Universität zu Köln

Zhang, Jingying, Liu, Yong-Xin ORCID: 0000-0003-1832-9835, Guo, Xiaoxuan, Qin, Yuan, Garrido-Oter, Ruben ORCID: 0000-0003-1769-892X, Schulze-Lefert, Paul and Bai, Yang (2021). High-throughput cultivation and identification of bacteria from the plant root microbiota. Nat. Protoc., 16 (2). BERLIN: NATURE RESEARCH. ISSN 1750-2799

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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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Zhang, Jingying UNSPECIFIED UNSPECIFIED UNSPECIFIED Liu, Yong-Xin UNSPECIFIED orcid.org/0000-0003-1832-9835 UNSPECIFIED Guo, Xiaoxuan UNSPECIFIED UNSPECIFIED UNSPECIFIED Qin, Yuan UNSPECIFIED UNSPECIFIED UNSPECIFIED Garrido-Oter, Ruben UNSPECIFIED orcid.org/0000-0003-1769-892X UNSPECIFIED Schulze-Lefert, Paul UNSPECIFIED UNSPECIFIED UNSPECIFIED Bai, Yang UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-585052
DOI:	10.1038/s41596-020-00444-7
Journal or Publication Title:	Nat. Protoc.
Volume:	16
Number:	2
Date:	2021
Publisher:	NATURE RESEARCH
Place of Publication:	BERLIN
ISSN:	1750-2799
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language HUMAN GUT MICROBIOTA; RHIZOSPHERE MICROBIOME; ARABIDOPSIS-THALIANA; CULTURE; COLLECTION; DIVERSITY; GENOME Multiple languages Biochemical Research Methods Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/58505