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High-throughput cultivation and identification of bacteria f

发布日期:2022-06-10 15:01 浏览次数:

Abstract

Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation from fresh root samples using limiting dilution to ensure that most cultured bacteria originated from only one microorganism. This is followed by strain characterization using a two-sided barcode polymerase chain reaction system to identify pure and heterogeneous bacterial cultures. Our approach overcomes multiple difficulties of traditional bacterial isolation and identification methods, such as obtaining bacteria with diverse growth rates while greatly increasing throughput. To facilitate data processing, we developed an easy-to-use bioinformatic pipeline called ‘Culturome’ (https://github.com/YongxinLiu/Culturome) and a graphical user interface web server (http://bailab.genetics.ac.cn/culturome/). This protocol allows any research group (two or three lab members without expertise in bioinformatics) to systematically cultivate root-associated bacteria within 8–9 weeks.
从生长于特定环境中的植物根部培养细菌,对于剖析植物根部微生物区系对植物生长和健康的功能至关重要。
本研究建立了一个简单的程序,使用有限的稀释度从新鲜的根样本中高通量分离细菌,以确保大多数培养的细菌只来自一种微生物。然后使用双面条形码聚合酶链式反应系统对菌株进行鉴定,以鉴定纯种和异种细菌培养物。该方法克服了传统细菌分离和鉴定方法的多重困难,例如获得不同生长速度的细菌,同时大大提高了吞吐量。为方便进行数据处理,本方法开发了一种易于使用的生物信息学技术,Culturome(https://github.com/YongxinLiu/Culturome)和图形用户界面网络服务器(http://bailab.genetics.ac.cn/culturome/)。该方法允许任何研究小组(两到三名没有生物信息学专业知识的实验室成员)在8-9周内系统地培养与根相关的细菌。

 
高通量分离与鉴定筛选基本流程


高通量筛选方法

High-throughput cultivation and identification of bacteria from the plant root microbiota

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