ArticleNature protocols2021
High-throughput cultivation and identification of bacteria from the plant root microbiota.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers, 2 of them syntheses that pooled it.
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Who cites it
122 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Principles for Rigorous Design and Application of Synthetic Microbial Communities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Pooled it
- A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities.Applied and environmental microbiology · 2022Pooled it
- Host genetic variation is associated with root-associated microbiome assembly and resistance to Fusarium oxysporum in tobacco.Plant physiology · 2026Article
- Unlocking the power ofmSystems · 2026Article
- A roadmap to create FAIR collections of microbial strains.Nature microbiology · 2026Review
- The metabolic and anatomical complexity of root microhabitats modulate their interaction with the microbiota.Nature communications · 2026Article
- Borborobacter xinjiangensis sp. nov., a moderately halophilic bacterium isolated from grapevine rootstock in Xinjiang, China.Archives of microbiology · 2026Article
- Review
- Beneficial microbes isolated from the strawberry rhizosphere: development of growth-promoting and anthracnose-suppressive SynComs.World journal of microbiology & biotechnology · 2026Article
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Discovery of specific rhizosphere bacteriaScience advances · 2026Article
- Rhizoplane microbiome: niche-specific recruitment and plant defense priming against bacterial wilt disease.Plant physiology · 2026Article
- Time-series dynamics and biocontrol potential of postharvest bacteria in litchi microbiota.Science China. Life sciences · 2026Article
- Rapid isolation of indigenous degraders combined with autochthonous bioaugmentation for in situ remediation of groundwater contaminated with complex organic pollutants: a pilot-scale study.Biodegradation · 2026Article
- Large-Scale Microbiome Profiling of Brown Algae Identifies a SpecificJournal of microbiology and biotechnology · 2026Article
- Distinct filtering processes shape bacterial and fungal communities and their co-occurrence patterns across garlic-associated compartments.Environmental microbiome · 2026Article
- The effects of feeding guild, seasonality, and warming on the gut microbiomes of Antarctic echinoderms.BMC microbiology · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Microbial profiling of five traditional Chinese medicines: culture-based identification vs. 16S rRNA sequencing.Journal of medical microbiology · 2026Article
- Review
62 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.