CRISPR-Cas is a prokaryotic defense system capable of protecting the cell from damaging foreign genetic elements. However, some genetic elements can be beneficial, which suggests the hypothesis that bacteria with CRISPR-Cas incur a cost of reduced intake of mutualistic plasmids and prophage. Here we present the first robust test of this hypothesis that controls for phylogenic and ecological biases in the distribution of CRISPR-Cas. We filtered the available genomic data (~7000 strains from ~2100 species) by first selecting all pairs of conspecific strains, one with and one without CRISPR-Cas (controlling ecological bias), and second by retaining only one such pair per bacterial family (controlling phylogenetic bias), resulting in pairs representing 38 bacterial families. Analysis of these pairs of bacterial strains showed that on average the CRISPR-Cas strain of each pair contained significantly fewer plasmids than its CRISPR-Cas negative partner (0.86 vs. 1.86). It also showed that the CRISPR-Cas positive strains had 31% fewer intact prophage (1.17 vs. 1.75), but the effect was highly variable and not significant. These results support the hypothesis that CRISPR-Cas reduces the rate of plasmid-mediated HGT and, given the abundant evidence of beneficial genes carried by plasmids, provide a clear example of a cost associated with the CRISPR-Cas system.

中文翻译：

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CRISPR-Cas在限制细菌中质粒获取和噬菌体整合中作用的系统发育测试。

CRISPR-Cas是一种原核防御系统，能够保护细胞免受外来遗传因素的破坏。然而，某些遗传因素可能是有益的，这提示了具有CRISPR-Cas的细菌会导致减少相互摄取质粒和原噬菌体的成本的假说。在这里，我们介绍了该假设的第一个稳健检验，该假设可控制CRISPR-Cas分布中的系统发育和生态偏差。我们通过首先选择所有成对的同种菌株来筛选可用的基因组数据（约2100个物种中的约7000个菌株），一个带有和不带有CRISPR-Cas（控制生态学偏见），然后每个细菌家族仅保留一个这样的对（控制系统发育偏向），从而代表38个细菌家族。对这些细菌菌株对的分析表明，平均每对CRISPR-Cas菌株包含的质粒比其CRISPR-Cas阴性伴侣的质粒少得多（0.86比1.86）。它也显示了CRISPR-Cas阳性菌株的完整原噬菌体减少了31％（1.17对1.75），但效果高度可变且不显着。这些结果支持以下假设：CRISPR-Cas降低了质粒介导的HGT的速率，并且鉴于质粒携带的有益基因的大量证据，提供了与CRISPR-Cas系统相关的成本的清晰示例。但效果变化很大，并不显着。这些结果支持以下假设：CRISPR-Cas降低了质粒介导的HGT的速率，并且鉴于质粒携带的有益基因的大量证据，提供了与CRISPR-Cas系统相关的成本的清晰示例。但效果变化很大，并不显着。这些结果支持以下假设：CRISPR-Cas降低了质粒介导的HGT的速率，并且鉴于质粒携带的有益基因的大量证据，提供了与CRISPR-Cas系统相关的成本的清晰示例。