School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK.
School of Science and Technology, Nottingham Trent University, UK.
Gut Microbes. 2022 Jan-Dec;14(1):2152306. doi: 10.1080/19490976.2022.2152306.
Individuals infected with harbor unique and diverse populations of quasispecies, but diversity between and within different regions of the human stomach and the process of bacterial adaptation to each location are not yet well understood. We applied whole-genome deep sequencing to characterize the within- and between-stomach region genetic diversity populations from paired antrum and corpus biopsies of 15 patients, along with single biopsies from one region of an additional 3 patients, by scanning allelic diversity. We combined population deep sequencing with more conventional sequencing of multiple single colony isolates from individual biopsies to generate a unique dataset. Single colony isolates were used to validate the scanning allelic diversity pipelines. We detected extensive population allelic diversity within the different regions of each patient's stomach. Diversity was most commonly found within non-coding, hypothetical, outer membrane, restriction modification system, virulence, lipopolysaccharide biosynthesis, efflux systems, and chemotaxis-associated genes. Antrum and corpus populations from the same patient grouped together phylogenetically, indicating that most patients were initially infected with a single strain, which then diversified. Single colonies from the antrum and corpus of the same patients grouped into distinct clades, suggesting mechanisms for within-location adaptation across multiple isolates from different patients. The comparisons made available by combined sequencing and analysis of isolates and populations enabled comprehensive analysis of the genetic changes associated with diversification and stomach region adaptation.
个体感染后携带独特且多样的准种群体，但人类胃的不同区域之间和内部的多样性以及细菌对每个位置的适应过程尚不清楚。我们应用全基因组深度测序技术，通过扫描等位基因多样性，对来自 15 名患者配对的胃窦和胃体活检组织以及另外 3 名患者单一区域活检组织中的个体胃内和胃间区域遗传多样性进行了特征描述。我们将群体深度测序与来自个体活检组织的多个单菌落分离株的常规测序相结合，生成了一个独特的数据集。单菌落分离株用于验证扫描等位基因多样性的流程。我们在每个患者胃的不同区域内检测到了广泛的群体等位基因多样性。多样性最常见于非编码、假设、外膜、限制修饰系统、毒力、脂多糖生物合成、外排系统和趋化相关基因中。来自同一患者的胃窦和胃体群体在系统发育上聚为一组，表明大多数患者最初感染了单一菌株，随后发生了多样化。来自同一患者胃窦和胃体的单菌落分为不同的分支，表明在来自不同患者的多个分离株之间存在适应同一位置的机制。通过对分离株和群体进行测序和综合分析，提供了可进行比较的机会，从而能够全面分析与 多样化和胃区域适应相关的遗传变化。
