Barberán Albert, Caceres Velazquez Hildamarie, Jones Stuart, Fierer Noah
Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona, USA.
Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.
mSphere. 2017 Aug 2;2(4). doi: 10.1128/mSphere.00237-17. eCollection 2017 Jul-Aug.
Cultivation in the laboratory is essential for understanding the phenotypic characteristics and environmental preferences of bacteria. However, basic phenotypic information is not readily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the (IJSEM) with all information made publicly available in an updatable database. Although the data span 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic strains from (mainly - and ), , , and isolated from soils, marine habitats, and plants. Most of the routinely measured traits tended to show a significant phylogenetic signal, although this signal was weak for environmental preferences. We demonstrated how this database could be used to link genomic attributes to differences in pH and salinity optima. We found that adaptations to high salinity or high-pH conditions are related to cell surface transporter genes, along with previously uncharacterized genes that might play a role in regulating environmental tolerances. Together, this work highlights the utility of this database for associating bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and emphasizes the need for more comprehensive and consistent measurements of traits across a broader diversity of bacteria. Cultivation in the laboratory is key for understanding the phenotypic characteristics, growth requirements, metabolism, and environmental preferences of bacteria. However, oftentimes, phenotypic information is not easily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the (IJSEM). We demonstrate how this database can be used to link bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and environmental preferences. The phenotypic database can be freely accessed (https://doi.org/10.6084/m9.figshare.4272392), and we have included instructions for researchers interested in adding new entries or curating existing ones.
在实验室中培养对于了解细菌的表型特征和环境偏好至关重要。然而，基本的表型信息并不容易获取。在此，我们汇编了《国际系统与进化微生物学杂志》（IJSEM）中描述的5000多种细菌菌株的表型和环境耐受性信息，并将所有信息公开提供在一个可更新的数据库中。尽管数据涵盖23个不同的细菌门，但大多数条目描述的是来自变形菌门（主要是α-、β-、γ-和δ-变形菌纲）、放线菌门、厚壁菌门、拟杆菌门，从土壤、海洋栖息地和植物中分离出的需氧、嗜温、嗜中性菌株。大多数常规测量的性状往往显示出显著的系统发育信号，尽管这种信号对于环境偏好来说较弱。我们展示了如何利用这个数据库将基因组属性与最适pH值和盐度的差异联系起来。我们发现，对高盐或高pH条件的适应与细胞表面转运蛋白基因以及可能在调节环境耐受性中发挥作用的先前未表征的基因有关。总之，这项工作突出了该数据库在将细菌分类学、系统发育或特定基因与测量的表型性状相关联方面的实用性，并强调了对更广泛的细菌多样性进行更全面和一致的性状测量的必要性。在实验室中培养是了解细菌的表型特征、生长需求、代谢和环境偏好的关键。然而，通常情况下，表型信息并不容易获取。在此，我们汇编了《国际系统与进化微生物学杂志》（IJSEM）中描述的5000多种细菌菌株的表型和环境耐受性信息。我们展示了如何利用这个数据库将细菌分类学、系统发育或特定基因与测量的表型性状和环境偏好联系起来。该表型数据库可免费访问（https://doi.org/10.6084/m9.figshare.4272392），并且我们为有兴趣添加新条目或整理现有条目的研究人员提供了说明。
