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Microbial Biomarker Discovery

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The Importance of Microbial Biomarker Discovery

Microbial Biomarker Discovery

The commensal microbes associated with humans or animals are critical to host health as they play a vital role in shaping host immunity and preventing infectious disease. Given the widespread presence of antimicrobial resistance, the promotion of a healthy microbiota in humans and animals is a global issue. Biomarker discovery has proven to be one of the most powerful and broadly applicable approach to translate molecular and genomic data into clinical practice. However, the bacterial genome is highly dynamic even within strains of the same genus. Therefore, the identification of clinically useful biomarkers in mixed microbial communities is very challenging. High-resolution techniques such as next-generation sequencing (NGS) and long-read sequencing are necessary for effective microbial biomarker discovery. Genomic methods can also be used to systematically discover potential biomarker genes through deep sequencing, literature-based data mining, and comparative genomics.

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Our Solution for Microbial Biomarker Discovery

We are dedicated to providing the highest-quality microbial genomics services to help you investigate microbe-microbe and host-microbe interactions within the human/animal microbial communities. We utilize next-generation sequencing (NGS) and long-read sequencing technologies to characterize microbial communities. We provide (full-length) 16S/18S/ITS sequencing and metagenomics for rapid detection of bacteria, archaea, fungi, and viruses, and a more comprehensive combination of microbial genomics services for further characterization of microbes, genes, or pathways of interest.

Main Research Directions

  • Microbiome-wide association studies linking dynamic microbial consortia with disease.
  • Discovery, validation, and identification of microbial biomarkers.

What Can We Do?

  1. 1. Microbial diversity analysis using (full-length) 16S/18S/ITS sequencing and metagenomics
  2. 2. Discovery of microbial biomarkers using microbial diversity analysis and metatranscriptomics
  3. 3. Further characterization of bacteria and fungi using microbial whole-genome sequencing and microbial epigenomics

Note: Our service is for research use only, not for disease diagnosis or treatment.

Detectable Objects

Bacteria, fungi, protozoan, viruses.

Detection Methods

Next-generation sequencing (NGS), long-read sequencing, quantitative PCR (qPCR), and other molecular biology techniques.

Detection Platforms

Illumina HiSeq/MiSeq, Nanopore MinIONTM, PacBio RSII, PacBio Sequel, Applied Biosystems real-time PCR platforms, et al.

Sample Requirement

    1. DNA sample: 1.8 < OD260/280 < 2.0 (without degradation or contamination)
    2. RNA sample: RIN ≥ 7.0, 28s/18s ≥ 1.5 (without degradation or contamination)

Workflow

The high-throughput sequencing analysis processFigure 1. The high-throughput sequencing analysis process.

Bioinformatics Analysis

Our bioinformatics analysis pipeline is flexible to your needs.

Taxonomic Assignment Species annotation
Rarefaction Curve
Shann-Wiener Curve
Rank Abundance Curve
Statistical Analysis Heatmap
VENN
Principal Components Analysis (PCA)
Comparative Analysis RDA/CCA
PCA/PCoA
LEfSe
Network Analysis
Functional analysis BLASTX, KEGG, eggNOG, CAZy, CARD, ARDB etc.
PICRUSt
TAX4Fun
Phylogenetic Analysis (Un)Weighted Unifrac
Phylogenetic Trees

References

  1. Yan X, Gurtler J, Fratamico P, et al. Comprehensive approaches to molecular biomarker discovery for detection and identification of Cronobacter spp.(Enterobacter sakazakii) and Salmonella spp. Appl. Environ. Microbiol, 2011, 77(5): 1833-1843.
  2. Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and explanation. Genome biology, 2011, 12(6): R60.

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