Sorouri Bahareh, Rodriguez Cynthia I, Gaut Brandon S, Allison Steven D
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.
Department of Earth System Science, University of California Irvine, Irvine, CA, United States.
Front Microbiol. 2023 Apr 17;14:1146165. doi: 10.3389/fmicb.2023.1146165. eCollection 2023.
Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about and facilitate applications in bioremediation.
微生物是否表现出栖息地偏好是微生物生态学中的一个基本问题。如果不同的微生物谱系具有不同的特征，那么这些谱系可能在其特征具有优势的栖息地中更频繁地出现。[具体细菌名称]是研究栖息地偏好与特征之间关系的理想细菌类群，因为这些细菌栖息于多样的环境和宿主中。在这里，我们下载了440个公开可用的基因组，根据分离来源将它们分配到不同栖息地，并研究它们的系统发育关系。我们试图解决以下问题：（1）栖息地与系统发育之间是否存在关系，以及（2）基于基因组的关键特征与栖息地偏好之间是否存在系统发育相关性。我们假设来自相似栖息地的[具体细菌名称]菌株会在系统发育分支中聚集在一起，并且在特定环境中提高适应性的关键特征应与栖息地相关。基于基因组的特征被分类到用于高生长产量、资源获取和胁迫耐受性的Y - A - S特征框架中。我们选择了252个高质量基因组，并基于404个核心基因的比对构建了一个具有12个明确分支的系统发育树。来自相同栖息地的[具体细菌名称]菌株在相同分支内聚集在一起，并且分支内的菌株共享相似的辅助基因簇。此外，基于基因组的关键特征频率在不同栖息地有所不同。我们得出结论，[具体细菌名称]的基因内容反映了栖息地偏好。这种关于环境和宿主与系统发育之间关系的知识也可能有助于未来对[具体细菌名称]的功能预测，并促进其在生物修复中的应用。
