The gut microbiota, including both bacterial and fungal communities, plays vital roles in the gut homeostasis of animals, and antibiotics can lead to disorders of these microbial communities. The use of anthelmintic treatment to control parasitic infection has long been a standard practice, although its impact on the gut microbiota of healthy sika deer is relatively unknown. This study used next-generation sequencing based on 16S/18S/ITS rRNA genes to investigate the shifts in fecal bacterial and fungal communities in parasite-free sika deer after treatment with fenbendazole and ivermectin tablets. The α-diversity of both bacterial and fungal communities was significantly decreased (P < 0.05) after treatment, as were the bacterial genus Bacteroides and fungal genus Candida (P < 0.05). The results of β-diversity, LEfSe analysis, core community’s analysis, taxonomic composition, and functional prediction of fungal and bacterial communities confirmed the substantial impacts of anthelmintic treatment on the function and structure of the intestinal microbiota of sika deer. Nevertheless, many lines of evidence, including β-diversity, LEfSe analysis and functional prediction analysis, suggested that the anthelmintics exerted more significant influences on fungal communities than on bacterial communities, suggesting that more attention should be paid to the changes in fungal communities of sika deer under anthelmintic treatment. The present study provides evidence to support the assumption that anthelmintic drugs modify the gut microbiota of deer and serves as the first trial to test the potential effects of anthelmintics on mycobiota in ruminants using high-throughput sequencing techniques.

肠道菌群（包括细菌和真菌群落）在动物的肠道稳态中起着至关重要的作用，抗生素可导致这些微生物群落的失调。长期以来，使用驱虫治疗来控制寄生虫感染一直是标准做法，尽管它对健康梅花鹿肠道菌群的影响相对未知。这项研究使用了基于16S / 18S / ITS rRNA基因的下一代测序技术，研究了使用芬苯达唑和伊维菌素片治疗的无寄生梅花鹿粪便细菌和真菌群落的变化。处理后，细菌和真菌群落的α-多样性均显着降低（P <0.05），细菌类杆菌和真菌属也是如此。念珠菌（P<0.05）。β多样性，LEfSe分析，核心群落分析，分类学组成以及真菌和细菌群落功能预测的结果证实了驱虫治疗对梅花鹿肠道菌群功能和结构的重大影响。然而，包括β多样性，LEfSe分析和功能预测分析在内的许多证据表明，驱虫药对真菌群落的影响远大于对细菌群落的影响，这表明应该更多地关注梅花真菌群落的变化。鹿在驱虫治疗下。