深度学习改变了菌体-宿主相互作用的发现,从元基因组数据中发现
Yiyan Yang1, Tong Wang1, Dan Huang1
1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
bioRxiv : the preprint server for biology
|July 16, 2025
概括
我们开发了PHILM,这是一个深度学习工具,用于从元基因组数据中预测菌体与宿主相互作用 (PHI). 菲尔姆显著提高了PHI预测的准确性,并为微生物组动态和疾病分类提供了新的见解.
科学领域:
- 微生物组研究的研究.
- 计算生物学是一种计算生物学.
- 病毒学 病毒学
背景情况:
- 微生物群落对于生态系统功能至关重要,菌体在塑造它们方面发挥着关键作用.
- 现有的从元基因组数据中推断菌体与宿主相互作用 (PHI) 的方法具有低灵敏度和有限的生态准确性.
研究的目的:
- 引入PHILM,这是一个新的深度学习框架,可以直接从元基因组分类学资料中预测PHI.
- 为了克服PHI推断当前计算方法的局限性.
主要方法:
- 开发了PHILM,这是一个使用元基因组分类学概况的深度学习框架.
- 通过生态模型和现实世界元基因组数据的合成数据集验证PHILM.
- 将PHILM与基于共丰度和基于汇编的PHI推断方法进行比较.
主要成果:
- 在推断PHI方面,PHILM在推断PHI方面始终优于基于共丰度的方法.
- 应用到一个大数据集,PHILM发现了90%以上的属级PHI,而不是基于组装的方法.
- 菲尔姆的潜伏表示有效地捕捉了微生物的继承并提高了疾病分类的准确性.
结论:
- 菲尔姆提供了一个强大的新计算框架,用于从元基因组数据中预测菌体与宿主相互作用.
- 该框架通过揭示复杂的菌体-宿主动态,为微生物组科学和翻译医学提供了重大进展.
相关概念视频
DNA Bacteriophages
158
Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
158
Lytic Cycle of Bacteriophages
72.1K
Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
72.1K
Lysogenic Cycle of Bacteriophages
63.3K
In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
63.3K
Viral Replication: Lysogenic Cycle
261
The lysogenic cycle is a crucial viral replication strategy that allows bacteriophages to persist within host cells without immediately destroying them. This process is primarily observed in temperate phages, such as bacteriophage lambda (λ), which infects Escherichia coli. The cycle allows the viral genome to persist across bacterial generations while keeping host cells viable.Integration of the Viral GenomeUpon infection, bacteriophage lambda attaches to the bacterial surface and injects...
261
Viral Replication: Lytic Cycle
282
Bacteriophages, or phages, are viruses that specifically infect bacteria. Among them, T-even bacteriophages, such as T4, exhibit a well-characterized lytic replication cycle in Escherichia coli (E. coli). This process ensures the rapid proliferation of the virus while ultimately leading to the destruction of the bacterial host.Attachment and DNA InjectionThe infection process begins with the recognition and binding of the T4 phage to the E. coli cell surface. Tail fibers of the phage...
282
Viruses of Archaea
81
Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...
81


