Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
mSystems. 2022 Jun 28;7(3):e0008322. doi: 10.1128/msystems.00083-22. Epub 2022 Apr 14.
The genus includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect species. We also identified similar predicted prophages in genomes of different species. Additionally, we examined CRISPR-Cas targeting of each genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel prophages, several of which may infect multiple species. These findings have important implications for understanding horizontal gene transfer between members of this genus. Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
该属包括两个致病物种，淋病奈瑟菌和脑膜炎奈瑟菌，以及许多共生物种。物种之间经常通过转化和同源重组以及多种类型的移动遗传元件（MGE）进行 DNA 交换。已经鉴定出少数噬菌体（噬菌体），但它们对细菌生理学的影响知之甚少。此外，人们对噬菌体可以感染的物种范围知之甚少。在这项研究中，我们使用三种病毒预测工具扫描了 21 种不同物种的 248 个基因组，并鉴定出 1302 个独特的预测原噬菌体。通过比较基因组学，我们发现许多预测与以前描述的感染物种的原噬菌体和其他 MGE 不同。我们还在不同物种的基因组中发现了相似的预测原噬菌体。此外，我们检查了每个基因组的 CRISPR-Cas 靶向和预测的原噬菌体。虽然 CRISPR 靶向染色体 DNA 在几种物种中似乎很常见，但我们发现，我们预测的 20%的原噬菌体比它们所在的细菌基因组的其余部分（即骨干）受到的靶向显著更多。此外，许多预测的原噬菌体都被其他物种编码的 CRISPR 间隔物靶向。然后，我们利用这些结果推断出已知原噬菌体和预测原噬菌体的其他宿主物种，这些预测原噬菌体相对于骨干受到高度靶向。总的来说，我们的结果表明，我们已经鉴定出了新型的原噬菌体，其中一些可能感染多种物种。这些发现对于理解该属成员之间的水平基因转移具有重要意义。耐多药淋病奈瑟菌是对人类健康的主要威胁。共生物种被认为是抗生素耐药性和毒力基因的储库，这些基因可导致致病性物种淋病奈瑟菌和脑膜炎奈瑟菌的感染。因此，了解可以介导该属内水平基因转移的移动遗传元件（MGE）的多样性以及这些 MGE 可以感染的物种范围非常重要。特别是，已知很少有噬菌体（噬菌体）感染 物种。在这项研究中，我们在共生和致病物种的基因组中鉴定出了大量候选噬菌体，其中许多似乎是新型噬菌体。重要的是，我们发现 CRISPR-Cas 系统广泛靶向预测的噬菌体，这可能反映了它们在不同物种之间的运动。揭示噬菌体的多样性和宿主范围对于了解它们如何影响其微生物宿主的进化至关重要。
