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C. Bradley1
1University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
The microbiome:
The microbiota is the sum of bacteria, fungi, viruses, and parasites living in and on a given habitat or host. Though the terms are often used interchangeably, the microbiome refers to the genetic component of these microbes, and unless otherwise specified often refers to bacterial communities. All our experiences in health and disease are altered by either the microbiota or their metabolites, including but not limited to smell, taste, touch, energy metabolism, nutrient absorption and barrier and immune function. The shared microbiota between people is also influenced by their environment and strongly influenced by their pets.
Advances in high-throughput (“next generation”) sequencing have allowed for culture-independent evaluation of these communities. The methods
most commonly utilized to examine the microbiome include targeted amplicon sequencing, whole genome metagenomics and other downstream analyses: transcriptomics or proteomics. Statistical methods used in ecology studies are often employed, examining both intraindividual (alpha diversity) and interindividual (beta) diversity metrics and changes in community composition/structure.
In veterinary studies, the most commonly used approach is targeted amplicon sequencing. This methodology
only allows for taxonomic identification and does not
give information as to function or metabolites of these communities. It utilizes a gene universally conserved by a kingdom or large group of microbes. In bacteria, the 16s (subunit) ribosomal RNA gene is commonly selected, and for fungi the 18s and ITS (internal transcribed sequences) of the rRNA gene are used. The 16s rRNA gene has both highly conserved regions allowing for primer set design and hypervariable regions (V1 through V9) that enable one to distinguish bacterial taxa.
Most studies of the microbiome take a census of what constitutes a given community and how it changes with a variable. This can be a daunting task with the number of potential influences on the microbiome such as location (i.e. body site), age, breed, environment, time, diet, bathing and health status. Community structure is often assessed with a description of a relative proportion of a given taxon compared to other taxa.
The skin microbiome
Our understanding of the skin microbiome is limited. Microbiomic studies of the skin face a number of challenges. Samples are generally procured from
surface swabs with low biomass. As such contaminants can have a dramatic effect on the study outcome necessitating careful collection and processing of samples along with numerous positive and negative controls. Regions of the 16s rRNA gene evaluated can also influence study outcome, making comparison across studies difficult. For example, the V4 region of the 16s rRNA gene has been demonstrated to underestimate the relative proportion of Proprionibacterium acnes
and Staphylococcus aureus in the skin microbiome compared to the V1-V3 region.
There are very few studies surveying the bacterial skin microbiome of dogs, and most of these characterize normal skin communities, with fewer examining
disease states. Information on the feline microbiome is extremely sparse. Microbiome studies of human skin
are slightly more abundant, and both differences and similarities with the companion animal microbiome
have been elucidated. In people there are dry, moist
and oily (sebaceous) microenvironments across the
skin associated with differing microbial communities.
In contrast, the microbiome of the haired skin of dogs
is much more homogenous. Interindividual variability
in both people and dogs is significant, influenced by
the individual, environment and life-style. The most abundant phyla in healthy dogs include Proteobacteria, Firmicutes, Actinobacteria, and Bacteroides. In health, there is generally a higher level of microbial diversity compared to disease states. Cutaneous diseases most commonly studied in the human microbiome field include atopic dermatitis (AD), acne, psoriasis. With a similar prevalence, pathogenesis, therapeutic considerations and associated bacterial disease, atopic dermatitis (AD) in humans and dogs (cAD) has been a recent line of investigation into the microbiome.
An Urban Experience

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