PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks
PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks
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DOI：
10.1016/j.cmpb.2022.106865
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发表时间：
2022-05-13
影响因子：
6.1
通讯作者：
Molina, Felipe
中科院分区：
文献类型：
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作者：
Diaz-Galian, Maria Victoria;Vega-Rodriguez, Miguel A.;Molina, Felipe
背景和目的：噬菌体疗法是一种用于医学和食品工业的复苏策略，用于裂解对健康造成损害或破坏食品的细菌。通常，噬菌体-细菌感染网络具有很大的尺寸，使得不可能手动研究所有可能的噬菌体鸡尾酒。因此，本文提出了一个R软件包称为PhageCocktail自动设计有效的噬菌体鸡尾酒从噬菌体-细菌infection networks.Methods：这个R软件包包括四种不同的方法设计噬菌体鸡尾酒：ExhaustiveSearch，ExhaustivePhi，precipteringSearch，和precipteringPhi。这四种方法进行了详细解释，并使用13个经验噬菌体细菌感染网络进行评估。更具体地说，分析了运行时间和预期成功（溶解细菌的分数）。结果：这四种方法在运行时间和结果质量方面存在差异。穷举搜索总是提供最好的噬菌体鸡尾酒，但它的运行时间可能很长。ExhaustivePhi只关注一种鸡尾酒大小，估计为最好的一种;因此，它的运行时间比ExhaustiveSearch少，但它可以产生比必要的更多的鸡尾酒。由于聚类技术的存在，QuantiteringSearch和QuantiteringPhi的速度非常快（通常不到1毫秒），能够提供即时的结果，但它们的准确性可能较低，产生的鸡尾酒预期成功率较低。结论：噬菌体-细菌感染网络越大，其分析就越复杂。因此，该工具为科学家和其他用户简化了这项任务，同时设计了高质量的噬菌体鸡尾酒。这个R包包括四种不同的方法;因此，用户可以根据他们对结果的速度和准确性的偏好来选择它们。(c)2022作者由Elsevier B. V.发布。这是CC BY许可下的开放获取文章（http：//creativecommons.org/licenses/by/4.0/）
Background and objective: Phage therapy is a resurgent strategy used in medicine and the food industry to lyse bacteria that cause damage to health or spoil a food product. Frequently, phage-bacteria infection networks have a large size, making it impossible to manually study all possible phage cocktails. Thus, this article presents an R package called PhageCocktail to automatically design efficient phage cocktails from phage-bacteria infection networks.Methods: This R package includes four different methods for designing phage cocktails: ExhaustiveSearch, ExhaustivePhi, ClusteringSearch, and ClusteringPhi. These four methods are explained in detail and are evaluated using 13 empirical phage-bacteria infection networks. More specifically, runtime and expected success (fraction of lysed bacteria) are analyzed.Results: The four methods have variations in terms of runtime and quality of the results. ExhaustiveSearch always provides the best possible phage cocktail, but its runtime could be long. ExhaustivePhi only focuses on one cocktail size, the one estimated as the best; thus, its runtime is less than ExhaustiveSearch, but it can produce cocktails with more phages than necessary. ClusteringSearch and ClusteringPhi are very fast (generally, less than one millisecond), providing always immediate results due to clustering techniques, but their accuracies can be lower, yielding cocktails with lower expected successes.Conclusions: The larger the phage-bacteria infection network is, the more complex its analysis is. Thus, this tool eases this task for scientists and other users while designing phage cocktails of good quality. This R package includes four different methods; therefore, users may choose among them, considering their preferences in speed and accuracy of results. (c) 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)