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Shotgun Metagenomic Sequencing

Shotgun metagenomic sequencing(Short Read Shotgun metagenomic sequencing and Long Read 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. Unlike the targeted approach used in the 16S/18S/ITS amplicon sequencing, shotgun metagenomic sequencing uses next-generation sequencing (NGS) and third-generation sequencing(TGS) 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, our services can help you determine the genomes, functions, and variations of microorganisms from diverse samples. Novogene’s 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.

Benefits of Novogene Shotgun Metagenomic Sequencing

Comprehensive Sequencing and Profiling
Comprehensive Sequencing and Profiling

Simultaneous sequencing of diverse microbes, delivering taxonomic and functional insights.

Advanced Analysis and Sample Diversity
Advanced Analysis and Sample Diversity

Supports diverse samples with combined short- and long-read strategies for genome-level insights.

Local Logistics and Fast Turnaround
Local Logistics and Fast Turnaround

Supported by local laboratory network that enables efficient sample handling, reduced shipping time, and faster project delivery.

Rigorous QC and Reliable Data
Rigorous QC and Reliable Data

Ensure accurate, stable, and reproducible results through comprehensive quality control processes.

Applications of Shotgun Metagenomic Sequencing

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

Microbiome Profiling Expert

Fully annotates microbial composition and function, revealing the blueprint of life within samples.

Targeted Microbial Radar

Accurately detects key microorganisms related to human health, environmental recovery, and energy synthesis.

Drug Discovery Probe

Deeply investigates the genetic makeup and metabolic mechanisms of microbes, providing foundational clues for drug development.

Interaction Decoder

Delves into microbe-host relationships, opening new pathways for novel drug discovery.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.


HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

ServiceSample TypeAmountVolumeConcentrationPurity
Shotgun Metagenomic SequencingTotal DNA≥ 200 ng≥20 μL≥ 10 ng/μLOD260/280 = 1.8-2.0.No degradation, no contamination. Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）HMW genomic DNA
(metagenomics)		≥5 μg≥50 μL≥80 ng/μLOD260/280=1.7~2.5.
OD260/230=1.1~2.6.
NC/QC=0.95~4.00
Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）HMW genomic DNA
(metagenomics)		≥5 μg≥50 μL≥80 ng/μLOD260/280=1.7~2.5.
OD260/230=1.1~2.6.
NC/QC=0.95~4.00
Fragments should be ≥10K
HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing PlatformIllumina NovaSeq PlatformsPacBio PlatformsNanopore Platforms
Sequencing StrategyPair-end 150 bpCCS (Circular Consensus Sequencing) ModeSingle-pass Sequencing
Recommended Sequencing Depth≥ 6Gb for simple environments
≥ 12Gb for complex environments		≥ 10Gb for simple environments≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options
(Choose among these three)		Standard Analysis(Assembly-based)• Data quality control (host contamination removal if required)
• Metagenome Assembly
• Gene Prediction
• Taxonomy Annotation
• Function Annotation (KEGG, eggNOG, CAZY…etc)
• Alpha and Beta Diversity Analyses
• Antibiotic Resistance Gene and Mobile Genetic Elements
• Annotation and Analyses		• Data quality control (host contamination removal if required)
• Metagenome Assembly
• Gene Prediction
• Taxonomy Annotation
• Function Annotation (KEGG, GO, CAZY…etc)
• Antibiotic Resistance Gene and Mobile Genetic Elements
• Annotation and Analyses		• Data quality control (host contamination removal if required)
• Metagenome Assembly
• Gene Prediction
• Taxonomy Annotation
• Function Annotation (KEGG, GO, CAZY…etc)
• Alpha and Beta Diversity Analyses
• Antibiotic Resistance Gene and Mobile Genetic Elements
• Annotation and Analyses
MetaPhlAn/HUMAnN (Reads-Mapping Based)• Data quality control (host contamination removal if required)
• Taxonomy Annotation
• Function Annotation (MetaCyc, KEGG, eggNOG, GO, etc.)
• Alpha and Beta Diversity Analyses
• Differential analysis between groups of species and function.		--
Kraken (Reads-Mapping Based)• Data quality control (host contamination removal if required)
• Taxonomy Annotation
• Function Annotation ( KEGG, eggNOG, GO, etc.)
• Alpha and Beta Diversity Analyses
• Differential analysis between groups of species and function.		--

Project Workflow

Novogene provides high-quality products and expert services throughout the entire project workflow. Every step is carefully designed and executed to meet rigorous scientific standards, ensuring exceptional research outcomes. To guarantee the accuracy and reliability of sequencing data, stringent quality control (QC) measures are implemented at each stage of the process. The workflow encompasses key steps such as sample preparation and quantification, fragmentation and library preparation, library quality control, sequencing, and bioinformatics analysis.

Project Workflow

Demo Results

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Novogene's Assembly-based Analysis Pipeline (Short read)
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Novogene's Assembly-based Analysis Pipeline (Long read-PacBio)
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Novogene's Assembly-based Analysis Pipeline (Long read-Nanopore)
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Core-Pan Genome Analysis

Rarefaction curves based on gene abundance data show pan- and core-genome gene counts obtained by random sampling. (a) Pan-genome curve; (b) Core-genome curve.

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Correlation analysis of samples

Spearman correlation coefficients assess sample consistency and data reliability. Blue bubbles indicate positive correlations, red bubbles indicate negative correlations, and darker colors represent stronger associations.

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Krona Visualization

Krona visualizes hierarchical data using interactive, zoomable pie charts, showing relative taxonomic abundance across levels.

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Metabolic Pathway

Nodes represent chemicals and rectangles represent enzymes. Rectangle color (blue–red) reflects unigene counts, with red indicating higher counts.

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Antibiotic Resistant Gene Annotation

Relative abundances of resistance genes were calculated and analyzed using the abundance table. Genes with multiple resistance types are labeled with abbreviations. The figure shows the percentage distribution of resistance genes across samples.

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