Du Yuhui, Qian Chengqian, Li Xianxin, Zheng Xinqian, Huang Shoucong, Yin Zhiqiu, Chen Tingjian, Pan Li
MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological slaEngineering, South China University of Technology, Guangzhou, 510006, Guangdong, PR China.
School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Guangzhou, 510006, Guangdong, PR China.
Curr Res Food Sci. 2024 Sep 21;9:100867. doi: 10.1016/j.crfs.2024.100867. eCollection 2024.
Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the group, is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of . Metagenomic read recruitment analyses demonstrated that members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.
了解食源性病原体在整个宿主相关栖息地的进化动态至关重要。细菌泛基因组作为动态实体，受到生态生活方式的强烈影响。作为该群体中表型多样的物种，[物种名称]同时被认为是一种新兴的食源性病原体和益生菌。这种了解甚少的物种是适应性泛基因组进化的合适研究模型。在本研究中，我们确定了[物种名称]关键遗传元件的生物地理分布、丰度、遗传多样性和基因型谱。宏基因组读数招募分析表明，[物种名称]成员在全球范围内分布，且在宿主相关栖息地中数量丰富。随后构建了高质量的[物种名称]泛基因组，以全面分析生态适应过程中涉及的进化动态。开放的泛基因组表明基因库具有灵活性，遗传多样性广泛。不同组分之间在系统发育关系、功能富集和选择压力程度上的显著差异表明，核心基因组和辅助基因组在生态力量驱动下具有不同的进化动态。纯化选择和基因丢失是[物种名称]泛基因组进化动态的主要特征。辅助基因组的可塑性表现为水平基因转移（HGT）、大量基因丢失以及较弱的纯化或正选择，这可能有助于特定生态位的适应。相比之下，虽然核心基因组主要经历纯化选择，但其与HGT和正选择突变的关联表明其在生态多样化中的潜在作用。此外，宿主适应性相关动态的特征是次生代谢物生物合成基因簇（BGCs）和编码碳水化合物活性酶（CAZyme）的基因丢失，以及通过HGT获得抗微生物耐药性（AMR）和毒力基因。本研究提供了一个泛基因组进化的案例研究，以调查生物地理特征所反映的生态适应，从而增进对食源性病原体种内多样性和进化动态的理解。
