Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia.
Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
Microb Genom. 2023 Sep;9(9). doi: 10.1099/mgen.0.001100.
Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the order. Despite identifying over 600 genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel species infecting WH2. These species, sp. 'tikkala' strain Bc01, sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.
拟杆菌是人类肠道中突出的细菌,在降解复杂多糖方面发挥着关键作用。它们的丰度受到属于目噬菌体的影响。尽管通过计算鉴定了超过 600 个基因组,但只有少数成功分离出来。继续努力分离更多的基因组可以深入了解噬菌体-宿主进化和感染机制。我们专注于废水样本,因为它们是感染各种宿主的噬菌体的潜在来源。对分离噬菌体的测序、组装和特征分析揭示了 14 个完整基因组,属于三种新的感染 WH2 的物种。这些物种,sp. 'tikkala' 菌株 Bc01、sp. 'frurule' 菌株 Bc03 和 'Rudgehvirus jaberico' 菌株 Bc11,跨越了两个科和三个属,显示出广泛的病毒产量。在测试所有成功培养的物种及其各自的细菌宿主后,我们发现它们与细菌宿主没有共同进化模式。此外,我们观察到基因相似性的变化,属内观察到更大的共享相似性。然而,尽管属于不同的属,这三个新物种共享一个独特的结构基因,该基因编码尾刺蛋白。当研究该基因与宿主相互作用之间的关系时,我们发现了纯化选择的证据,表明其功能重要性。此外,我们的分析表明,这种尾刺蛋白结合在细菌宿主表面上存在的 TonB 依赖性受体上。综合这些观察结果,我们的发现深入了解了噬菌体-宿主相互作用,并提出了三个物种作为在人类肠道病毒组中最占优势的成员之一进行受控感染实验的理想系统。