Impact of winter enclosures on the gut bacterial microbiota of red deer in the Bavarian Forest National Park

High numbers of red deer (Cervus elaphus) pose a challenge for natural forests because of their high browsing intensities, especially during winter months. To mitigate this human–wildlife conflict, conservation management in Central Europe involves luring red deer into fenced winter-feeding sites. The supplementary diet provided in these so-called winter enclosures strongly differs from the natural diet of red deer. Dietary shifts, however, can lead to an imbalance of the gut microbiota, which could promote bacterial pathogens. Moreover, increased inter-individual contact in winter enclosures enhances the exchange of symbiotic but also pathogenic bacteria. In this study, we used high-throughput sequencing of the 16S rRNA gene in fecal samples of red deer inhabiting the Bavarian Forest National Park to investigate differences in the gut bacterial microbiota between individuals in winter enclosures and individuals that ranged freely in the forests in winter. We also investigated the occurrence of potential zoonotic bacterial pathogens in both study groups. Our results revealed that proportions of bacterial taxa, alpha- and beta-diversities, and relative abundances of amplicon sequence variants in the gut bacterial microbiota of the two groups differed. These differences were attributed to the enrichment of bacterial taxa involved in the digestion of the supplementary food and to different natural diets consumed before entering the winter enclosures. We detected sequences with high similarities to known red deer pathogens in both study groups, but their relative abundances were low, which suggests that the population of red deer of the National Park Bavarian Forest is healthy.

高密度的马鹿（Cervus elaphus）因其高强度的取食行为，尤其在冬季，对天然林造成了生存挑战。为缓解这一人兽冲突，中欧的野生动物保护管理实践会将马鹿诱引至设有围栏的冬季投喂点。这些被称为‘冬季围栏区’的投喂点所提供的补充日粮，与马鹿的天然采食食谱存在显著差异。然而饮食结构的改变可能引发肠道微生物群失衡，进而助长病原菌的增殖。此外，冬季围栏区内个体间接触频率提升，会促进共生菌乃至病原菌的传播交换。本研究以巴伐利亚森林国家公园内的马鹿粪便样本为研究材料，通过16S rRNA基因高通量测序技术，对比分析了冬季处于围栏投喂区与自由活动于林间的马鹿个体间肠道细菌菌群的差异，同时调查了两个研究组中潜在人畜共患病原菌的检出情况。研究结果显示，两组马鹿的肠道细菌菌群在细菌类群占比、α多样性与β多样性，以及扩增子序列变体（amplicon sequence variants）的相对丰度上均存在显著差异。此类差异主要源于两组马鹿肠道内参与补充日粮消化的细菌类群富集程度不同，以及进入冬季围栏区前采食的天然食谱存在差异。本研究在两个研究组中均检测到与已知马鹿病原菌高度同源的序列，但这些序列的相对丰度较低，这表明巴伐利亚森林国家公园内的马鹿种群整体健康状况良好。