The honey bee is associated with a diverse community of microbes (viruses, bacteria, fungi, and protists), commonly known as the microbiome. Here, we present data on honey bee microbiota from two localities having different surrounding landscapes – mountain (the Rhodope Mountains) and lowland (the Danube plain). The bacterial communities of abdomen of adult bees were studied using amplicon sequencing of the 16S rRNA gene. The composition and dominance structure and their variability within and between localities, alpha and beta diversity, and core and differential taxa were compared at different hierarchical levels (operational taxonomic units to phylum). Seven genera (Lactobacillus, Gilliamella, Bifidobacterium, Commensalibacter, Bartonella, Snodgrassella, and Frischella), known to include core gut-associated phylotypes or species clusters, dominated (92–100%) the bacterial assemblages. Significant variations were found in taxa distribution across both geographical regions and within each apiary. Lactobacillus (Firmicutes) prevailed significantly in the mountain locality followed by Gilliamella and Bartonella (Proteobacteria). Bacteria of four genera, core (Bartonella and Lactobacillus) and non-core (Pseudomonas and Morganella), dominated the bee-associated assemblages of the Danube plain locality. Several ubiquitous bacterial genera (e.g., Klebsiella, Serratia, and Providencia), some species known also as potential and opportunistic bee pathogens, had been found in the lowland locality. Beta diversity analyses confirmed the observed differences in the bacterial communities from both localities. The occurrence of non-core taxa contributes substantially to higher microbial richness and diversity in bees from the Danube plain locality. We assume that the observed differences in the microbiota of honey bees from both apiaries are due to a combination of factors specific for each region. The surrounding landscape features of both localities and related vegetation, anthropogenic impact and land use intensity, the beekeeping management practices, and bee health status might all contribute to observed differences in bee microbiota traits.

蜜蜂与多种微生物群落（病毒、细菌、真菌和原生生物）相关，通常称为微生物组。在这里，我们提供了来自两个具有不同周围景观的地方的蜜蜂微生物群的数据——山区（罗多彼山脉）和低地（多瑙河平原）。使用 16S rRNA 基因的扩增子测序研究了成年蜜蜂腹部的细菌群落。在不同的层次级别（操作分类单元到门）比较了组成和优势结构及其在地点内部和地点之间的变异性、α和β多样性以及核心和差异类群。已知包括核心肠道相关系统发育型或物种簇的七个属（乳杆菌属、吉利亚梅拉属、双歧杆菌属、共生杆菌属、巴尔通体属、斯诺德格拉斯氏菌属和弗里斯凯氏菌属）在细菌组合中占主导地位（92-100%）。两个地理区域和每个养蜂场内的类群分布存在显着差异。乳杆菌（厚壁菌门）在山区占主导地位，其次是吉利亚门氏菌和巴尔通氏菌（变形菌门）。四个属的细菌，核心（巴尔通体和乳杆菌）和非核心（假单胞菌和摩根氏菌），在多瑙河平原地区与蜜蜂相关的组合中占主导地位。在低地地区发现了几种普遍存在的细菌属（例如克雷伯氏菌属、沙雷氏菌属和普罗维登斯氏菌属），其中一些物种也被称为潜在和机会性蜜蜂病原体。β多样性分析证实了两个地区细菌群落的观察到的差异。非核心类群的出现极大地提高了多瑙河平原地区蜜蜂的微生物丰富度和多样性。我们假设观察到的两个养蜂场蜜蜂微生物群的差异是由于每个地区特有因素的组合造成的。两个地点的周围景观特征和相关植被、人为影响和土地利用强度、养蜂管理实践和蜜蜂健康状况都可能导致观察到的蜜蜂微生物群特征的差异。