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New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance.
Journal of Microbiological Methods ( IF 1.7 ) Pub Date : 2020-06-27 , DOI: 10.1016/j.mimet.2020.105996
Jade A Ezzedine 1 , Cécile Chardon 1 , Stéphan Jacquet 1
Affiliation  

Appropriate use and specific primers are important in assessing the diversity and abundance of microbial groups of interest. Bdellovibrio and like organisms (BALOs), that refer to obligate Gram-negative bacterial predators of other Gram-negative bacteria, evolved in terms of taxonomy and classification over the past two decades. Hence, some former primers have become inadequate while others are yet to be designed, for both PCR (especially with the advent of NGS) and qPCR approaches. Thus, to study BALOs' abundance and diversity in a variety of aquatic ecosystems, we designed in silico specific primer sets for each BALO genera and tested them in vitro on a variety of cultures and environmental samples. Also, we performed Sanger and Nano Miseq sequencing to reveal the exact degree of specificity of the most promising primers set. Here we report our success in designing specific primers for some BALOs genera, i.e. Bdellovibrio (PCR), Bacteriovorax (qPCR), Peredibacter (PCR).



中文翻译:

新的16S rRNA引物可揭示Bdellovibrio以及类似生物的多样性和丰度。

适当的使用和特定的引物对于评估目标微生物群的多样性和丰富性很重要。蛭弧菌和类似生物(BALOs),引用责成等革兰阴性菌的革兰阴性细菌的天敌,在分类学和分类方面,在过去二十年中发展而来。因此,对于PCR(特别是随着NGS的出现)和qPCR方法,一些以前的引物已经不足,而其他引物还没有被设计。因此,为了研究BALO在各种水生生态系统中的丰度和多样性,我们为每个BALO属设计了计算机专用的引物对,并进行了体外测试各种文化和环境样本。此外,我们进行了Sanger和Nano Miseq测序,以揭示最有前途的引物组的确切特异性。在这里,我们报告了我们成功设计了一些BALO属的特异性引物,Bdellovibrio (PCR),Bacteriovorax(qPCR),Peredibacter(PCR)。

更新日期:2020-07-02
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