Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria.
Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria.
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DOI：
10.1128/mbio.01766-23
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发表时间：
2023-12-19
期刊：
影响因子：
6.4
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Liu, Jett;Jaffe, Alexander L.;Chen, Linxing;Bor, Batbileg;Banfield, Jillian F.
在人类微生物群中，细叶菌、潜行菌和糖菌是候选辐射门（CPR）的成员，它们与人类口腔健康和疾病的关系越来越密切。我们分析了这些细菌基因组中CRISPR-Cas系统的多样性，并通过将它们的间隔序列清单与大型噬菌体序列数据库相匹配，寻找能够感染它们的噬菌体。细叶杆菌和潜存杆菌将典型的TGA终止密码子编码为甘氨酸，并被认为被共享宿主替代遗传密码的噬菌体感染。然而，出乎意料的是，其他预测的细叶杆菌和潜行杆菌噬菌体不使用替代遗传密码。其中一些噬菌体可能同时感染编码的CPR细菌和标准编码的细菌。这些噬菌体通常依赖于TGA以外的其他终止密码子，因此应该能够在任何一种细菌宿主类型中产生活的基因产物。通过避免获得帧内终止密码子，这些噬菌体可能具有更广泛的宿主范围。有趣的是，我们还预测，一些糖菌的噬菌体是由放线菌编码的间隔物靶向的，放线菌门包括已知的外共生糖菌宿主。在这里，我们描述了假定的糖菌噬菌体，这是特别重要的，因为糖菌影响一些人类口腔疾病。此外，我们还分析了两种候选辐射门（CPR）谱系，即细叶细菌（Gracilibacteria）和潜存细菌（abconditabobacteria）的推定噬菌体，因为它们使用了另一种遗传密码。在本研究中鉴定的噬菌体中，一些是来自CPR和非CPR细菌的间隔物的目标，另一些是使用标准遗传密码的细菌和使用替代遗传密码的细菌的目标。这些发现代表了对可能的噬菌体复制策略的新见解，并与寻求操纵含有CPR细菌的微生物组的噬菌体疗法相关。
Within human microbiomes, Gracilibacteria, Absconditabacteria, and Saccharibacteria, members of Candidate Phyla Radiation (CPR), are increasingly correlated with human oral health and disease. We profiled the diversity of CRISPR-Cas systems in the genomes of these bacteria and sought phages that are capable of infecting them by matching their spacer inventories to large phage sequence databases. Gracilibacteria and Absconditabacteria recode the typical TGA stop codon to glycine and are putatively infected by phages that share their host’s alternate genetic code. Unexpectedly, however, other predicted phages of Gracilibacteria and Absconditabacteria do not use an alternative genetic code. Some of these phages may infect both alternatively coded CPR bacteria and standard-coded bacteria. These phages typically rely on other stop codons besides TGA and thus should be capable of producing viable gene products in either bacterial host type. By avoiding the acquisition of in-frame stop codons, these phages may have a broadened host range. Interestingly, we additionally predict that some phages of Saccharibacteria are targeted by spacers encoded in Actinobacteria, a phylum that includes known hosts for episymbiotic Saccharibacteria. Here, we profiled putative phages of Saccharibacteria, which are of particular importance as Saccharibacteria influence some human oral diseases. We additionally profiled putative phages of Gracilibacteria and Absconditabacteria, two Candidate Phyla Radiation (CPR) lineages of interest given their use of an alternative genetic code. Among the phages identified in this study, some are targeted by spacers from both CPR and non-CPR bacteria and others by both bacteria that use the standard genetic code as well as bacteria that use an alternative genetic code. These findings represent new insights into possible phage replication strategies and have relevance for phage therapies that seek to manipulate microbiomes containing CPR bacteria.
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DOI：
10.1073/pnas.1810625115
发表时间：
2018-11-27
影响因子：
11.1
作者：
Bor B;McLean JS;Foster KR;Cen L;To TT;Serrato-Guillen A;Dewhirst FE;Shi W;He X
通讯作者：
He X
影响因子：
28.3
作者：
Devoto, Audra E.;Santini, Joanne M.;Banfield, Jillian F.
通讯作者：
Banfield, Jillian F.
影响因子：
7.6
作者：
Bor, B.;Collins, A. J.;Dewhirst, F. E.
通讯作者：
Dewhirst, F. E.
影响因子：
5.8
作者：
Crisci MA;Chen LX;Devoto AE;Borges AL;Bordin N;Sachdeva R;Tett A;Sharrar AM;Segata N;Debenedetti F;Bailey M;Burt R;Wood RM;Rowden LJ;Corsini PM;van Winden S;Holmes MA;Lei S;Banfield JF;Santini JM
通讯作者：
Santini JM
影响因子：
64.8
作者：
Al-Shayeb, Basem;Sachdeva, Rohan;Banfield, Jillian F.
通讯作者：
Banfield, Jillian F.