The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.
The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.
复制标题
DOI：
10.1038/s41598-020-80826-9
复制
发表时间：
2021-01-18
影响因子：
4.6
通讯作者：
Han K
中科院分区：
文献类型：
--
作者：
Jeong J;Yun K;Mun S;Chung WH;Choi SY;Nam YD;Lim MY;Hong CP;Park C;Ahn YJ;Han K
微生物组研究的主要目标之一是表征栖息在标本中的微生物群落。用于阅读16 S rRNA基因的部分区域的短读段测序平台通过降低下一代测序（NGS）的成本负担而最常用，但是由于其长度太短而不能考虑序列相似性而在物种水平上的错误分类仍然是一个挑战。Loop Genomics最近提出了一种新的基于16 S全长的合成长读段测序技术（sFL 16 S）。我们使用24个人类胃肠道微生物群样品比较了基于16 S全长的合成长读段（sFL 16 S）和V3-V4短读段（V3 V4）方法。我们的sFL 16 S和V3 V4测序数据的比较分析表明，它们在除物种水平外的所有分类分辨率上都高度相似。在物种水平上，我们证实sFL 16 S在α多样性、相对丰度频率和鉴定准确性分析中表现出比V3 V4更好的分辨率。此外，通过比较两种方法对双歧杆菌、拟杆菌和Alistipes的鉴定准确性，证明sFL 16 S可以克服由于16 S可变区序列相似性不同而导致的微生物错误鉴定。因此，本研究表明，新的sFL 16 S方法是克服V3 V4方法弱点的合适工具。
Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
登录
查看更多内容
影响因子：
4.6
作者：
Frank JA;Pan Y;Tooming-Klunderud A;Eijsink VGH;McHardy AC;Nederbragt AJ;Pope PB
通讯作者：
Pope PB
结合16S rRNA基因变量区域可以实现高分辨率微生物社区分析。
影响因子：
15.5
作者：
Fuks G;Elgart M;Amir A;Zeisel A;Turnbaugh PJ;Soen Y;Shental N
通讯作者：
Shental N
影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP
影响因子：
5
作者：
D'Argenio, Valeria;Salvatore, Francesco
通讯作者：
Salvatore, Francesco