斯坦福大学Ami S. Bhatt团队取得一项新突破。他们报道了长读宏基因组学揭示了人类肠道微生物组中的噬菌体动力学。2025年11月26日出版的《自然》杂志发表了这项成果。

使用深度长读体宏基因组测序，研究人员追踪了6名健康个体粪便样本中噬菌体整合的动态，时间跨度为2年。尽管大多数噬菌体能够稳定地整合到宿主中，但大约5%的噬菌体是动态地从持久性细菌宿主中获得或丢失的。在一个样本中，该课题组发现有和没有给定的噬菌体的细菌宿主同时共存。

此外，当检测到噬菌体诱导时，主要发生在低水平（与宿主区域相比覆盖率为1 - 3倍），这符合理论预期。课题组人员发现了同一噬菌体与不同分类科细菌整合的多个实例，挑战了噬菌体对特定物种或菌株的宿主特异性的教条。最后，该课题组描述了一类新的“IScream噬菌体”，它们共同选择细菌IS30转座介导它们的动员，代表了一种以前未被认识的噬菌体对自私细菌元素的驯化形式。综上所述，这些发现阐明了人类肠道微生物组中噬菌体-细菌动力学的基本方面，并扩展了他们对驱动水平基因转移和微生物基因组可塑性的进化机制的理解。

据了解，肠道噬菌体深刻影响微生物生态和健康；然而，他们没有得到充分的研究。

附：英文原文

Title: Long-read metagenomics reveals phage dynamics in the human gut microbiome

Author: Wirbel, Jakob, Hickey, Angela S., Chang, Daniel, Enright, Nora J., Dvorak, Mai, Chanin, Rachael B., Schmidtke, Danica T., Bhatt, Ami S.

Issue&Volume: 2025-11-26

Abstract: Gut bacteriophages profoundly impact microbial ecology and health1,2,3; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1–3× coverage compared to the host region), in line with theoretical expectations4. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain5. Finally, we describe a new class of ‘IScream phages’, which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage–bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.

DOI: 10.1038/s41586-025-09786-2

Source: https://www.nature.com/articles/s41586-025-09786-2