Apostolopoulos, Glaeser et al. (2021) — PLoS ONE
Description and Comparison of the Skin and Ear Canal Microbiota of Non-Allergic and Allergic German Shepherd Dogs Using Next Generation Sequencing
Published: August 05, 2026
Atopic dermatitis is one of the most common skin diseases in dogs — chronic, complex, and frequently misunderstood as simply an allergic reaction to environmental triggers. A study using next-generation sequencing to profile the skin and ear canal microbiota of allergic and non-allergic German Shepherd dogs has revealed that the bacterial community living on the skin surface differs measurably between affected and healthy dogs even when neither is in an active flare. And the factor with the strongest influence on skin microbiome composition turns out to be something most owners would not immediately think of: which household the dog lives in. 🐾
Researchers Neoklis Apostolopoulos, S. Glaeser, N. Thom, and their team characterised bacterial communities at four body sites — the axilla, front dorsal interdigital skin, groin, and ear canals — in non-allergic and allergic German Shepherds using 16S rRNA gene amplicon sequencing. Crucially, the allergic dogs included in the study were not in acute flare and had no concurrent skin infection at the time of sampling. This design choice was deliberate: by studying the microbiome in a stable, non-inflamed state, the researchers could identify baseline microbial differences that exist independent of acute disease rather than simply documenting the bacterial changes associated with active inflammation.
What the Microbiome Differences Actually Look Like
In non-allergic German Shepherds, the bacterial microbiota across all four body sites showed no significant differences from each other — the skin community was broadly consistent whether samples came from the armpit, between the toes, the groin, or the ear canal. Actinobacteria was the dominant phylum across these sites, and Macrococcus species were notably abundant on non-allergic skin.
Allergic dogs showed a different pattern across multiple dimensions. At the axilla specifically, allergic dogs showed lower bacterial species richness compared to non-allergic dogs — reduced diversity in the skin community at this site even without active disease. Across the different body sites, allergic dogs also showed body-site-specific differences in bacterial community composition compared to non-allergic dogs, where non-allergic dogs showed more consistency across sites. In allergic dogs, Proteobacteria was the dominant phylum rather than Actinobacteria, and Sphingomonas species were more abundant on allergic skin while Macrococcus was more abundant on healthy skin.
The shift from Actinobacteria-dominated to Proteobacteria-dominated skin microbiome in allergic dogs is a finding with broader context in the atopic dermatitis literature. Actinobacteria include genera associated with skin barrier support and competitive exclusion of pathogenic species. A community structure that is less rich in diversity and different in dominant phylum — even in the absence of acute inflammation — suggests that the microbiome disruption in atopic dogs is a baseline characteristic of the disease state rather than purely a consequence of active flares.
The Household Effect That Outweighed Everything Else ⚠️
The metadata analysis produced the most unexpected finding in the dataset. Forward step redundancy analysis — a statistical approach that identifies which variables most strongly explain community composition variation — revealed that the household the dogs came from had the strongest impact on skin microbiome composition. This effect was stronger than sex, health status, or body site combined.
This means that two German Shepherds living in the same household share more similar skin microbiomes than two German Shepherds of the same sex, the same health status, or sampled at the same body site from different households. The shared living environment — floors, bedding, human contact, cleaning products, outdoor access, diet, and the entire microbial ecosystem of the home — appears to be the dominant shaper of what bacterial communities colonise the skin.
For owners of allergic dogs, this finding carries direct practical implications. The household environment is not simply a backdrop to the dog’s skin health — it is one of its primary determinants. The microbial landscape the dog is exposed to daily through their bedding, resting surfaces, contact with human skin, and outdoor environments is continuously shaping the skin bacterial community in ways that may either support or undermine barrier function and immune regulation. This is not a finding that suggests owners can simply swap to a different shampoo and resolve atopic dermatitis. It is a finding that points toward the home environment as a modifiable variable in the long-term management of the condition.
What This Means for Managing Atopic Dermatitis in Predisposed Breeds 🐕
German Shepherds are among the breeds with elevated prevalence of atopic dermatitis, alongside Labrador and Golden Retrievers, Bulldogs, and West Highland White Terriers. The genetic predisposition is real. But this research adds a layer of environmental modifiability to the picture that genetic risk alone does not capture.
A dog whose skin microbiome is shifting toward the low-diversity, Proteobacteria-dominated profile associated with atopic disease — even before visible skin symptoms are present — may benefit from interventions aimed at supporting microbial diversity rather than simply suppressing immune response. Regular washing of bedding, attention to the microbial environment of resting surfaces, probiotic approaches targeting skin microbiome health, and dietary strategies supporting skin barrier function are all variables with mechanistic rationale grounded in what this research documents.
At Zoeta Dogsoul, physical foundation includes the invisible microbial layer that mediates between the dog’s immune system and the world it lives in. A dog with atopic dermatitis is a dog whose physical experience — persistent itch, inflammation, discomfort — is shaping their behavioural state and their capacity for engagement every day. The research covered in this series consistently shows that load shows — and chronic skin disease is a form of load that operates beneath the surface of behaviour in ways that attentive owners can learn to recognise and address.
NeuroBond is built on seeing the whole animal. The microbiome on the surface of that animal is part of the whole — and understanding that the home environment shapes it as powerfully as the dog’s genetics is a piece of knowledge that changes what attentive ownership can actually do. 🐾
Source: Apostolopoulos, N., Glaeser, S., Thom, N., et al. (2021). Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing. PLoS ONE. Published May 3, 2021.
