Novel association of Psychrobacter and Pseudomonas with malodour in bloodhound dogs, and the effects of a topical product composed of essential oils and plant-derived essential fatty acids in a randomized, blinded, placebo-controlled study

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.

Comparison of canine colostrum and milk using a multi-omics approach

BACKGROUND

A mother's milk is considered the gold standard of nutrition in neonates and is a source of cytokines, immunoglobulins, growth factors, and other important components, yet little is known about the components of canine milk, specifically colostrum, and the knowledge related to its microbial and metabolic profiles is particularly underwhelming. In this study, we characterized canine colostrum and milk microbiota and metabolome for several breeds of dogs and examined profile shifts as milk matures in the first 8 days post-whelping.

RESULTS

Through untargeted metabolomics, we identified 63 named metabolites that were significantly differentially abundant between days 1 and 8 of lactation. Surprisingly, the microbial compositions of the colostrum and milk, characterized using 16S rRNA gene sequencing, were largely similar, with only two differentiating genera. The shifts observed, mainly increases in several sugars and amino sugars over time and shifts in amino acid metabolites, align with shifts observed in human milk samples and track with puppy development.

CONCLUSION

Like human milk, canine milk composition is dynamic, and shifts are well correlated with developing puppies' needs. Such a study of the metabolic profile of canine milk, and its relation to the microbial community, provides insights into the changing needs of the neonate, as well as the ideal nutrition profile for optimal functionality. This information will add to the existing knowledge base of canine milk composition with the prospect of creating a quality, tailored milk substitute or supplement for puppies.

Psychrobacter raelei sp. nov., isolated from a dog with peritonitis

A strain belonging to the genus Psychrobacter, named PraFG1T, was isolated from the peritoneal effusion of a stray dog during necropsy procedures. The strain was characterized by the phylogenetic analyses based on the nucleotide sequences of 16S and 23S rRNA genes and of gyrB, which placed the strain in the genus Psychrobacter. The nucleotide sequence of the chromosome confirmed the placement, showing an average nucleotide identity of 72.1, 77.7, and 77.5 % with the closest related species, namely Psychrobacter sanguinis, Psychrobacter piechaudii, and Psychrobacter phenylpyruvicus, respectively, thus indicating a novel species. The polyphasic characterization by biochemical and fatty acid profiling as well as MALDI-TOF supported those findings. The strain was halotolerant, capable of growing within a temperature range between 4 and 37 °C, it was positive for catalase and oxidase, indole producing, nitrate reducing, and not able to use 5-keto-d-gluconic acid as a carbon source. Taken together, the data suggest that strain PraFG1T could be considered as representing a novel species, with the name Psychrobacter raelei sp. nov. (type strain PraFG1T=CIP 111873T=LMG 32233T).

Tolerability and the effect on skin Staphylococcus pseudintermedius density of repeated diluted sodium hypochlorite (bleach) baths at 0.005% in healthy dogs

BACKGROUND

Dilute sodium hypochlorite (bleach) baths at 0.005% concentration twice weekly have been shown to markedly reduce the severity of atopic dermatitis in children, yet no tolerability and efficacy data are available for this treatment in dogs.

OBJECTIVES

To determine the local tolerability and the longitudinal effect on the density of Staphylococcus pseudintermedius of repeated diluted bleach baths on healthy dog skin.

ANIMALS

Four healthy hound cross-bred dogs.

METHODS

Bleach baths (0.005%; twice weekly for 15 min) were applied to four healthy hound cross-bred dogs over four weeks (eight baths). Local tolerability was assessed for axillae, abdomen and legs by an investigator before, immediately after and 24 h after each bath. The longitudinal effect on density of S. pseudintermedius from axillae and groin was analysed through quantitative PCR before treatment [at Day (D)-7 and -3], during treatment on D4, D11 and D25, and on D30.

RESULTS

There was no erythema or scaling after the baths in any dog. Copy numbers of S. pseudintermedius in axillae, groin and both (axillae and groin together) were not significantly different at any time point during the study.

CONCLUSIONS AND CLINICAL RELEVANCE

Repeated 0.005% hypochlorite bleach baths over four weeks were safe and well-tolerated in healthy dogs without significant changes in the density of S. pseudintermedius.

Biocidal effects of a wipe-down procedure using common veterinary cleansers on microbial burden within working canine exterior coats

Introduction

Recent work demonstrating reduction of aerosolized contamination via a wipe-down procedure using common veterinary antiseptics offers promise regarding health concerns associated with cross-contamination from working canines to humans. While mechanical reduction can be achieved via a wipe-down procedure, the biocidal impact on flora within the exterior coat is unknown.

Methodology

This study assessed the biocidal impact of antiseptics on the exterior bacterial community of the canine. Lint-free towels were saturated with 2% chlorhexidine gluconate scrub, or 7.5% povidone-iodine scrub diluted at a 1:4 ratio. Treatments were rotated across the dorsal aspect of kennel housed Foxhounds (n = 30). Sterile swabs were collected in triplicate prior to, and following wipe down, stored in Amies solution at 4°C, plated onto nutrient agar and reduction in colony forming units (CFU) was measured across both treatments. Statistical analysis utilizing PROC GLM examined effects of treatment (p ≤ 0.05). Molecular analysis of the 16S rRNA gene was completed for 3 hounds.

Results

Reduction in CFU was measured (p < 0.001) for both antiseptics. Qualitative molecular data indicated that both antiseptics had a biocidal effect on the dominant microbial community on the exterior coat with gram-positive, spore-forming taxa predominating post-treatment.

Conclusion

Effective wipe-down strategies using common veterinary cleansers should be further investigated and incorporated to safeguard working canine health and prevent cross-contamination of human personnel.

Essential Oils and Melatonin as Functional Ingredients in Dogs

Simple Summary

Phytogenics are plant-based compounds with beneficial actions in feed technology and/or animal health. These so-called plant secondary metabolites are very diverse and with wide possible applications in humans and animals. Among them, essential oils (EOs) are the most used in feed for livestock and pets. Lately, melatonin has acquired new and interesting applications in dogs. Recent studies using EOs and/or melatonin in dog feeding and their involvement in health aspects are presented.

Abstract

The use of nutraceuticals or functional ingredients is increasingly widespread in human food; their use is also widespread in animal feed. These natural compounds generally come from plant materials and comprise a wide range of substances of a very diverse chemical nature. In animals, these compounds, so-called phytogenics, are used to obtain improvements in feed production/stability and also as functional components with repercussions on animal health. Along with polyphenols, isoprenoid compounds represent a family of substances with wide applications in therapy and pet nutrition. Essential oils (EOs) are a group of complex substances with fat-soluble nature that are widely used. Melatonin is an indolic amine present in all living with amphiphilic nature. In this work, we present a review of the most relevant phytogenics (polyphenol, isoprenoid, and alkaloid compounds), their characteristics, and possible uses as nutraceuticals in dogs, with special emphasis on EOs and their regulatory aspects, applied in foods and topically. Additionally, a presentation of the importance of the use of melatonin in dogs is developed, giving physiological and practical aspects about its use in dog feeding and also in topical application, with examples and future projections. This review points to the combination of EOs and melatonin in food supplements and in the topical application as an innovative product and shows excellent perspectives aimed at addressing dysfunctions in pets, such as the treatment of stress and anxiety, sleep disorders, alopecia, and hair growth problems, among others.

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.

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.

Characterization of microbiota diversity of engorged ticks collected from dogs in China

BACKGROUND

Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs.

OBJECTIVES

To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China.

METHODS

A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied.

RESULTS

After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs.

CONCLUSIONS

The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.

Topical effect of a specific spot-on treatment made of natural ingredients in rabbits (Oryctolagus cuniculus) with skin problems: A pilot study

Background and Aim:

Rabbits often experience skin diseases. The beneficial effects of plant extracts and essential oils are well known in other species, but the properties of these natural ingredients have not been evaluated in rabbits in vivo. The objective of the current study was to evaluate the effect of a topical, commercial solution made of essential oils, plant-extracted polyunsaturated fatty acids, and Vitamin E on rabbits suffering from skin problems.

Materials and Methods:

Thirty New Zealand rabbits (no sex distinction) were included in this study, with an average weight of 2–3 kg. The rabbits were divided into two groups: The first group was treated with a topical solution made from natural ingredients, and the second was a control group. The rabbits’ hair and skin conditions were evaluated on days 1, 14, 28, and 35 after treatment. Data were analyzed using a Kruskal–Wallis range test.

Results:

Significant differences were determined in terms of glossy hair variability on days 28 and 35 (p≤0.0001). On days 14-35, hair loss was determined to have reduced (p=0.001), and flaking and odor improved in the treatment group, showing increased scores and significant differences (p=0.0001). By contrast, the control group showed stable overall skin and hair score and an increase in the dryness score.

Conclusion:

The topical application of essential oils and polyunsaturated fatty acids with Vitamin E was able to improve hair shine and skin hydration and reduce flaking, bad odor, and hair loss, improving the general, and cutaneous aspect of rabbits.

Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.

Antifungal in vitro Activity of Essential Oils against Clinical Isolates of Malassezia pachydermatis from Canine Ears: A Report from a Practice Laboratory

BACKGROUND

The yeast Malassezia pachydermatis is a commensal but also the most isolated pathogenic yeast in canine otitis externa. Essential oils (EOs) exhibit antimicrobial activity and thus could be an alternative for treatment of otitis.

OBJECTIVE

The aim of this study was to analyse the in vitro efficacy of EOs against M. pachydermatis isolates from canine ears.

MATERIALS AND METHODS

Twenty-two EOs were tested for their in vitro activity against 15 M. pachydermatis isolates by agar disc diffusion. In addition, diluted EOs were tested and volatile antifungal activity was analysed by vapour assay.

RESULTS

Most EOs showed in vitro efficacy against M. pachydermatis. A different susceptibility pattern of tested isolates was found. Overall, the most potential EO was lemon grass. Also, cinnamon leaf, clove, manuka, Indian melissa, oregano, palmarosa, and winter savory oil exhibited a strong antifungal activity. Volatile activity was proven by the inhibiting effect in vapour assay.

CONCLUSION

EOs show in vitro activity against M. pachydermatis. This study gives scientific background for the use of EOs in veterinary medicine. Diverse susceptibility patterns of different M. pachydermatis strains emphasise the helpfulness of an aromatogram as one lead for the best choice of an EO for therapy.

The skin microbiome of vertebrates

The skin constitutes the primary physical barrier between vertebrates and their external environment. Characterization of skin microorganisms is essential for understanding how a host evolves in association with its microbial symbionts, modeling immune system development, diagnosing illnesses, and exploring the origins of potential zoonoses that affect humans. Although many studies have characterized the human microbiome with culture-independent techniques, far less is known about the skin microbiome of other mammals, amphibians, birds, fish, and reptiles. The aim of this review is to summarize studies that have leveraged high-throughput sequencing to better understand the skin microorganisms that associate with members of classes within the subphylum Vertebrata. Specifically, links will be explored between the skin microbiome and vertebrate characteristics, including geographic location, biological sex, animal interactions, diet, captivity, maternal transfer, and disease. Recent literature on parallel patterns between host evolutionary history and their skin microbial communities, or phylosymbiosis, will also be analyzed. These factors must be considered when designing future microbiome studies to ensure that the conclusions drawn from basic research translate into useful applications, such as probiotics and successful conservation strategies for endangered and threatened animals.

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon

Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples often contain DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to assess long-amplicon PCR-based approaches for assigning taxonomy at the genus and species level. We use Nanopore sequencing with two different markers: full-length 16S rRNA (~1,500 bp) and the whole rrn operon (16S rRNA-ITS-23S rRNA; 4,500 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities (HM-783D, Bei Resources; D6306, ZymoBIOMICS™) and two pools of low-biomass samples (dog skin from either the chin or dorsal back), using the MinION™ sequencer 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using the WIMP workflow on EPI2ME or Minimap2 software with rrn database. Results: The full-length 16S rRNA and the rrn operon were used to retrieve the microbiota composition at the genus and species level from the bacterial isolate, mock communities and complex skin samples. For the Staphylococcus pseudintermedius isolate, when using EPI2ME, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the rrn operon marker, and in ~68% of the cases with the 16S rRNA gene. In both skin microbiota samples, we detected many species with an environmental origin. In chin, we found different Pseudomonas species in high abundance, whereas in dorsal skin there were more taxa with lower abundances. Conclusions: Both full-length 16S rRNA and the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, using the rrn operon would be the best choice.

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon

Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota composition of the samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the16S-ITS-23S genetic marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA gene represented better the abundances of a microbial community; whereas, 16S-ITS-23S obtained better resolution at the species level. Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, targeting the 16S-ITS-23S of the rrn operon would be the best choice.