Soil Microbiome Analysis

Soil-based microorganisms act as a central factor in the promotion of soil health, quality and fertility and agricultural sustainability. Still, most soil microorganisms are still poorly described and not fully understood. Advances in NGS technology and metagenomic approaches have greatly expanded our ability to characterize and modify the beneficial microbes, explore the structural and functional diversity of soil microorganisms and broaden our understanding of how native ecosystems will respond to environmental change.

Soil Microbiome Analysis

Potential Research Directions of Soil Microbiota Analysis

• Explore various microbial interactions for improving soil fertility, restoring degraded systems, and also for augmenting the microbially mediated eco-system functions to meet the sustainable development goals.
• Reveal the genetic structure, gene prediction, proposed functions, and metabolic pathways of the analyzed soil microbial communities.
• Explore microbial communities including the culture-independent study of the soil microbiome.

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 soil 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
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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. And we offer full-service for microbiome which has been successfully achieved involve soil microbiome analysis, sediment microbiome analysis and humus microbiota analysis.

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 Objects

Soil, sediment and humus

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. Dubey, R. K., Tripathi, V., Prabha, R., Chaurasia, R., Singh, D. P., Rao, C. S., … Abhilash, P. C. (2019). Bioinformatics Tools for Soil Microbiome Analysis.SpringerBriefs in Environmental Science, 61–70.
2. Jansson, J. K., & Hofmockel, K. S. (2018). The soil microbiome — from metagenomics to metaphenomics. Current Opinion in Microbiology, 43, 162–168.

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