Extreme environments Microbiome Analysis

Extreme environments represent unique ecosystems that provide a particularly interesting natural context because of the specific challenges to maintain basic life functions under challenging conditions. Bacteria adopt various strategies to acquire multiple systems so as to thrive against harsh environment such as glacial, deserts, hot springs, ocean bottoms, oligothrophic seas, hydrothermal vents, rocks of the earth's mantle. High-throughput DNA sequencing approaches promise to reveal new insights into diverse environmental and host-associated microbial communities. Omics-driven approaches in combination with high-throughput DNA sequencing technology are nowadays considered reliable and cost-effective tool for the study of the functional and mechanistic underpinnings of metaorganism biology in extreme environments.

Extreme Environments Microbiota Analysis

Potential Research Directions of Extreme environments Microbiota Analysis

• Explore the roles of extremophiles in ecosystems, including climate regulation.
• Explore the way extremophiles preserve their biological functions
• Explore the usefulness of "extremozymes" for biotechnologies
• Explore the extremophilic organisms and the limits of life

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 extreme environments 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
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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

Reference
1. Bang, C. , Dagan, T. , Deines, P. , Dubilier, N. , Duschl, W. J. , & Fraune, S. , et al. (2018). Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?. Zoology, 1-19.

For research use only.

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