Global overview and major challenges of host prediction methods for uncultivated phages
Global overview and major challenges of host prediction methods for uncultivated phages
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DOI：
10.1016/j.coviro.2021.05.003
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发表时间：
2021-06-12
影响因子：
5.9
通讯作者：
Roux, Simon
中科院分区：
文献类型：
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作者：
Coclet, Clement;Roux, Simon
细菌群落在地球所有生物群系中发挥着关键作用，影响着人类健康和全球生态系统功能。它们是在病毒，即噬菌体或“噬菌体”施加的强大限制下这样做的。噬菌体可以重塑细菌群落结构，影响细菌种群的长期进化，并在感染过程中改变宿主细胞代谢。宏基因组学方法，即对环境DNA或RNA进行鸟枪测序，最近使噬菌体基因组多样性的大规模探索成为可能，产生了数百万个噬菌体基因组，现在可以进一步分析和表征。然而，一个主要的挑战是缺乏这些噬菌体的直接宿主信息。目前已经提出了几种方法和工具，仅根据基因组序列信息从生物信息学上预测未培养噬菌体的潜在宿主。在这里，我们回顾了这些不同的方法，并强调了它们独特的优势和局限性。我们还概述了正在提出的验证和完善这些生物信息学预测的补充实验分析。
Bacterial communities play critical roles across all of Earth's biomes, affecting human health and global ecosystem functioning. They do so under strong constraints exerted by viruses, that is, bacteriophages or 'phages'. Phages can reshape bacterial communities' structure, influence long-term evolution of bacterial populations, and alter host cell metabolism during infection. Metagenomics approaches, that is, shotgun sequencing of environmental DNA or RNA, recently enabled large-scale exploration of phage genomic diversity, yielding several millions of phage genomes now to be further analyzed and characterized. One major challenge however is the lack of direct host information for these phages. Several methods and tools have been proposed to bioinformatically predict the potential host(s) of uncultivated phages based only on genome sequence information. Here we review these different approaches and highlight their distinct strengths and limitations. We also outline complementary experimental assays which are being proposed to validate and refine these bioinformatic predictions.