Root-Associated Microbiome Analysis

Root microbiota affect plant host fitness and productivity in a variety of ways. Root-associated microbiomes, as a source of benefits for the plant, play pivotal roles in the plant–soil ecosystem by influencing plant nutrition and productivity. Rhizosphere bacteria can alter plant growth by eliciting induced systemic tolerance to protect plants against abiotic stresses. Advances in NGS technology and metagenomic approaches allow not only for the taxonomic profiling of the root-associated microbial communities but also for the functional characterization of the microbiome.

Root Associated Microbiome Analysis

Potential Research Directions of Root-Associated Microbiota Analysis

• Explore the composition of root-associated microbial communities
• Explore the interactions of plants with beneficial and pathogenic microbes
• Explore the overrepresentation of specific fungal phyla in the rhizosphere correlates with their increased activity around the roots.
• Explore the effect of root exudates on root-associated microbiome
• Explore the interplay between plant immunity and the microbiome
• Explore the prospect of using synthetic communities to promote plant health

Technical Platforms

With our next-generation sequencing (NGS) technology, PacBio SMRT sequencing, and Nanopore sequencing platforms, we have the tool to identify, quantify and analysis the root-associated microbiota. With this high-throughput technology we can perform complete metagenomics studies capable of surveying the genomes of entire communities, including those of unculturable organisms.

Illumina Hiseq Illumina Miseq Ion PGM PacBio SMRT system
Gut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome Analysis
Nanopore system PCR-DGGE Real-time qPCR Clone library
Gut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome Analysis

What Can Creative Biogene Do?

Creative Biogene offers extensive microbiome analysis portfolio includes not only consultancy, study design, sampling solutions and sequencing, but also downstream bioinformatic and biostatistical analyses. 

Project Workflow

High-throughput sequencing analysis process

Fig.1 High-throughput sequencing analysis process

High-throughput sequencing analysis process

Fig.2 PCR-DGGE analysis process

Service Specifications

Sample requirements and preparation

• Sample: Genomic DNA
• Quality requirements: ≥ 300 ng, ≥ 10 ng/μL, OD260/280=1.8-2.0, non-degradative
• Shipment: Dry ice or ice packs
• Repeated freeze-thaw cycles should be avoided

Detectable Microorganisms

• Bacteria
• Fungi
• Viruses

Basic analysis

• Sequence Filtering and Trimming
• Sequence Length Distribution
• OTU Clustering and Species Annotation
• Diversity Index
• Shannon-Wiener Curve
• Rank-Abundance Curve
• Rarefraction Curve
• Multiple Contrast
• Heatmap
• Principal Components Analysis (PCA)

Routine analysis

• Heatmap
• VENN
• Principal Components Analysis (PCA)
• Microbial Community Structure Analysis
• α Diversity Index Analysis
• Matastats Analysis
• Weighted Unifrac test
• CCA/RDA Analysis

Advanced data analysis

• Phylogenetic Tree
• LDA-Effect Size (LEfSe)
• Network Analysis
• Correlation Analysis

References
1. Fuhrman JA. 2009. Microbial community structure and its functional implications. Nature 459:193–199.
2. Zhou, J. , He, Z. , Yang, Y. , Deng, Y. , & Alvarez-Cohen, L. . (2015). High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio, 6(1).
3. Blandino, G., Inturri, R., Lazzara, F., Rosa, M.D., & Malaguarnera, L. (2016). Impact of gut microbiota on diabetes mellitus. Diabetes & metabolism, 42 5, 303-315.

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