Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene

SIMPLE SUMMARY: There are millions of snake envenoming cases annually worldwide, which is an important but often neglected tropical disease. The morbidity and mortality from snake bites are not only caused by the venom toxins but also the secondary infection from bacteria from the snake itself or an external source. Therefore, if we do not understand the actual pathogens of infection, the expected treatment efficacy is reduced. In this study, we investigated the microbiota carried in the oral cavity of seven wild venomous snakes in Taiwan using full-length 16S rRNA next-generation sequencing. The results showed that non-pathogenic bacteria and pathogenic bacteria were similar in dominance in the oral cavity of snakes, Gram-negative bacteria were more common than Gram-positive bacteria, and the microbiota were significantly different between the Elapidae and Viperidae families of snakes. Our findings will assist in resolving the diversity of oral microbiomes in snakes and can be applied to the veterinary medicine and clinical therapy of venomous snakebites. ABSTRACT: A venomous snake’s oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake’s oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.