The application of riboswitch sequencing for human gut bacterial classification and identification
The application of riboswitch sequencing for human gut bacterial classification and identification
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核糖开关测序在人体肠道细菌分类鉴定中的应用
DOI：
10.1016/j.ympev.2022.107409
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发表时间：
2022-01-24
影响因子：
4.1
通讯作者：
Li，Sanshu
中科院分区：
文献类型：
--
作者：
Wu，Yaoyao;Zhang，Deying;Li，Sanshu
细菌，特别是肠道细菌在人类健康和疾病中发挥着重要作用。由于种间分辨率低，16S 核糖体 RNA (rRNA) 对许多细菌属的分类失败了。鉴于核糖开关在细菌中广泛分布，它们可能有助于 16S rRNA 区分密切相关的物种。我们发现，在16S rRNA无法区分的28类物种中，其中8类可以被TPP核糖开关和其他核糖开关分开。而且，16S rRNA数据库中的物种与这些核糖开关数据库有重叠，因此，使用核糖开关数据库可以帮助16S rRNA更好地识别物种。此外，我们使用 Klenow DNA 聚合酶和一对短引物来促进 TPP 核糖开关的文库构建以进行测序。测序结果表明，TPP核糖开关可以检测到与16S rRNA相似的主要门。因此，TPP 核糖开关和其他核糖开关类别有可能应用于肠道细菌分类。
Bacteria, especially gut bacteria play important roles in human health and diseases. The classification of many bacterial genera by the 16S ribosomal RNA (rRNA) has failed due to its low inter-species resolution. Given the wide distribution of riboswitches in bacteria, they may help 16S rRNA differentiate closely related species. We found that among 28 groups of species that could not be distinguished by 16S rRNA, eight of them could be separated by the TPP riboswitch and other riboswitches. Moreover, the species in the 16S rRNA database and these riboswitch databases overlap, therefore, using riboswitch databases can help 16S rRNA better identify species. In addition, we used Klenow DNA polymerase and a pair of short primers to facilitate the library construction of TPP riboswitches for sequencing. The sequencing results showed that the TPP riboswitch could detect the major phyla similar to those detected by 16S rRNA. Therefore, the TPP riboswitch and other riboswitch classes could potentially be applied to gut bacteria classification.