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metagenomics shotgun sequencing

Shotgun Metagenomics Sequencing CapitalBio

Metagenome refers to the sum of all microbial genetic materials in specified environment. Metagenome sequencing can determine all microorganisms in specified environment, especially conduct sequence determine and excavate functional gene for the genome which is difficult to culture the microorganism and research new gene with specified function.

Workflow Specifications Bioinformatics Analysis

shotgun metagenomics

PlatformNovaSeq 6000
Read lengthPaired-end 150bp
Sequencing Depth


Sample RequirementsPurity: OD260/280: 1.8~2.0, no impurities contamination such as RNA and protein

DNA amount ≥1.6μg

DNA Concentration ≥50ng/μL

Integrity:The volume shall greater than 30μL and DNA shall have obvious main band without impurities contamination such as degradation, RNA and protein


Metagenome Sequencing

16S rDNA Segment Sequencing

Test Area

Test the whole genomic DNA sequence

Test the 16S hypervariable region and usually as V3+V4

Identified Depth

Species level

Genus level

Research Purpose

Except achieving the 16S rDNA research purpose, functional genome analysis, inter-specimen gene difference, metabolic network of researched species can also be conducted

Research the microflora structure, abundance, diversity, evolution relationship and microflora difference etc.

How Is Metagenomics Shotgun Sequencing Different From 16s?

CapitalBio utilizes shotgun metagenomic sequencing, a technique that differs significantly from 16S rRNA sequencing. While 16S rRNA sequencing targets a specific region of DNA, shotgun metagenomic sequencing reads all genomic DNA present in a sample. This comprehensive approach allows for the identification and profiling of a wide range of microorganisms, including bacteria, fungi, and viruses. Therefore, for microbiome studies, shotgun sequencing provides a more complete and detailed picture of microbial diversity and function.

Advantages Of Shotgun Metagenomics Sequencing

CapitalBio employs shotgun metagenomic sequencing due to its numerous advantages. This method is faster as it eliminates the need for the mapping process, thus accelerating the sequencing timeline. Shotgun metagenomic sequencing also requires less DNA, making it more efficient and cost-effective, especially when dealing with scarce or precious samples. Furthermore, the cost of shotgun sequencing is significantly lower than other methods that require a map, making it a more economical choice. Overall, shotgun metagenomic sequencing offers a comprehensive, efficient, and cost-effective solution for studying microbial diversity and function.

Applications Of Shotgun Metagenomic Sequencing

  • Environmental Microbiology: Through metagenomic whole genome shotgun sequencing, Capitabio enables researchers to analyze environmental samples in unprecedented detail. This deep shotgun metagenomic sequencing approach helps in identifying microbial communities present in soil, water, and air, providing insights into their roles in ecosystem functions and biogeochemical cycles.

  • Human Health and Disease: Capitabio’s shotgun sequencing metagenomics services play a crucial role in exploring the human microbiome. By employing shotgun metagenomic sequencing analysis, researchers can uncover the complex interactions between microbial communities and human health, aiding in the discovery of novel diagnostics and therapeutics for a wide range of diseases.

  • Agriculture and Food Safety: Leveraging shotgun metagenomic sequencing definition and applications, Capitabio supports advancements in agricultural practices and food safety. Whole metagenome shotgun sequencing allows for the examination of microbial communities in crops and livestock, enhancing yield, disease resistance, and understanding pathogen contamination in food products.

  • Antibiotic Resistance Tracking: The rise of antibiotic-resistant bacteria poses a significant challenge to public health. Capitabio’s shotgun sequencing metagenomics services are instrumental in tracking and studying the spread of antibiotic resistance genes. Shotgun metagenomic analysis offers a powerful tool for monitoring resistance patterns, guiding the development of strategies to combat antibiotic resistance effectively.

What Analytics Are Included in Shotgun Metagenomic Sequencing Services?

  • Taxonomic Profiling: Utilizing shotgun sequencing metagenomics, Capitabio offers detailed taxonomic profiling, identifying the diverse array of microorganisms present in a sample down to the species level. This analysis leverages the power of metagenomic whole genome shotgun sequencing to provide a comprehensive overview of microbial diversity.

  • Functional Analysis: Beyond identifying what is present, shotgun metagenomic sequencing analysis delves into the functional capabilities of microbial communities. This includes understanding metabolic pathways, resistance genes, and potential virulence factors, offering insights into how microbes interact with their environment or host.

  • Comparative Metagenomics: Capitabio’s services include comparative metagenomic analysis, allowing for the comparison of microbial communities across different samples or conditions. This deep shotgun metagenomic sequencing approach helps in identifying significant changes in microbiome composition or function, which can be crucial for ecological studies, disease research, and more.

  • Microbial Abundance and Diversity Metrics: Through shotgun sequencing metagenomics, Capitabio quantifies the abundance and diversity of microbial species within a sample. Metrics such as alpha and beta diversity provide valuable information on the richness and evenness of microbial communities, essential for ecological and health-related research.

  • Strain-Level Resolution and Pathogen Detection: Leveraging the precision of whole metagenome shotgun sequencing, Capitabio’s shotgun sequencing metagenomics services can achieve strain-level resolution in microbial identification. This capability is critical for tracking pathogen outbreaks, understanding microbial evolution, and studying microbiome dynamics.

Comparing Shotgun Metagenomics and Whole Transcriptome Shotgun Sequencing

Shotgun Metagenomics Sequencing and Whole Transcriptome Shotgun Sequencing (WTSS) are both high-throughput sequencing technologies, but they focus on different biological questions and application areas.

Shotgun Metagenomics Sequencing is primarily used to study the genomic composition of microbial communities in environmental samples or within organisms. This method allows for the direct extraction and sequencing of DNA from samples without the need for culturing the microbes. It provides genetic information about all the microbes present in the sample, enabling researchers to understand the diversity, structure, and function of microbial communities and how they respond to environmental changes.

On the other hand, Whole Transcriptome Shotgun Sequencing (WTSS), also known as RNA-Seq, focuses on the complete set of transcripts (i.e., RNA molecules) in an organism at a specific time point or under specific conditions. By sequencing and analyzing RNA molecules, researchers can understand patterns of gene expression, regulatory mechanisms, and expression differences under various conditions, thereby revealing gene functions and regulatory networks.

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