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Shotgun Metagenomics

Unlock the full potential of microbiome research with our advanced Shotgun Metagenomic Sequencing services. By sequencing all DNA present in a sample, shotgun metagenomics provides the most comprehensive and highest-resolution analysis of microbial communities. This untargeted approach allows for the detection and quantification of bacteria, viruses, fungi, and other microorganisms at the species, subspecies, and strain levels, as well as the characterization of functional genes, antimicrobial resistance (AMR) genes, and virulence factors.

Shotgun Metagenomics

Unlock the full potential of microbiome research with our advanced Shotgun Metagenomic Sequencing services. By sequencing all DNA present in a sample, shotgun metagenomics provides the most comprehensive and highest-resolution analysis of microbial communities. This untargeted approach allows for the detection and quantification of bacteria, viruses, fungi, and other microorganisms at the species, subspecies, and strain levels, as well as the characterization of functional genes, antimicrobial resistance (AMR) genes, and virulence factors.

Our Shotgun Metagenomics Services

At Cmbio, we offer both shallow and deep shotgun sequencing options to suit the specific requirements of your study. Whether you're conducting exploratory research, clinical trials, or large-scale population studies, our services are designed to deliver accurate, high-quality data that empowers your research.
 

Shallow Shotgun Sequencing

Ideal for large cohort studies and projects where cost-effectiveness is crucial, our shallow shotgun sequencing service provides consistent species and strain-level resolution of bacteria at a sequencing depth of approximately 3 million reads per sample. This approach offers better resolution than traditional 16S rRNA gene sequencing and is particularly well-suited for gut microbiome research.

Advantages of Shallow Shotgun Sequencing:

  • Cost-Effective: Enables large-scale studies without compromising data quality.

  • Enhanced Resolution: Provides species-level identification with improved diversity detection across multiple kingdoms, including bacteria, viruses, fungi, and protists.

  • Suitable for Low Biomass Samples: Effective for samples with low microbial content, such as swabs.

  • Ideal for Routine Testing: Supports microbiome-based diagnostics and routine surveillance.

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Deep Shotgun Sequencing

For projects requiring extensive coverage and detailed characterization of microbial communities, our deep shotgun sequencing service offers sequencing depths ranging from 6 million to over 100 million reads per sample. This approach builds upon the benefits of shallow shotgun sequencing, providing additional advantages for in-depth analysis.

Advantages of Deep Shotgun Sequencing:

In addition to all the benefits of shallow shotgun sequencing, deep shotgun sequencing offers:

  • Higher Resolution: Achieves species, subspecies, and strain-level identification with greater accuracy.

  • Enhanced Multi-Kingdom Profiling: Provides comprehensive profiling of bacteria, viruses, bacteriophages, fungi, and protists with increased sensitivity.

  • Detailed Functional Insights: Enables characterization of antimicrobial resistance genes, virulence factors, plasmids, and functional pathways at a deeper level.

  • Improved Detection of Low-Abundance Organisms: Increased sequencing depth enhances the detection of rare or low-abundance microorganisms and genes.

  • De Novo Strain Profiling: Enables engraftment and strain tracking analysis, essential for probiotic- and FMT studies.

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Applications of Shotgun Metagenomics

 

Human Health and Disease Research

Explore the role of the microbiome in various health conditions.

Clinical Trials and Pharmaceutical Studies

Analyze clinical samples for primary or exploratory endpoints.

Biomarker Discovery and Patient Stratification

Identify microbial markers for drug development and personalized medicine.

Epidemiology and Strain Tracking

Monitor the spread of pathogens and antimicrobial resistance.

Infectious Disease Diagnostics

Support clinical metagenomics for rapid pathogen identification.

Fecal Microbiota Transplantation (FMT)

Screen donor and recipient samples for safety and efficacy.

Agricultural and Environmental Research

Investigate microbial communities in soil, water, and other environmental samples.

Food Safety and Spoilage Studies

Detect and characterize microbial contaminants in food products.

Our Shotgun Metagenomics Workflow
 

Sample Processing

Our CLIA-certified and GCP-compliant facilities is equipped to handle samples from around the globe. We provide:

  • Customized DNA Extraction: Optimized protocols based on sample type to ensure minimal bias, optimal yield, and high purity.

  • Sample Tracking: Barcoding and accessioning through our LIMS system for secure sample management.

Library Preparation and Sequencing

Depending on your study requirements, we offer sequencing on various Illumina and Element platforms. We provide flexible sequencing depth options to meet the specific needs of your project.

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Bioinformatics and Data Analysis

Access your data and do your own analysis through the Cosmos-HUB, our user-friendly platform offering:

  • High-Resolution Taxonomic Profiling: Species and strain-level identification across multiple kingdoms.

  • Functional Analysis: Detection of AMR genes, virulence factors, plasmids, and functional pathways.

  • Interactive Visualizations: Heatmaps, PCA plots, alpha and beta diversity analyses.

  • Data Accessibility: Downloadable reports, QC metrics, and raw data files.

Or collaborate with our experienced science team to receive publication-ready bioinformatics analyses tailored specifically to your study and needs. Our team offers:

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  • In-Depth Data Interpretation: We provide detailed analysis and interpretation of your metagenomic data, aligning results with your research objectives and hypotheses.

  • Advanced Statistical Analysis: Utilizing both leading proprietary and public statistical workflows, we perform differential abundance testing, diversity analysis, and predictive modeling to uncover significant patterns and correlations in your data.

  • Custom Visualizations: Creation of high-quality, publication-ready figures and charts, including complex visualizations like network diagrams, heatmaps, and correlation matrices.

  • Scientific Reporting: Preparation of detailed reports that include methodology, results, discussion, and conclusions, formatted to meet the standards of leading scientific journals.

  • Collaborative Consultation: Direct communication with our scientists to discuss findings, refine analyses, and ensure that the interpretations align with your expectations.

  • Data Integration Services: Integration of metagenomic data with other datasets such as metabolomics, proteomics, or clinical metadata to provide a holistic understanding of your study.

Our science team is dedicated to enhancing the impact of your research by providing personalized support and expertise. We work closely with you to ensure that the bioinformatics analyses not only meet but exceed the requirements for publication and presentation in scientific venues.
 

Turnaround Time and Support

We understand the importance of timely results and provide both:

  • Standard Turnaround: Flexible timelines based on project size and complexity.

  • Expedited Services: Accelerated processing options for time-sensitive projects.

Our team will provide regular updates on your project's status and is available to address any questions or special requirements.

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