**Background:** The rising incidence of inflammatory disorders, including allergies, is linked to insufficient immune education by diverse microbiota and to Western dietary patterns. The 'diet hypothesis' emphasizes the role of dietary factors, gut microbiota, and immune system interactions in allergy development. Pet dogs share their owners' lifestyle, have simpler diets, and exhibit analogous allergy patterns to humans, making them a suitable model. This study aimed to investigate how diet, lifestyle, and living environment influence the gut microbiota of dogs and whether these factors are associated with owner-reported atopic symptoms.
**Methods:** The study included 155 privately owned pet dogs (96 Finnish Lapphunds, 59 Labrador Retrievers) in Finland. Faecal samples were collected by owners in November 2014 and frozen immediately. DNA was extracted and the V1-V3 regions of the bacterial 16S rRNA gene were sequenced. OTUs were clustered at 99% similarity and classified using the SILVA database. Cumulative-sum scaling was used for normalization. Owners completed a validated questionnaire on atopic symptoms, diet, lifestyle, environment, and antibiotic use. Diet was categorized into: (i) non-heat-processed low-carbohydrate raw (NHeP-LC-R), (ii) heat-processed high-carbohydrate dry kibble (HeP-HC-D), and (iii) heat-processed high-carbohydrate moist food (HeP-HC-M). Statistical analyses included distance-based redundancy analysis (db-RDA) and multiple regression on distance matrices (MRM) for beta-diversity, and zero-inflated lognormal models for differential abundance testing, with false discovery rate correction.
**Key Results:** Atopy was significantly associated with gut microbial composition (p=0.019). In healthy dogs (n=125), an OTU of Prevotella_9 was more abundant (mean global relative abundance 0.87%; 0.94% in healthy vs. 0.61% in atopic). In atopic dogs (n=30), OTUs of Escherichia-Shigella were enriched (mean relative abundance 0.24% overall; 0.05% in healthy vs. 1.03% in atopic). Breed was the main source of inter-individual variation in microbiota (15.7%, p=0.0012). In Finnish Lapphunds, diet (percentage of NHeP-LC-R items) was the strongest factor (R²=0.044, p=0.0001), with NHeP-LC-R diet associated with increased Bacteroides and Lachnospiraceae, and decreased Faecalibacterium and Prevotella_9. In Labrador Retrievers, severity of atopic symptoms (p=0.032) and antibiotic use (R²=0.031, p=0.032) were more strongly associated with microbiota than diet. Antibiotic use was tightly coupled with atopy: 50% of atopic dogs vs. 3% of healthy dogs had received antibiotics. Alpha diversity (Shannon index) was lower in dogs with >33.3% NHeP-LC-R diet (p=0.0003). Oral exposure to dirt showed a trend toward association with microbiota (R²=0.010, p=0.067) but was not significantly related to atopy.
**Clinical Implications:** The study demonstrates that diet and antibiotic use are major determinants of canine gut microbiota composition, and that atopic dogs have a distinct microbial signature characterized by Escherichia-Shigella enrichment and reduced Prevotella_9. The strong association between antibiotic use and atopy suggests antibiotics may predispose to or exacerbate allergic disease, consistent with human literature reporting a 41% increased risk of atopic dermatitis with early-life antibiotic exposure. The finding that HeP-HC-D diet (kibble) was associated with Prevotella and Faecalibacterium—known short-chain fatty acid producers—raises questions about potential protective effects, though SCFAs were not measured. The results support the use of pet dogs as a translational model for studying lifestyle-microbiota-allergy relationships in humans, given the shared environment and analogous disease patterns. Limitations include the cross-sectional design, owner-reported atopy diagnosis, incomplete antibiotic timing data, and inability to fully disentangle the effects of diet, antibiotics, and atopy on microbiota.