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首页> 美国卫生研究院文献>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes >OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes
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OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes

机译：OTUX：特定于V区域的OTU数据库用于改进16S rRNA OTU挑选和微生物组的高效跨研究分类学比较

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摘要

Many microbiome studies employ reference-based operational taxonomic unit (OTU)-picking methods, which in general, rely on databases cataloguing reference OTUs identified through clustering full-length 16S rRNA genes. Given that the rate of accumulation of mutations are not uniform throughout the length of a 16S rRNA gene across different taxonomic clades, results of OTU identification or taxonomic classification obtained using ‘short-read’ sequence queries (as generated by next-generation sequencing platforms) can be inconsistent and of suboptimal accuracy. De novo OTU clustering results too can significantly vary depending upon the hypervariable region (V-region) targeted for sequencing. As a consequence, comparison of microbiomes profiled in different scientific studies becomes difficult and often poses a challenge in analysing new findings in context of prior knowledge. The OTUX approach of reference-based OTU-picking proposes to overcome these limitations by using ‘customized’ OTU reference databases, which can cater to different sets of short-read sequences corresponding to different 16S V-regions. The results obtained with OTUX-approach (which are in terms of OTUX-OTU identifiers) can also be ‘mapped back’ or represented in terms of other OTU database identifiers/taxonomy, e.g. Greengenes, thus allowing for easy cross-study comparisons. Validation with simulated datasets indicates more efficient, accurate, and consistent taxonomic classifications obtained using OTUX-approach, as compared with conventional methods.
机译：许多微生物组研究采用基于参考的操作生物分类单位（OTU）挑选方法，这些方法通常依赖于数据库，该数据库对通过对全长16S rRNA基因进行聚类确定的参考OTU进行分类。鉴于跨不同分类进化枝的16S rRNA基因的全长突变积累率不一致，使用“短读”序列查询（由下一代测序平台生成）获得OTU鉴定或分类分类的结果可能不一致并且准确性不佳。从头OTU聚类结果也可能会大大不同，具体取决于测序的目标高变区（V区）。结果，比较在不同科学研究中描述的微生物组变得困难，并且常常在现有知识的背景下分析新发现时提出挑战。 OTUX的基于参考的OTU选择方法建议通过使用“定制的” OTU参考数据库来克服这些限制，这些数据库可以满足与不同16S V区域相对应的短读序列的不同集合。使用OTUX方法获得的结果（以OTUX-OTU标识符表示）也可以“映射”或以其他OTU数据库标识符/分类法表示，例如Greengenes，因此可以轻松进行跨研究比较。与传统方法相比，使用模拟数据集进行的验证表明，使用OTUX方法获得的分类效率更高，更准确且一致性更高。

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