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Shallow Shotgun Metagenomic

Shallow shotgun metagenomic sequencing (SSMS) bridges the gap found between shotgun metagenomic sequencing and 16S/18S/ITS amplicon sequencing. Shallow shotgun metagenomic sequencing provides taxonomy information on the total genomic DNA from all organisms from a sample while avoiding the need for isolation and cultivation of microorganisms. This is crucial as nearly 99% of all microorganisms cannot be cultivated within a laboratory. While shotgun metagenomic remains the gold standard for high-resolution microbiome analysis, SSMS is a powerful alternative to amplicon sequencing. SSMS uses next-generation sequencing (NGS) to provide species-level taxonomy across different taxa with little to no PCR bias or restricted by amplification region.

Novogene’s shallow shotgun metagenomic sequencing services provide the ability to detect, characterize and compare the diversity of metagenomic samples with less than 3Gb of raw data. This approach is suitable for community microbial ecology studies, and understanding microbial-microbial interactions and pathogenesis, among many others. At Novogene, we provide high-quality data with publication-ready results that can be suitable for different research objectives.


By providing a less-biased and higher taxonomy profiling from metagenomic samples, shallow shotgun metagenomic sequencing can be used in many different research topics:

  • Species-level annotation of microbial composition
  • Detection of commensal or pathogenic microbes for understanding microbe-host relationship.
  • Analyze samples from physiological fluids or tissues in relation to human health.
  • Suitable for large-scale human microbiome cohort studies.


  • Shallow shotgun metagenomic sequencing can sequence multiple microorganisms in a single run without the need for isolation and cultivation. Similarly, shallow shotgun metagenomic sequencing has limited PCR bias as amplification of specific target regions for either prokaryotes or eukaryotes is not required. Instead, the sequencing results provide comprehensive information on microbial diversity and composition.
  • Novogene has extensive experience providing metagenomic sequencing services to help clients obtain information from a variety of samples through short-read sequencing. At Novogene, shallow shotgun metagenomic sequencing services provide flexibility and cost-effectiveness in experimental design at a lower sequencing depth through reads-based analysis of metagenomic data with Kraken2.

Specifications: DNA Sample Requirements

Sample Type Amount Volume Concentration Purity
Total DNA ≥ 200 ng ≥20 μL ≥ 10 ng/μL A260/280 = 1.8-2.0

Note: Sample amounts displayed are for reference only. For detailed information, please contact us with your customized requests.

Specifications: Sequencing and Analysis

Sequencing Platform Illumina NovaSeq 6000
Read Length Pair-end 150 bp
Recommended Sequencing Depth 1-3 Gb
Standard Data Analysis
  • Species Annotation
  • Krona Presentation
  • Taxonomic abundance heatmap
  • PCA and NMDS
  • PCoA
  • Anosim
  • Sample Clustering
  • Metastats and LEfSe

Note: Data output and analysis contents listed are for reference only. For detailed information, please contact us.

Project Workflow

In order to ensure the accuracy and reliability of the sequencing data, quality control (QC), consistent with our high scientific standards, is performed at each step of the procedure. The shotgun metagenomic sequencing workflow comprises these main steps: sample preparation and quantification, fragmentation and library preparation, library quality control, sequencing, and bioinformatics analysis.

Taxonomic Abundance Bar Graph

Taxonomic Abundance Bar Graph

Krona For Microbiome Abundance

Novogene Metagenomic Heatmap for the Relation Among Samples

Taxonomic Abundance For Clustering Heatmap

Novogene Metagenomic Venn Figures for Gene Number among samples

PCA And NMDS Analysis Results Based On Taxonomic Relative Abundance

Novogene Metagenomic Gene Number & Abundance Clustering Heatmap in genus level
Novogene Metagenomic Gene Number & Abundance Clustering Heatmap in genus level

PCoA Analysis At The Phylum Level Based On Bray-Curtis Dissimilarity

Novogene Metagenomic Anosim Analysis at Phylum Level

Hierarchical clustering on Taxonomxy Abundance

Novogene Metagenomic Linear Discriminant Analysis (LDA) & Cladogram

ANOSIM Analysis

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

MetaStats Analysis

Novogene Metagenomic eggNOG Annotation

Inter-Group Differences Analysis Using LEfSe Or LDA Effect Size (LEfSe) Analysis

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