当暴露于相似的环境或从事某些生活方式时,远亲的生物可能会进化出相似的特征。乳杆菌科(LAB)家族的几个成员经常从花生态中分离出来,主要来自蜜蜂和花朵。在一些花卉LAB物种(此后称为蜜蜂相关)中,独特的基因组(例如,基因组减少)和表型(例如,最近记录了对果糖的偏好,而不是葡萄糖或果糖)特征。这些特征在远亲物种中发现,提出了这样的假设,即特定的基因组和表型性状在适应花环境期间融合进化。为了检验这个假设,我们检查了369种蜜蜂相关和非蜜蜂相关LAB的代表性基因组。系统学分析揭示了LAB中花生态位的七个独立生态转变。在这些蜜蜂相关的实验室中,我们观察到无处不在,基因组大小显著减少,基因库,和GC含量。使用机器倾斜,我们可以用94%的准确率区分蜜蜂和非蜜蜂相关的物种,基于缺乏参与新陈代谢的基因,渗透胁迫,或DNA修复。此外,我们发现机器学习分类器最重要的基因似乎丢失了,独立,在多个与蜜蜂相关的谱系中。其中一个基因,adhE,编码与果聚糖进化相关的双功能醛-醇脱氢酶,一种罕见的表型性状,最近在许多花卉LAB物种中发现。这些结果表明,与蜜蜂相关的LAB中独特表型的独立进化很大程度上是由同一组基因的独立丢失驱动的。
■几种乳酸菌(LAB)物种与蜜蜂密切相关,并表现出独特的生化特性,具有食品应用和蜜蜂健康的潜力。使用基于机器学习的方法,我们的研究表明,LAB对蜜蜂环境的适应伴随着由基因丢失深深塑造的独特的基因组轨迹。这些基因丢失中的一些独立发生在远亲物种中,并且与它们的一些独特的生物技术相关性状有关。例如果糖优先于葡萄糖(果糖)。这项研究强调了机器学习在识别适应指纹和检测收敛进化实例方面的潜力。此外,它揭示了蜜蜂相关细菌的基因组和表型特征,从而加深了对蜜蜂健康积极影响的认识。
Distantly related organisms may evolve similar traits when exposed to similar environments or engaging in certain lifestyles. Several members of the Lactobacillaceae (LAB) family are frequently isolated from the floral niche, mostly from bees and flowers. In some floral LAB species (henceforth referred to as bee-associated), distinctive genomic (e.g., genome reduction) and phenotypic (e.g., preference for fructose over glucose or fructophily) features were recently documented. These features are found across distantly related species, raising the hypothesis that specific genomic and phenotypic traits evolved convergently during adaptation to the floral environment. To test this hypothesis, we examined representative genomes of 369 species of bee-associated and non-bee-associated LAB. Phylogenomic analysis unveiled seven independent ecological shifts towards the floral niche in LAB. In these bee-associated LAB, we observed pervasive, significant reductions of genome size, gene repertoire, and GC content. Using machine leaning, we could distinguish bee-associated from non-bee-associated species with 94% accuracy, based on the absence of genes involved in metabolism, osmotic stress, or DNA repair. Moreover, we found that the most important genes for the machine learning classifier were seemingly lost, independently, in multiple bee-associated lineages. One of these genes, adhE, encodes a bifunctional aldehyde-alcohol dehydrogenase associated with the evolution of fructophily, a rare phenotypic trait that was recently identified in many floral LAB species. These results suggest that the independent evolution of distinctive phenotypes in bee-associated LAB has been largely driven by independent loss of the same set of genes.
UNASSIGNED: Several lactic acid bacteria (LAB) species are intimately associated with bees and exhibit unique biochemical properties with potential for food applications and honeybee health. Using a machine-learning based approach, our study shows that adaptation of LAB to the bee environment was accompanied by a distinctive genomic trajectory deeply shaped by gene loss. Several of these gene losses occurred independently in distantly related species and are linked to some of their unique biotechnologically relevant traits, such as the preference of fructose over glucose (fructophily). This study underscores the potential of machine learning in identifying fingerprints of adaptation and detecting instances of convergent evolution. Furthermore, it sheds light onto the genomic and phenotypic particularities of bee-associated bacteria, thereby deepening the understanding of their positive impact on honeybee health.