Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions.

IF 5.1 Q1 ECOLOGY
ISME communications Pub Date : 2025-02-04 eCollection Date: 2025-01-01 DOI:10.1093/ismeco/ycaf017
Marta Proença, Luís Tanoeiro, James G Fox, Filipa F Vale
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Abstract

Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from H. canis, H. equorum, H. jaachi, and the gastric prophage from H. himalayensis-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.

胃和肠肝环境中的噬菌体动力学:揭示生态障碍和适应性转变。
噬菌体捕食在塑造细菌遗传多样性中起着至关重要的作用,而噬菌体也起着类似的作用。然而,对幽门螺杆菌属中噬菌体的流行率和遗传变异性的研究仍不充分。幽门螺杆菌种类在临床上具有重要意义,并占据不同的消化系统区域,胃种(如幽门螺杆菌)居住在胃粘膜中,肠肝种定居在各种脊椎动物的肝脏和肠道中。在这里,我们通过分析343个非幽门螺杆菌基因组中前噬菌体的存在和多样性,绘制它们的分布,比较胃和肠肝前噬菌体的基因组特征,并探索它们与宿主的进化关系,来解决这一知识空白。我们鉴定并分析了119个新的完整噬菌体和78个不完整的噬菌体。我们的分析揭示了胃和肠肝物种之间的显著差异。胃前噬菌体表现出高度的共生性,并聚集在少数群体中,表明其遗传结构更为保守。相比之下,肠肝噬菌体在基因顺序和内容上表现出更大的多样性,反映了它们对不同宿主环境的适应性。中国幽门螺杆菌(Helicobacter cinaedi)尤为突出,它在肠肝菌中拥有大量的噬菌体,形成了一个独特的内聚群。系统发育分析揭示了几种噬菌体和它们的细菌宿主之间的共同进化关系——尽管有例外,如犬嗜血杆菌、马瘟嗜血杆菌、豺嗜血杆菌和喜马拉雅嗜血杆菌的胃噬菌体——表明了更复杂的共同进化动力学,如宿主跳跃、重组和水平基因转移。从这项研究中获得的见解增强了我们对幽门螺杆菌前噬菌体动力学的理解,强调了它们在细菌适应、毒力和宿主特异性中的作用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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