Oral Microbiome Dysbiosis and Candidate Stomatitis-Associated Bacteria in Captive Sharp-Nosed Pit Viper (Deinagkistrodon acutus)

Many reptiles face the threat of stomatitis, and the farming industry of the sharp-nosed pit viper (Deinagkistrodon acutus) has suffered significant losses as a result, through impaired growth and mortality of affected animals and the cost of empirical antimicrobial treatment. In this study, full-length 16S sequencing was used to analyze the oral microbiomes of 18 captive sharp-nosed pit vipers with stomatitis (ST group) and 13 healthy individuals (NST group) from the same breeding facility. Shannon (p = 0.01) and Simpson (p = 0.005) indices differed significantly between groups, whereas ACE (p = 0.23) and Chao1 (p = 0.215) did not, indicating a change in community evenness rather than in detected richness. PERMANOVA indicated that stomatitis status was associated with differences in oral microbial community composition (R2 = 0.194, p < 0.001), and PERMDISP detected no statistically significant difference in within-group dispersion between the groups (p = 0.90). ANCOM-BC identified Porphyromonas and Filifactor as genera significantly enriched in stomatitis, with Porphyromonas also recovered by MaAsLin2 and LEfSe, and Porphyromonas pogonae being the dominant species-level enrichment. In contrast, biomarkers of the healthy group included Campylobacter, Bacteroides, Granulicatella, Mycoplasma, and Wolinella. Genus-level records of previously reported pathogen associations were returned for Porphyromonas and Filifactor, whereas neither focal species had a species-level record. FAPROTAX analysis revealed that microbial functions in diseased individuals were concentrated in chemoheterotrophy and fermentation. In summary, stomatitis in sharp-nosed pit vipers was associated with altered oral microbial community composition, including higher relative abundances of several anaerobic taxa and lower relative abundances of taxa prevalent in apparently healthy animals. Whether Porphyromonas pogonae and Filifactor alocis contribute to lesion development or instead reflect the lesion-associated environment requires targeted culture, quantitative validation and functional investigation. Our study is the first to investigate the oral microbiota of captive sharp-nosed pit vipers using full-length 16S sequencing, providing a basis for culture-based validation and susceptibility testing of these candidate taxa.