Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter.
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter.
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DOI：
10.1093/nar/gkab133
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发表时间：
2021-04-06
影响因子：
14.9
通讯作者：
Moineau S
中科院分区：
文献类型：
--
作者：
Dion MB;Plante PL;Zufferey E;Shah SA;Corbeil J;Moineau S
由于病毒元基因组学，最近发现了数以千计的新噬菌体。这些噬菌体极其多样化，它们的基因组序列通常与任何已知的噬菌体都不相似。要了解它们的生态影响，重要的是确定它们的细菌宿主。CRISPR间隔区可用于预测未知噬菌体的宿主，因为间隔区代表了过去噬菌体与细菌相互作用的生物记录。然而，还没有建立指南来标准化基于CRISPR间隔区的寄主预测。此外，目前还没有使用间隔区对大型病毒数据集进行宿主预测的工具。在这里，我们开发了一套工具，其中包括预测未知噬菌体宿主的所有必要步骤。我们创建了一个包含1100万个间隔区的数据库和一个在大型病毒数据集上执行宿主预测的程序。我们的宿主预测方法使用生物学标准，灵感来自CRISPR-CA作为适应性免疫系统的自然工作方式，这使得结果很容易解释。我们使用9484个已知宿主的噬菌体对性能进行了评估，获得了49%的召回率和669%的准确率。我们还发现，这种宿主预测方法对感染肠道相关细菌的噬菌体产生了更高的性能，表明它很适合于肠道病毒的表征。
Thousands of new phages have recently been discovered thanks to viral metagenomics. These phages are extremely diverse and their genome sequences often do not resemble any known phages. To appreciate their ecological impact, it is important to determine their bacterial hosts. CRISPR spacers can be used to predict hosts of unknown phages, as spacers represent biological records of past phage–bacteria interactions. However, no guidelines have been established to standardize host prediction based on CRISPR spacers. Additionally, there are no tools that use spacers to perform host predictions on large viral datasets. Here, we developed a set of tools that includes all the necessary steps for predicting the hosts of uncharacterized phages. We created a database of >11 million spacers and a program to execute host predictions on large viral datasets. Our host prediction approach uses biological criteria inspired by how CRISPR–Cas naturally work as adaptive immune systems, which make the results easy to interpret. We evaluated the performance using 9484 phages with known hosts and obtained a recall of 49% and a precision of 69%. We also found that this host prediction method yielded higher performance for phages that infect gut-associated bacteria, suggesting it is well suited for gut-virome characterization.
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影响因子：
3
作者：
Edgar RC
通讯作者：
Edgar RC
影响因子：
14.9
作者：
Grissa, Ibtissem;Vergnaud, Gilles;Pourcel, Christine
通讯作者：
Pourcel, Christine
影响因子：
14.9
作者：
Chen IA;Chu K;Palaniappan K;Pillay M;Ratner A;Huang J;Huntemann M;Varghese N;White JR;Seshadri R;Smirnova T;Kirton E;Jungbluth SP;Woyke T;Eloe-Fadrosh EA;Ivanova NN;Kyrpides NC
通讯作者：
Kyrpides NC
影响因子：
14.9
作者：
Couvin D;Bernheim A;Toffano-Nioche C;Touchon M;Michalik J;Néron B;Rocha EPC;Vergnaud G;Gautheret D;Pourcel C
通讯作者：
Pourcel C
影响因子：
11.3
作者：
Edwards RA;McNair K;Faust K;Raes J;Dutilh BE
通讯作者：
Dutilh BE