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Omics Research // Metagenomics

Shotgun Metagenomic Sequencing

A comprehensive method for characterizing the identity and potential function of the entire microbial community

What Is Shotgun Metagenomic Sequencing?

Shotgun metagenomics is a high-throughput sequencing technology that comprehensively assesses the total genomic content in all microorganisms present in a sample.

This is a widely used method to understand the taxonomical composition, diversity, and metabolic functions of a given sample. In combination with bioinformatics analyses, shotgun metagenomics can be used to identify bacteria, fungi, and viruses present in a sample. It can survey the composition and function of microorganisms in soil, water, and microbiome samples.

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Why Is Shotgun Metagenomic Sequencing Important?

The ability to assess the entire genomic content of a sample and identify the metabolic pathways and associated functions of a community make this approach a standard to describe samples from diverse sources.

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What Can You Do?
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Clinical Microbiology

Identify unknown microorganisms and pathogens in outbreaks or human diseases

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Microbial Ecology

Discover new microorganisms and genes by mapping a functional profile of microbial communities and their internal and environmental interactions

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Drug Development

Identify novel genes, biological compounds, antibiotics, and enzymes with clinical and industry applications

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Disease Factors

Categorize associations between the human microbiome and disease states

Shotgun Metagenomic Sequencing Technologies

Biotechnological Discovery

Profile high-complexity environments for all genomes contained in a diverse sample using de novo assembly.

Metagenomic Profiling

Sequence all strains of your microbial sample in one quick and easy approach.

On-Going Promotions

We're always adding new deals — check in often for updated promotions!

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Shotgun Metagenomics Best Practices

Starting Material

DNA extraction from stool, swabs, saliva, urine, media, and moreSample QC >2 ng

Get your high-quality genomic DNA isolated from most sample types at Psomagen.

Library Preparation

Short Read

  • DNA Prep Library Kit
  • 2 ng genomic DNA
  • Library QC > 10nM at ~600 bp

Long Read

  • PacBio Microbial Library (Avg. size 20 kb)
  • 5 µg genomic DNA
  • Library QC > 20nM at 3~50Kb

Sequencing Instrumentation & Read Length

Short Read

  • Illumina NovaSeq 6000 S4 or HiSeq X
  • 2 x 151 bp read length
  • 3 GB raw sequencing data

Long Read

  • PacBio Sequel Ile

Psomagen standardly runs 12.5 ng of DNA for amplicon sequencing, with additional DNA required to perform quality control checks

For taxonomy identification, Psomagen standardly provides 100,000 read sequencing depth per sample using a 2 x 300 bp read length on a MiSeq Sequencer

Psomagen can only guarantee raw sequencing depth

Bioinformatic Analysis

  • Assembly and OTU clustering
  • Taxonomic assignment
  • Species abundance
  • Diversity statistics

Data Delivery

All sequencing run data is delivered as demultiplexed .fastq files

If an entire flow cell or lane is purchased, raw data can be delivered as BCL files if requested at the time of purchase

Why Our Clients Choose Psomagen

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Superior Data Quality

Exceeds manufacturer benchmarks

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Fast Turnaround

Starting at one week for sequencing projects

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US-Based Processing

Sequencing and customer support in Rockville, MD

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Ph.D. Level Support

Expert assistance every step of the way, with real-time project updates through our online system

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Automated Workflows

Increase scalability and improve reproducibility

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CLIA-Certified, CAP-Accredited Labs

Clinical research options available (inquire for more information)

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Complete Sequencing Solutions

From extraction to data analysis, with many sample types accepted

Quotes From Our Clients

I chose Psomagen because of the price and US-based labs. We've used Psomagen before and were very satisfied. The people were responsive and helpful and the work done was very good.

Professor

University Research Laboratory

I chose Psomagen because of the price and US-based labs. We've used Psomagen before and were very satisfied. The people were responsive and helpful and the work done was very good.

Professor

University Research Laboratory

I chose Psomagen because of the price and US-based labs. We've used Psomagen before and were very satisfied. The people were responsive and helpful and the work done was very good.

Professor

University Research Laboratory

We're Ready for Your Order!

Here's what to expect in your project's life cycle. If you have a question during sequencing, it's easy to get in touch!

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Request a Consultation

Create an account through our client portal and get in touch with your local field team to start designing a project.

We’ll help drive your research forward with the right tools for your research needs.

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Place an Order

After finalizing the scope of work, the official quote will be issued for signing. Then, your sales representative will send specific shipping instructions.

Once all the samples and necessary documents are ready, we can start your project. Need more analysis? Reach out to our bioinformatics experts to dig deeper.

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QC and Data Delivery

All Psomagen sequencing projects come with a built-in QC step to ensure you get the information you need. An account manager will update you on your project's progress in a timely manner.

You can also see some project information and securely view all valid reports on the client portal site.

Customer Publications and Other Resources

Association of SNPs in the PAI1 Gene with Disease Recurrence and Clinical Outcome in Bladder Cancer
Genomic-based microsatellite development for Ternstroemia (Pentaphylacaceae) and transferability to other Ericales
Antifungal In Vitro Activity of Phoradendron sp. Extracts on Fungal Isolates from Tomato Crop
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