILCs directly respond to tissue-derived signals and are instrumental in barrier immunity. Epithelial cells produce alarmins such as thymic stromal lymphopoietin (TSLP) and interleukins (IL)-33 and IL-25, all of which activate group 2 ILCs (ILC2s), which produce type 2 cytokines, such as IL-5 and IL-13, boosting type 2 immune reactions. Dysregulation of the epithelial-ILC crosstalk results in allergic inflammation. This review highlights our understanding of the active interactions between the host epithelial and immune cells, and microbiota, providing a foundation for novel therapeutic strategies for inflammatory skin diseases.

Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome

Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin “archaeomes” dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum, formerly Thaumarchaeota). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 samples by high-throughput sequence data, with most of the archaeon-positive samples associated with nonhuman mammalian skin. Only 5.9% of human-associated skin sample data sets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal amplicon sequence variants (ASVs) was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome data sets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downward recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome.

IMPORTANCE The current state of research on mammalian skin-associated archaea is limited, with the few papers focusing on potential skin archaeal communities often in disagreement with each other. As such, there is no consensus on the prevalence or taxonomic composition of archaea on mammalian skin. Mammalian skin health is in part influenced by its complex microbiota and consortium of bacteria and potential archaea. Without a clear foundational analysis and characterization of the mammalian skin archaeome, it will be difficult for future research to explore the potential impact of skin-associated archaea on skin health and function. The current work provides a much-needed analysis of the mammalian skin archaeome and contributes to building a foundation from which further discussion and exploration of the skin archaeome might continue.

Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes

In 2016, a new species name Cutibacterium acnes was coined for the well-documented species, Propionibacterium acnes, one of the most successful and clinically important skin commensals. The nomenclatural changes were brought about through creation of the genus Cutibacterium, when a group of propionibacteria isolates from the skin were transferred from the genus Propionibacterium and placed in the phylum Actinobacteria. Almost simultaneously, the discovery of two novel species of Cutibacterium occurred and the proposal of three subspecies of C. acnes were reported. These dramatic changes that occurred in a long-established taxon made it challenging for the non-specialist to correlate the huge volume of hitherto published work with current findings. In this review, we aim to correlate the eco-specificity and pathophysiological properties of these newly circumscribed taxa. We envisage that this information will shed light on the pathogenic potential of new isolates and enable better assessment of their clinical importance in the foreseeable future. Currently, five species are recognized within the genus: Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, Cutibacterium modestum (previously, "Propionibacterium humerusii"), and Cutibacterium namnetense. These reside in different niches reflecting their uniqueness in their genetic makeup. Their pathogenicity includes acne inflammation, sarcoidosis, progressive macular hypomelanosis, prostate cancer, and infections (bone, lumbar disc, and heart). This is also the case for the three newly described subspecies of C. acnes, which are C. acnes subspecies acnes (C. acnes type I), subspecies defendens (C. acnes type II), and subspecies elongatum (C. acnes type III). C. acnes subspecies acnes is related to inflamed acne and sarcoidosis, while subspecies defendens to prostate cancer and subspecies elongatum to progressive macular hypomelanosis. Because the current nomenclature is based upon polyphasic analyses of the biochemical and pathogenic characteristics and comparative genomics, it provides a sound basis studying the pathophysiological roles of these species.

Atopic Dermatitis in Domestic Animals: What Our Current Understanding Is and How This Applies to Clinical Practice

Atopic dermatitis is a clinical syndrome that affects both people and animals. Dogs closely mimic the complexity of the human skin disease, and much progress has been made in recent years in terms of our understanding of the role of skin impairment and the identification of new treatments. Cats and horses also develop atopic syndromes which include both cutaneous and respiratory signs, yet studies in these species are lagging. It is now recognized that atopic dermatitis is not a single disease but a multifaceted clinical syndrome with different pathways in various subgroups of patients. Appreciating this complexity is clinically relevant as we develop more targeted treatments which may work well in some patients but not in others. Different phenotypes of atopic dermatitis have been described in dogs, and it is possible that phenotypes related to breed and age may exist in other animals similar to how they are described in people. The awareness of different mechanisms of disease leads to the desire to correlate different phenotypes with specific biomarkers and responses to treatment. In this review, the current understanding and updated information on atopic syndrome in animals are described, highlighting opportunities for further studies in the future.

Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor

The epidermis forms a barrier that defends the body from desiccation and entry of harmful substances, while also sensing and integrating environmental signals. The tightly orchestrated cellular changes needed for the formation and maintenance of this epidermal barrier occur in the context of the skin microbiome. Using germ-free mice, we demonstrate the microbiota is necessary for proper differentiation and repair of the epidermal barrier. These effects are mediated by microbiota signaling through the aryl hydrocarbon receptor (AHR) in keratinocytes, a xenobiotic receptor also implicated in epidermal differentiation. Mice lacking keratinocyte AHR are more susceptible to barrier damage and infection, during steady-state and epicutaneous sensitization. Colonization with a defined consortium of human skin isolates restored barrier competence in an AHR-dependent manner. We reveal a fundamental mechanism whereby the microbiota regulates skin barrier formation and repair, which has far-reaching implications for the numerous skin disorders characterized by epidermal barrier dysfunction.

Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves (Canis lupus)

The host-associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site-specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site-specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long-term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.

Longitudinal study of the cutaneous microbiota of healthy horses

BACKGROUND

Next-generation sequencing techniques have revealed that human and animal skin is colonised by a rich and diverse population of bacteria, and that microbial composition varies between different body sites and individuals. Very little is known about the normal microbiota of healthy equine skin.

HYPOTHESIS/OBJECTIVES

To describe the taxonomic distributions of cutaneous bacterial microbiota in a population of healthy horses in Ontario, Canada, and to evaluate the effects of body site, individual and time of year on microbial diversity and community composition.

ANIMALS

Samples were collected from four body sites (dorsum, ventral abdomen, pastern and groin) from 12 clinically healthy horses from the same farm. Samples were collected from all individuals at four time points (winter, spring, summer, autumn) within a calendar year.

METHODS AND MATERIALS

Illumina sequencing of the V4 region of the 16S rRNA gene was performed following DNA extraction. Data were analysed using mothur software.

RESULTS

Bacteria from 38 phyla and 1,665 genera were identified. Alpha diversity was higher in the winter and summer than spring and autumn although this was not statistically significant. Community membership and structure clustered more based on season than skin site.

CONCLUSIONS AND CLINICAL IMPORTANCE

Healthy equine skin is inhabited by a marked diversity of microbiota. Individuals living in a similar environment share overlapping cutaneous microbial populations. These populations vary significantly over time and between body sites.

Malassezia species dysbiosis in natural and allergen-induced atopic dermatitis in dogs

Malassezia dermatitis and otitis are recurrent features of canine atopic dermatitis, increasing the cost of care, and contributing to a reduced quality of life for the pet. The exact pathogenesis of secondary yeast infections in allergic dogs remains unclear, but some have proposed an overgrowth of M. pachydermatis to be one of the flare factors. The distribution of Malassezia populations on healthy and allergic canine skin has not been previously investigated using culture-independent methods. Skin swabs were collected from healthy, naturally affected allergic, and experimentally sensitized atopic dogs. From the extracted DNA, fungal next-generations sequencing (NGS) targeting the ITS region with phylogenetic analysis of sequences for species level classification, and Malassezia species-specific quantitative real-time polymerase chain reaction (qPCR) were performed. M. globosa was significantly more abundant on healthy canine skin by both methods (NGS P < .0001, qPCR P < .0001). M. restricta was significantly more abundant on healthy skin by NGS (P = .0023), and M. pachydermatis was significantly more abundant on naturally-affected allergic skin by NGS (P < .0001) and on allergen-induced atopic skin lesions by qPCR (P = .0015). Shifts in Malassezia populations were not observed in correlation with the development of allergen-induced skin lesions. Differences in the lipid dependency of predominant Malassezia commensals between groups suggests a role of the skin lipid content in driving community composition and raises questions of whether targeting skin lipids with therapeutics could promote healthy Malassezia populations on canine skin.

Preventive use of a topical anti-inflammatory glucocorticoid in atopic dogs without clinical sign of otitis does not affect ear canal microbiota and mycobiota

BACKGROUND

Otitis externa is associated with a lack of bacterial/fungal diversity in atopic dermatitis. Clinical experience has shown that use of topical corticosteroids in the ear canal (EC) can prevent otitis. No data are available on the impact of this treatment on the EC microbiota.

HYPOTHESIS/OBJECTIVES

To observe the bacterial/fungal diversity in the EC and the clinical effect of topical corticosteroids administered over a four week period in atopic dogs without active otitis.

ANIMALS

Ten atopic dogs without active otitis.

METHODS AND MATERIALS

Mometasone was applied in the right EC, while the left was used as control. A clinical and cytological evaluation of the EC was performed. Swabs of each EC were analysed using next-generation sequencing methods.

RESULTS

At the beginning of the trial, variations in microbiota and mycobiota were observed between dogs and also within individuals. Statistically, no significant difference was observed in alpha and beta diversity between the treated and the untreated group over time. Clinically, right and left EC diversities were no different at Day (D)28 (P = 0.28). A significant difference was noted between D0 and D28 for the treated ears (P = 0.012) and not for the untreated ears (P = 0.63). No cytological evidence of microbes was found for treated ECs at D28.

CONCLUSIONS AND CLINICAL RELEVANCE

These data suggest that the use of topical corticosteroids as proactive treatment is unlikely to increase the risk of secondary microbial overgrowth. The positive clinical effect of this proactive treatment seems to be supported through cytological and otoscopic improvement.

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing

Atopic dermatitis is one of the most common skin diseases in dogs. Pathogenesis is complex and incompletely understood. Skin colonizing bacteria likely play an important role in the severity of this disease. Studying the canine skin microbiota using traditional microbiological methods has many limitations which can be overcome by molecular procedures. The aim of this study was to describe the bacterial microbiota of the skin and ear canals of healthy non-allergic and allergic German shepherd dogs (GSDs) without acute flare or concurrent skin infection and to compare both. Bacterial 16S rRNA gene amplicon sequence data revealed no differences of bacterial community patterns between the different body sites (axilla, front dorsal interdigital skin, groin, and ear canals) in non-allergic dogs. The microbiota at the different body sites of non-allergic GSDs showed no significant differences. Only for the samples obtained from the axilla the bacterial microbiota of allergic dogs was characterized by a lower species richness compared to that of non-allergic dogs and the bacterial community composition of the skin and ear canals of allergic dogs showed body site specific differences compared to non-allergic dogs. Actinobacteria was the most abundant phylum identified from the non-allergic dogs and Proteobacteria from allergic dogs. Macrococcus spp. were more abundant on non-allergic skin while Sphingomonas spp. were more abundant on the allergic skin. Forward step redundancy analysis of metadata indicated that the household the dogs came from had the strongest impact on the composition of the skin microbiome followed by sex, host health status and body site.

Advances in our understanding of canine atopic dermatitis

Canine atopic dermatitis (cAD) is a genetically inherited clinical syndrome that encompasses a diversity of mechanisms and can have a variety of triggers. Development of clinical disease is the result of genetic factors and environmental conditions, which shape the resulting immunological response. Clinical disease becomes evident once a threshold of inflammatory response is achieved. Skin barrier impairment plays a role in promoting cutaneous dysbiosis and increased allergen penetration. Keratinocytes shape the response of dendritic cells and subsequent lymphocytic response. Thymic stromal lymphopoietin is one of the links between the damaged skin barrier and the modulation of a T-helper (Th)2 response. It is still unclear whether mutations in skin barrier genes exist in atopic dogs, as they do in humans, or whether the observed alterations are purely secondary to inflammation. A dysregulated immune response with increased Th2, Th17 and CD4+ CD25+ regulatory T cells has been reported. A variety of cytokines [interleukin(IL)-31, IL-34, Macrophage migration inhibitory factor] are proposed as potential biomarkers and treatment targets because they are increased in the serum of atopic dogs when compared to controls, although a correlation between serum levels of these factors and severity of disease is not always present. The main issue with many published studies is that atopic dogs are always only compared to normal controls. Thus, it is unclear whether the changes that we find are truly a signature of cAD or merely a manifestation of nonspecific broad inflammatory responses. Studies considering comparison with other inflammatory diseases different from cAD are urgently needed to correctly identify what is specific to this complicated syndrome.

Clinical and Genetic Findings in 28 American Cocker Spaniels with Aural Ceruminous Gland Hyperplasia and Ectasia

American Cocker Spaniels (ACSs) develop aural ceruminous gland hyperplasia and ectasia more often than dogs of other breeds. Data on the cause and development of these breed characteristic histopathological changes are lacking. We performed video-otoscopic examinations and dermatological work-up on 28 ACSs, obtained aural biopsies from each dog and assessed the statistical associations between the presence of ceruminous gland hyperplasia and ectasia and disease history, clinical or microbiological findings and underlying cause of otitis externa (OE). Histological lesions of ceruminous gland hyperplasia and ectasia were observed in aural biopsies from 6/13 clinically healthy ears and 13/15 ears with OE from 19/28 examined dogs. Nine of 28 dogs had histologically normal ceruminous glands (odds ratio [OR] 6.2, 95% confidence interval [CI] 1.1-36.6). Bacterial growth in microbiological culture of aural exudate (OR 14.1, 95% CI 2.1-95.3) was associated with ceruminous glandular changes, whereas previous history of OE, cutaneous findings or underlying allergies were not. Pedigree analysis and a genome-wide association study (GWAS) were performed on 18 affected and eight unaffected dogs based on histopathological diagnosis. While the GWAS indicated a tentative, but not statistically significant, association of ceruminous gland hyperplasia and ectasia with chromosome 31, a larger cohort is needed to confirm this preliminary result. Based on our results, ceruminous gland hyperplasia and ectasia may also precede clinical signs of OE in ACSs and a genetic aetiological component is likely Further studies with larger cohorts are warranted to verify our preliminary results.

Preliminary evaluation of two bathing methods for the management of Malassezia overgrowth in dogs with atopic dermatitis

BACKGROUND

Antifungal shampoos are widely used for canine Malassezia dermatitis. Few studies have evaluated effective bathing methods for atopic dogs with Malassezia overgrowth.

OBJECTIVES

To evaluate the efficacy of an emollient bathing product (AFLOAT VET) and 2% miconazole/2% chlorhexidine shampoo (2% MIC/CHX) in atopic dogs, and to evaluate the influence on skin barrier function of both products in healthy dogs.

ANIMALS

Sixteen atopic dogs with secondary Malassezia overgrowth and 11 healthy dogs.

METHODS AND MATERIALS

This study was a randomized, single-blinded trial. The dogs were randomly treated with either emollient bathing or 2% MIC/CHX, twice weekly for four weeks. Clinical assessment used the Canine Atopic Dermatitis Extent and Severity Index, 4^th iteration (CADESI-04), pruritus Visual Analog Scale (pVAS), and cytological evaluation of yeast numbers at Day (D)0, D14 and D28. Skin barrier function was determined by measuring transepidermal water loss (TEWL) after a single bathing procedure with each product in the healthy dogs.

RESULTS

The pVAS scores and yeast counts were significantly reduced on D28 compared with D0 in both groups (P < 0.05). CADESI-04 was significantly decreased on D28 in the emollient bathing group (P = 0.003). There were no significant differences in each endpoint score between the groups. In healthy dogs, TEWL was significantly increased after bathing in both groups (P < 0.01).

CONCLUSION

An emollient bathing product can be effective for Malassezia overgrowth in dogs with atopic dermatitis. Bathing with shampoo products might affect skin barrier function even when using an emollient product.