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Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos

机译：评估16S rRNA基因引物以研究老化烤烟的细菌群落结构和功能

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Selection of optimal primer pairs in 16S rRNA gene sequencing is a pivotal issue in microorganism diversity analysis. However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F–1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degradation of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.Electronic supplementary materialThe online version of this article (10.1186/s13568-018-0713-1) contains supplementary material, which is available to authorized users.
机译：在16S rRNA基因测序中选择最佳引物对是微生物多样性分析中的关键问题。然而，已经投入了有限的努力来研究特定的引物组，以分析老化的烤烟（AFT）的细菌多样性以及预测细菌群落的功能。在这项研究中，评估了四个引物对在基于AFT中16S rRNA基因序列确定细菌群落结构中的性能，并使用通过未观察到的状态重建进行的系统进化研究（PICRUSt）预测了基因的功能。结果显示，覆盖扩增区域V5V6V7的引物组799F–1193R提供了更精确的AFT细菌群落结构图，叶绿体和线粒体基因的共扩增水平较低，并且与使用其他引物相比，其属更广。此外，功能基因预测表明AFTs的微生物组参与了各种感兴趣的途径。在AFT中检测到大量参与氮代谢的功能基因，这反映出参与降解有害氮化合物并为他人产生含氮营养素的细菌水平很高。此外，参与有价值的代谢物生物合成和有毒化合物降解的功能基因还提供了这样的信息，即AFTs具有庞大的微生物和基因库，可用于进一步研究。所有这些发现为从事烟草相关样品细菌多样性评估的研究人员提供了重要参考。电子补充材料本文的在线版本（10.1186 / s13568-018-0713-1）包含补充材料，可以通过授权使用用户。

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