Data from: 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.

高密度马鹿（Cervus elaphus）因高强度的啃食行为，尤其在冬季，对天然林构成严峻挑战。为缓解这一人兽冲突，中欧地区的野生动物保护管理工作常将马鹿诱引至带围栏的冬季投喂点。这类被称为冬季围栏投喂点的区域所提供的补充日粮，与马鹿的天然食料存在显著差异。然而，饮食结构的改变可能引发肠道微生物群失衡，进而促发细菌性致病菌的增殖。此外，冬季围栏投喂点内个体间接触频次的提升，会促进共生菌乃至致病菌的传播交换。本研究以栖息于巴伐利亚森林国家公园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，对比分析了冬季栖息于围栏投喂点与自由活动于林间的马鹿个体间肠道细菌微生物群的差异；同时探究了两个试验组中潜在人畜共患细菌性致病菌的检出情况。研究结果显示，两组马鹿的肠道细菌微生物群在细菌类群占比、α多样性与β多样性，以及扩增子序列变异（amplicon sequence variant，ASV）的相对丰度上均存在显著差异。上述差异主要源于与补充日粮消化相关的细菌类群的富集，以及马鹿进入冬季围栏投喂点前采食的天然食料存在差异。两个试验组中均检出与已知马鹿致病菌高度同源的序列，但其相对丰度较低，这表明巴伐利亚森林国家公园的马鹿种群整体健康状况良好。