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Microbial Diversity Analysis of Extreme Environments

Microbial Diversity Analysis of Extreme Environments

The importance of microbial diversity analysis in extreme environments

The extreme environment such as volcanoes, glaciers, and deep seas, is an indispensable part of the natural environment. Its condition is too harsh for human, plants, and animals to exist. However, there is probably a large number of microorganisms living in such places, which are called extremophiles. These microorganisms represent the limits to adapt to the environment and are treasures of biological genetics and functional diversity. They not only play an important role in the origin and evolution of life, but also have great applications in studying specialized genotypes, physiological mechanisms and metabolites, revealing the mechanism of these microorganisms to colonize hostile ecosystems. The enzymes isolated from them are currently being exploited for their commercial interest and industrial applications. At present, extreme microbes have become a hot field of international research.

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Accelerate microbial research in extreme environments

With the development of next-generation sequencing and bioinformatics tools, it is possible and much easier to conduct systematic classification, gene function analysis, and pathway analysis in extreme environments. We provide a broad array of microbial genomics solutions to help researchers explore the diversity of microbial community structures in extreme environments and maybe find resources that have great potential for industrial applications.

Microbial identification and quantification

16S ribosomal RNA (16S rRNA), the most common housekeeping genetic marker in bacteria, is ideal for bacterial detection and bacterial diversity analysis. 18S rRNA and ITS are ideal for fungal detection and diversity analysis. We provide both short-read and full-length 16S/18S/ITS amplicon sequencing and qPCR services for microbial identification and quantification in extreme environments.
Microbial diversity analysis

We utilize 16S/18S/ITS amplicon sequencing and metagenomics to help you simultaneously detect dominant species, rare species, and unknown species in your sample, and obtain the microbial community composition and relative abundance. In order to improve identification accuracy and alignment rate, we also provide long-read sequencing services utilizing PacBio SMRT sequencing or Nanopore sequencing.
Bioinformatics analysis

After sequencing, we process the data through our powerful bioinformatics analysis platform. First, the raw data is filtered out or trimmed, and the qualified data is retained for alignment, assembly, taxonomic assignment, diversity analysis, phylogenetic analysis, network analysis, correlation analysis, functional prediction and so on.

The main research direction of extremophiles:

Discovery of new microbial species.
Discovery of new genes, enzymes, or metabolites that have application potential.
Microbial function analysis and gene function analysis.
The molecular mechanism of microbial adaptation.
Microbial evolution studies.

What can we do?

1. Identification of extremophiles
2. Quantitation of extremophiles
3. Studying the evolution and function of extremophiles, and the relationship between microorganisms and the environment

Note: Our service is for research use only, and not for therapeutic or diagnostic use.

Detectable Objects

Bacteria, eukaryotes, archaebacteria.

Detection Methods

Next-generation sequencing, third-generation sequencing, PCR denaturing gradient gel analysis (PCR-DGGE), real-time PCR

Technical Platforms

Illumina HiSeq/MiSeq, Ion PGM, PacBio sequencing, Nanopore sequencing, PCR-DGGE, Real-time qPCR, clone library etc.

Sample Requirement

DNA ≥ 300 ng, 1.8<OD_260/280<2.2, concentration ≥ 10 ng/μl, Volume ≥ 10 μl.
Ensure that the DNA is not degraded or slightly degraded. Avoid repeated freezing and thawing during sample storage and shipment.
Please use enough dry ice or ice packs during shipment.
Nucleic acid samples should be stored at -20 °C.

Workflow

Figure 1. High-throughput sequencing analysis process

Figure 2. PCR-DGGE analysis process

Bioinformatics Analysis

Basic Analysis	Routine Analysis (According to Customer Requirements)	Advanced Data Analysis
Sequence Filtering and Trimming	Heatmap	Phylogenetic Tree
Sequence Length Distribution	VENN	LDA-Effect Size (LEfSe)
OTU Clustering and Species Annotation	Principal Components Analysis (PCA)	Network Analysis
Diversity Index	Microbial Community Structure Analysis	Correlation Analysis
Shannon-Wiener Curve	α Diversity Index Analysis
Rank-Abundance Curve	Matastats Analysis
Rarefraction Curve	Weighted Unifrac test
Multiple Contrast	CCA/RDA Analysis
Heatmap
Principal Components Analysis (PCA)