Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

Rands Chris M.; Brüssow Harald; Zdobnov Evgeny M.

摘要

Summary > Negativicutes are gram‐negative bacteria characterized by two cell membranes, but they are phylogenetically a side‐branch of gram‐positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from gram‐negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co‐evolved vertically with their hosts and thus resemble gram‐positive Firmicute prophages. We predicted and characterized 485 prophages (mostly Caudovirales ) from gram‐negative Firmicute genomes plus 2977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to support our predictions. The majority of identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu‐like candidate prophage and no clear P2‐like prophages were identified in Negativicutes, both common in Proteobacteria. Given this collective evidence, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence‐related prophages, which occasionally harboured antibiotic resistance genes, were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales), possibly suggesting horizontal cross‐order phage infection between human gut commensals. Our results reveal ancient genomic signatures of phage and bacteria co‐evolution despite horizontal phage mobilization. </abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> <div class="translation abstracttxt"> <span class="zhankaihshouqi fivelineshidden" id="abstract"> <span>机译：</span><Abstract Type =“Main”XML：Lang =“en”> <标题类型=“main”>概述</ title> >否定克肾阴性细菌，其特征是两个细胞膜，但它们是侧面的只包含单个膜的革兰肯积极的分支。我们询问病毒（噬菌体）是否患有革兰氏阴性植物的病毒（噬菌体）被水平获得，鉴于其细菌宿主的共同外细胞结构，或者如果否定的腔噬菌体与其宿主垂直进化，因此类似于革兰氏阳性的更加预言。我们预测并从革兰氏阴性型素质素加上2977个螺旋曲面预测并表征了485个（主要是剖腹产）（大多是剖宫产，</ i>），我们使用来自183个人粪便样本的病毒序列数据来支持我们的预测。大多数已识别的否定型预言是与其他常压的睫毛与序列关系和基因组组织（裂解模块的位置）相比来自其他常规的植物。在噬菌体中常见的否定性，只鉴定了单一穆式候选的候选先知和没有明确的P2样本。鉴于这种集体证据，不太可能从植物中获得否定的噬菌体。在两个不同的否定抗性序列（Veillonellales和acidaminococales）中鉴定了与抗生素抗性基因的序列相关的血管，可能表明人肠道之间的水平交互噬菌体感染。尽管水平噬菌体动员，我们的结果揭示了脑袋和细菌共同进化的古代基因组特征。 </ p> </ abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> </div> <div class="record"> <h2 class="all_title" id="enpatent33" >著录项</h2> <ul> <li> <span class="lefttit">来源</span> <div style="width: 86%;vertical-align: text-top;display: inline-block;"> <a href='/journal-foreign-22868/'>《Environmental microbiology》</a> <b style="margin: 0 2px;">|</b><span>2019年第11期</span><b style="margin: 0 2px;">|</b><span>共13页</span> </div> </li> <li> <div class="author"> <span class="lefttit">作者</span> <p id="fAuthorthree" class="threelineshidden zhankaihshouqi"> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Rands Chris M.&option=202" target="_blank" rel="nofollow">Rands Chris M.;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Brüssow Harald&option=202" target="_blank" rel="nofollow">Brüssow Harald;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Zdobnov Evgeny M.&option=202" target="_blank" rel="nofollow">Zdobnov Evgeny M.;</a> </p> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zkzz" style="display: none;">展开▼</span> </div> </li> <li> <div style="display: flex;"> <span class="lefttit">作者单位</span> <div style="position: relative;margin-left: 3px;max-width: 639px;"> <div class="threelineshidden zhankaihshouqi" id="fOrgthree"> <p>Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical SchoolGeneva Switzerland;</p> <p>Department of Biosystems Laboratory of Gene TechnologyKU LeuvenLeuven Belgium;</p> <p>Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical SchoolGeneva Switzerland;</p> </div> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zhdw" style="display: none;">展开▼</span> </div> </div> </li> <li > <span class="lefttit">收录信息</span> <span style="width: 86%;vertical-align: text-top;display: inline-block;"></span> </li> <li> <span class="lefttit">原文格式</span> <span>PDF</span> </li> <li> <span class="lefttit">正文语种</span> <span>eng</span> </li> <li> <span class="lefttit">中图分类</span> <span><a href="https://www.zhangqiaokeyan.com/clc/183.html" title="微生物学">微生物学;</a></span> 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href="/academic-degree-domestic_mphd_thesis/020315283879.html">革兰阴性菌与革兰阳性菌所致腹膜透析相关性腹膜炎耐药性分析和危险因素研究</a> <b>[A] </b> <span> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=刘庆倩&option=202" target="_blank" rel="nofollow" class="tuijian_auth tuijian_authcolor"> . 刘庆倩</a> <span> . 2018</span> </span> </div> </li> </ul> <ul style="display: none;"> <li> <div> <b>1. </b><a class="enjiyixqcontent" href="/patent-detail/06120112909754.html">一种治疗耐药性革兰阴阳性菌的化合物及其制备方法</a> <b>[P]</b> . <span> 中国专利： CN112939860A </span> <span> . 2021-06-11</span> </div> </li> <li> <div> <b>2. </b><a class="enjiyixqcontent" href="/patent-detail/061204010228.html">药品中耐胆盐革兰阴性菌能力验证样品及其制备方法</a> <b>[P]</b> . <span> 中国专利： CN107142303B </span> <span> . 2020.09.22</span> </div> </li> <li> <div> <b>3. </b><a class="enjiyixqcontent" href="/patent-detail/06130401697597.html">Determination of multi-dimensional location, species and genomic copy number by comparative fluorescence imaging of three stained microbial 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