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Shotgun Metagenomic Sequencing

Introduction to Shotgun Metagenomic Sequencing

Shotgun metagenomic sequencing provides information on the total genomic DNA from all organisms in a sample, avoiding the need for isolation and cultivation of microorganisms or amplification of target regions. This is crucial because it is believed that nearly 99% of all microorganisms cannot be cultivated in the laboratory. Differently from the targeted approach used in the 16S/18S/ITS amplicon sequencing, shotgun metagenomic sequencing uses next-generation sequencing (NGS) technology to provide not only information on the taxonomic annotations of each organism but also the functional profiling, gene prediction and microbial interaction of the whole community.

With extensive experience and well-developed bioinformatics pipelines, Novogene can help you determine the genomes, functions, and variations of microorganisms from diverse samples. Novogene shotgun metagenomic sequencing service delivers high-quality data, publication-ready results, and personalized analysis to meet different research objectives. Novogene offers comprehensive metagenomics solutions from the study of community structure and species classification to system evolution, gene function, and metabolic network of environmental microorganisms.

How does of Shotgun Metagenomic Sequencing work?

From taxonomic profiling to functional analysis and metabolic network, shotgun metagenomic sequencing can be used in many different research topics, including:

  • Annotation of microbial composition and function
  • Detection of microbes of interest related to human health, environmental recovery, and energy synthesis
  • Deep investigation of the genetic makeup and metabolism of microbes for drug development
  • Investigation of the microbe-host relationship, which can also be related to the development of new drugs

Advantages of Novogene Shotgun Metagenomic Sequencing

Shotgun metagenomic sequencing helps to sequence multiple prokaryote and eukaryote microorganisms can be sequenced – all in a single run – without specific isolation and cultivation of microorganisms and the amplification of target regions for either prokaryotes or eukaryotes. The sequencing results provide complete information not only on microbial diversity but also functional diversity in the sample.

Novogene has rich experience providing metagenomic sequencing services to help clients study many different types of samples, including soil, fecal, and water. Long reads assembly service is now also provided with Novogene’s significantly improved new metagenome assembly pipeline. It is now possible to achieve even a complete map of some bacteria and fungi, to better support taxonomy resolution and function annotation.

Metagenomic Specifications: DNA Sample Requirements

Sample Type Amount Concentration Purity
Genomic DNA ≥ 200ng ≥ 10 ng/μL OD 260/280 = 1.8-2.0

Note: Sample amounts displayed are for reference only. Download the Service Specifications or Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Metagenomic Specifications: Sequencing and Analysis

Sequencing Platform Illumina NovaSeq 6000
Read Length Pair-end 150bp
Recommended Sequencing Depth ≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis
  • Data Quality Control
  • De novo Assembly
  • Gene Functional Annotation
  • Comparative Analysis between multiple samples
  • Note: Sequencing depths and analysis contents listed are for reference only. Download the Service Specifications to learn more. For detailed information, please contact us.

    Project Workflow of Novogene Metagenomic Sequencing Services

    In order to keep the accuracy and reliability of the sequencing data, quality control (QC) is performed at each step of the procedure. Each step is performed in agreement with a high scientific standard to ensure high-quality analysis results. The shotgun metagenomic sequencing workflow comprises four main steps, from sample preparation and quantification, fragmentation and library preparation, library quality control, sequencing, and bioinformatics analysis.

    Featured publications with Novogene Shotgun Metagenomic Sequencing service

    Shotgun Metagenomic Sequencing is a flexible approach to obtain microbial genomes among environments (de novo assembly), as well as gene functions (function annotation), and how they interact with each other (pathway analysis). Here presents a list of academic publications that have used Novogene Shotgun Metagenomic Sequencing services.

    Core-pan Gene Rarefaction Curve

    Novogene Metagenomic Sequencing Core-pan Gene Rarefaction Curve


    Heatmap for the Relation among samples

    Novogene Metagenomic Heatmap for the Relation Among Samples


    Venn Figures for Gene Number among samples

    Novogene Metagenomic Venn Figures for Gene Number among samples


    Gene Number & Abundance Clustering Heatmap in genus level

    Novogene Metagenomic Gene Number & Abundance Clustering Heatmap in genus level


    Anosim Analysis at Phylum Level

    Novogene Metagenomic Anosim Analysis at Phylum Level


    Linear Discriminant Analysis (LDA) & Cladogram

    Novogene Metagenomic Linear Discriminant Analysis (LDA) & Cladogram


    Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation

    Novogene Metagenomic Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation


    Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG) Annotation

    Novogene Metagenomic eggNOG Annotation


    PCA & NMDS Analysis Results based on relative abundance of gene functions

    Novogene Metagenomic PCA & NMDS Analysis Results based on relative abundance of gene functions


    Comparison Plot for Metabolic Pathway of multi-samples

    Novogene Metagenomic Comparison Plot for Metabolic Pathway of multi-samples