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.
Applications
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.
Benefits
- 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 |
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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
Krona For Microbiome Abundance
Taxonomic Abundance For Clustering Heatmap
PCA And NMDS Analysis Results Based On Taxonomic Relative Abundance
PCoA Analysis At The Phylum Level Based On Bray-Curtis Dissimilarity
Hierarchical clustering on Taxonomxy Abundance
ANOSIM Analysis
MetaStats Analysis
Inter-Group Differences Analysis Using LEfSe Or LDA Effect Size (LEfSe) Analysis
