Ellegaard Kirsten M, Tamarit Daniel, Javelind Emelie, Olofsson Tobias C, Andersson Siv G E, Vásquez Alejandra
Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
Department of Laboratory Medicine, Medical Microbiology, Lund University, Medicon Village, Scheelevägen 2, SE-223 62, Lund, Sweden.
BMC Genomics. 2015 Apr 11;16(1):284. doi: 10.1186/s12864-015-1476-6.
In the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore important to elucidate the diversity and role of this microbiota in the honeybee. In this study, we have sequenced the genomes of eleven strains of lactobacilli and bifidobacteria isolated from the honey crop of the honeybee A. mellifera.
Single gene phylogenies confirmed that the isolated strains represent the diversity of lactobacilli and bifidobacteria in the gut, as previously identified by 16S rRNA gene sequencing. Core genome phylogenies of the lactobacilli and bifidobacteria further indicated extensive divergence between strains classified as the same phylotype. Phylotype-specific protein families included unique surface proteins. Within phylotypes, we found a remarkably high level of gene content diversity. Carbohydrate metabolism and transport functions contributed up to 45% of the accessory genes, with some genomes having a higher content of genes encoding phosphotransferase systems for the uptake of carbohydrates than any previously sequenced genome. These genes were often located in highly variable genomic segments that also contained genes for enzymes involved in the degradation and modification of sugar residues. Strain-specific gene clusters for the biosynthesis of exopolysaccharides were identified in two phylotypes. The dynamics of these segments contrasted with low recombination frequencies and conserved gene order structures for the core genes. Hits for CRISPR spacers were almost exclusively found within phylotypes, suggesting that the phylotypes are associated with distinct phage populations.
The honeybee gut microbiota has been described as consisting of a modest number of phylotypes; however, the genomes sequenced in the current study demonstrated a very high level of gene content diversity within all three described phylotypes of lactobacilli and bifidobacteria, particularly in terms of metabolic functions and surface structures, where many features were strain-specific. Together, these results indicate niche differentiation within phylotypes, suggesting that the honeybee gut microbiota is more complex than previously thought.
在蜜蜂（西方蜜蜂）中，肠道细菌群落始终由八种不同的细菌系统型定殖。人工饲养的蜂群具有相当大的经济价值，因此阐明这种微生物群在蜜蜂中的多样性和作用非常重要。在本研究中，我们对从西方蜜蜂的蜜胃中分离出的11株乳酸杆菌和双歧杆菌进行了基因组测序。
单基因系统发育分析证实，分离出的菌株代表了肠道中乳酸杆菌和双歧杆菌的多样性，这与之前通过16S rRNA基因测序确定的结果一致。乳酸杆菌和双歧杆菌的核心基因组系统发育分析进一步表明，分类为同一系统型的菌株之间存在广泛的差异。系统型特异性蛋白质家族包括独特的表面蛋白。在各系统型中，我们发现基因含量多样性水平非常高。碳水化合物代谢和转运功能贡献了高达45%的辅助基因，一些基因组中编码用于摄取碳水化合物的磷酸转移酶系统的基因含量高于任何先前测序的基因组。这些基因通常位于高度可变的基因组片段中，这些片段还包含参与糖残基降解和修饰的酶的基因。在两个系统型中鉴定出了用于胞外多糖生物合成的菌株特异性基因簇。这些片段的动态变化与核心基因的低重组频率和保守的基因顺序结构形成对比。CRISPR间隔序列的匹配几乎只在各系统型内发现，这表明各系统型与不同的噬菌体群体相关。
蜜蜂肠道微生物群被描述为由数量有限的系统型组成；然而，本研究中测序的基因组表明，在所有三种已描述的乳酸杆菌和双歧杆菌系统型中，基因含量多样性水平非常高，特别是在代谢功能和表面结构方面，其中许多特征是菌株特异性的。总之，这些结果表明各系统型内存在生态位分化，这表明蜜蜂肠道微生物群比以前认为的更复杂。
