Feline chronic gingivostomatitis (FCGS) remains a poorly understood clinical condition with significant impact on the quality of life of affected cats. An understanding of the pathogenesis of this inflammatory disease will enable the development of improved and targeted therapeutics beyond full-mouth extractions. Here, we collected sterile noninvasive plaque samples at ten distinct sites within the oral cavity in cats with FCGS (n = 12), healthy cats (n = 9), or cats with other oral conditions (n = 11). We used 16S rRNA gene sequencing (V1–V9) to profile bacteria in the oral microbiome. We found that the microbiomes of cats with FCGS were distinct from those of healthy cats at multiple oral sites, indicating that dysbiosis is present throughout the oral cavity. The microbiomes of cats varied depending on their oral diagnoses, confirming that the various dental diseases impact the microbiome in different ways. Lastly, microbiome data obtained from swabs of the oral cavity were similar to those obtained using endodontic paper point plaque samples, suggesting this approach as another valuable method of sampling. Given these additional insights, future studies can focus on targeted therapeutics so that extraction of healthy teeth will no longer be the standard of care for this challenging condition.

Feline chronic gingivostomatitis (FCGS) is a chronic mucosal and gingival inflammatory disease in which pathogenesis remains unclear. Interactions between the host inflammatory process, the host immune response, and the oral microbiome are implicated in this pathogenesis. To begin to understand this disease and the impact of the microbiome to host inflammatory disease states, we collected sterile noninvasive plaque biofilm samples from ten distinct sites within the oral cavity in cats with stomatitis (n = 12), healthy cats (n = 9), and cats with tooth resorption or periodontitis (n = 11). Analysis of full-length 16S rRNA gene sequences indicated that the microbiomes of cats with FCGS presented marked dysbiosis at multiple oral sites. Additionally, microbiome beta diversity varied with oral condition, indicating that stomatitis, periodontitis, and/or tooth resorption influence the microbiome differently. Lastly, we found that the microbiomes of swabs taken from the oral cavity were comparable to those taken from plaque using endodontic paper points, validating this as another sampling method. Collectively, our work furthers our understanding of the dysbiosis and composition of bacteria in the oral microbiome in FCGS, with hopes of contributing to the prevention, diagnosis, and treatment of this challenging condition in felines.