Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments.

中文翻译：

---

使用 Hi-C 追踪人类肠道中的微生物进化揭示了广泛的水平基因转移、持久性和适应性。

尽管水平基因转移对于细菌的快速进化很重要，但缺乏将移动遗传元件可靠地分配给自然群落（如人类肠道微生物群）中的微生物宿主。我们使用高通量染色体构象捕获结合实验噪声的概率建模来解析来自两名参与者的 88 个菌株级宏基因组组装的远端肠道细菌基因组，包括 12,251 个辅助元素。对每个参与者相隔 10 年收集的两个样本进行比较，揭示了辅助元素的广泛原位交换以及核心基因组适应性进化的证据。辅助元素在 218 名成年人的远端肠道宏基因组中主要是混杂和普遍的。