Zhai Yiting, Wei Chaochun
Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Front Microbiol. 2022 Aug 23;13:948138. doi: 10.3389/fmicb.2022.948138. eCollection 2022.
() is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of . An open pangenome of was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.
（）是一种分离良好且经过培养的乳酸菌，但如果仅利用分离出的基因组，对该分类群进行基于基因组的分析将是不完整的，因为在某些生态位中仍存在未培养的菌株。在本研究中，我们采用非培养方法从食品和人类肠道宏基因组中获得了93个高质量的宏基因组组装基因组（MAG）。然后，我们将这些MAG与70个公开可用的分离基因组整合，构建了一个统一的基因组目录。有了这个全面的资源，我们评估了基因组多样性和系统发育关系，以进一步探索（）的遗传和功能特性。利用我们的基因组目录生成了一个开放的泛基因组，总共包含13066个基因，其中5448个基因在分离基因组中未被鉴定。基于核心基因组的系统发育分析表明，我们收集的（）菌株被分为两个主要分支，对应于两个亚种，同时发现了一些未培养的系统发育谱系。基于我们泛基因组的辅助基因的主成分分析也表明了物种差异。这些各种分析进一步揭示了该分类群在基因组和基因水平上意外的高多样性，并给出了其种群结构和进化的线索。（）在食品发酵中有着长期安全使用的历史，被认为是重要的益生菌微生物之一。获得（）的完整遗传信息对食品和健康产业很重要。然而，它可以自然栖息于乳制品以外的许多环境中，包括排水和人类肠道样本。在这里，我们展示了一个由163个从各种环境中获得的高质量基因组构建的开放泛基因组，包括从环境宏基因组中获得的MAG和分离基因组。这项研究将（）的遗传信息扩展了约三分之一，包括在未培养菌株中发现的5000多个新基因。（）这个更完整的基因库对于进一步理解其遗传和功能特性至关重要。这些特性可用于为乳制品发酵或其他行业赋予额外价值。
