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A Bioinformatics Guide to Plant Microbiome Analysis.

Rares Lucaciu¹, Claus Pelikan¹, Samuel M Gerner¹

¹Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.

Frontiers in Plant Science

|November 12, 2019

Summary

This summary is machine-generated.

This review provides practical guidelines for molecular plant-microbiome studies, focusing on experimental and computational methods. It details how to optimize sequencing and omics techniques for accurate plant holobiont analysis.

Keywords:

computational experimental holobiont microbiome omics plant

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Published on: June 17, 2012

Area of Science:

Plant science
Microbiome research
Molecular biology

Background:

Plants host diverse microbial communities essential for survival.
Understanding plant-microbe interactions is crucial for plant health.
Molecular analysis requires careful consideration of contamination and experimental design.

Purpose of the Study:

To review state-of-the-art techniques for molecular plant-microbiome studies.
To provide practical guidelines for experimental and computational aspects.
To enhance the quality and accuracy of plant holobiont research.

Main Methods:

Review of sequencing and omics techniques (amplicon sequencing, shotgun metagenomics, transcriptomics, metaproteomics, metabolomics).
Discussion of primer and database selection for amplicon sequencing.
Highlighting bioinformatic workflows for data assembly, binning, and genome annotation.
Emphasis on data integration and complementarity.

Main Results:

Identified critical factors for successful molecular plant-microbiome studies.
Outlined strategies to overcome limitations in genome database resources.
Provided insights into adapting omics methods for specific research needs.
Stressed the importance of careful sample preparation to minimize contamination.

Conclusions:

Accurate molecular analysis of the plant holobiont requires optimized experimental and computational strategies.
Adherence to practical guidelines ensures high-quality data for microbiome research.
Future research should focus on data integration to deepen understanding of plant-microbe interactions.