Shotgun Metagenomic Sequencing

What Is Shotgun Metagenomic Sequencing?

Metagenome shotgun sequencing (MGS) involves sequencing all DNA from a microbial community, including bacteria, archaea, fungi, and viruses.

Unlike 16S Amplicon Sequencing, MGS provides a comprehensive, unbiased view of the community's composition and functional potential (e.g., metabolic pathways) and allows for the identification of critical genes, such as Antibiotic Resistance Genes (ARGs), at strain-level resolution.

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.

Psomagen's MGS service combines deep sequencing data with advanced bioinformatics to answer not just "who is there?" but precisely "what they are doing?"

What Can You Do?

Clinical Microbiology

Identify unknown microorganisms and pathogens in outbreaks or human diseases

Microbial Ecology

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

Drug Development

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

Disease Factors

Categorize associations between the human microbiome and disease states

deep genomic coverage

Illumina NovaSeq X Plus

Leveraging the ultra-high-throughput Illumina NovaSeq X Plus platform, Psomagen ensures the deep sequencing coverage necessary to accurately profile complex microbial communities.

Unbiased Discovery: By sequencing all nucleic acids and not just those in highly conserved genes, we offer comprehensive coverage of all community members, including viruses and eukaryotes.
High-Resolution Taxa Identification: Extensive assembly and binning capabilities allow for strain-level taxonomic and functional assignment.

More about the Platform

Choose Your Service Tier

Standard Value vs. Custom Flexibility

Psomagen offers two shotgun metagenomics project paths to meet your budget and research requirements:

	Standard Service			Custom Service
Key Uses	Lowest cost per Gb for: Common research needs Predictable budgeting			Maximum flexibility for: Unique samples Deep sequencing Integrated multi-omics projects
Data Output	1 Gb (clean data)	5 Gb (clean data)	10 Gb (clean data)	Consultation available — reach out here!
Recommended Depth	Pilot studies, low complexity	Standard diversity and functional profiling	High quality functional and taxonomic resolution
Sequencing Platform	Illumina NovaSeq X Plus
Read Length	2 x 150 bp paired-end
Deliverables	Raw FASTQ Basic analysis

Bioinformatics analysis options

1. Core Analysis Pipelines: Mapping vs. Assembly

We offer two powerful analysis pipelines. The choice depends on your research goal: accurate profiling of known functions (mapping) or discovery of novel genomes (assembly).

Mapping-Based Analysis (Recommended Standard)

This is our standard, rapid, highly accurate pipeline for profiling microbial communities. Reads are mapped directly against curated, industry-leading reference databases.

Host DNA Depletion: The first critical step is removing host DNA to focus analysis on the microbial data.
Taxonomy Profiling (MetaPhlAn4): Uses species-specific marker genes for highly accurate taxonomic classification and abundance.
Functional Profiling (HUMAnN3): Identifies the abundance of gene families, pathways (MetaCyc, KEGG, Kofam, EggNOG).

Assembly-Based Analysis (MAGs & Novel Discovery)

For researchers focused on novel gene discovery or reconstructing genomes from unknown species.

Process: Reads are assembled into longer contigs, which are then "binned" to create Metagenome-Assembled Genomes (MAGs).
Functional Annotation (DRAM): MAGs are annotated to analyze the metabolic functions of complex, uncultured microbial genomes.
Recommendations: Assembly from short-read data is computationally intensive. For projects focused on generating high-quality MAGs, we recommend our metagenome long-read sequencing service for superior results.

2. Standard Report Deliverables

Our standard service includes raw data and basic analysis (QC & taxonomy) as the default delivery. If you require only raw data (FASTQ files) without basic analysis, please inquire about a price discount.

Result Type	File Format	Basic Report	Advanced Report	Core Deliverables
Raw Data	FASTQ	Default	Default	Raw sequencing data.
QC & Taxonomy	HTML, XLSX, PNG	+	+	QC stats, taxonomy abundance matrix, diversity analysis.
Functional Analysis	HTML, XLSX, PNG	-	+	Gene family abundance (heatmap), pathway abundance (heatmap).
Statistical Analysis	HTML, PNG	-	Optional	LEfSe, PCoA biplot, Venn diagram, advanced heatmaps.

Advanced Analysis Options (Custom Add-ons)

Comparative Genomics: Genome-level comparison and phylogenomic analysis across samples.
Statistical Modeling: Multivariate statistics, correlation analysis, and machine learning for biomarker discovery.

Our Analysis Pipeline

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

Stool, swabs, saliva, urine, environmental media (soil, water), and more.

DNA extraction available as an add-on service.

Sample QC Requirements

For gDNA submission:

Concentration: >10 ng/µL
Quality check: DNA integrity is verified via gel electrophoresis or TapeStation. High molecular weight (HMW) DNA is preferred.

Lower input amounts may be accepted for specific low-input protocols (consultation required).

Library Preparation

Standard Protocol: Illumina DNA Prep

Input DNA: Flexible input (typically ~100–500 ng recommended for standard workflows).
Library QC: Verified for size distribution (~350-500 bp insert size) and concentration using TapeStation/Bioanalyzer.

Sequencing Instrumentation & Read Length

Platform: Illumina NovaSeq X Plus
Read Length: 2 x 150 bp Paired-End (PE)

Guaranteed Output

We guarantee raw data (Gb) output per sample as specified in the project quote.

Data output options:

1 Gb: pilot studies, low-complexity samples.
5 Gb: standard depth for taxonomic profiling and functional analysis.
10 Gb: high-resolution profiling, strain-level detection, and detecting rare species.
Flexible options available.

Bioinformatic Analysis

Standard Analysis Pipeline (mapping-based):

QC: Adapter trimming and low-quality read filtering.
Host Removal: Removal of host DNA (e.g., human) sequences.
Taxonomic Profiling: Species-level identification using marker gene databases (e.g., MetaPhlAn4).
Functional Profiling: Pathway and gene family abundance analysis (e.g., HUMAnN3, MetaCyc, KEGG, UniRef).
Diversity Analysis: Alpha and Beta diversity metrics.

Advanced/Custom Analysis (assembly-based):

De novo assembly and binning (MAGs).
Comparative genomics and statistical modeling (LEfSe, etc.).

Data Delivery

Format: Demultiplexed .fastq files (raw data).
Method: Secure sFTP download or AWS S3 bucket transfer.
Reports: Interactive HTML report and comprehensive Excel tables (Taxonomy, Function, Diversity) included with analysis packages.
Raw data only: Available at a discounted rate for clients with their own bioinformatics pipelines.

Why Our Clients Choose Psomagen

Superior Data Quality

Exceeds manufacturer benchmarks

Fast Turnaround

Starting at one week for sequencing projects

US-Based Processing

Sequencing and customer support in Rockville, MD

Ph.D. Level Support

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

Automated Workflows

Increase scalability and improve reproducibility

CLIA-Certified, CAP-Accredited Labs

Clinical research options available (inquire for more information)

Complete Sequencing Solutions

From extraction to data analysis, with many sample types accepted

Customer Publications and Other Resources

More Customer Publications

Omics Research // Metagenomics