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Sequencing ServicesShallow Shotgun Sequencing


Shallow Shotgun Sequencing Services & Solutions

Through extensive R&D, the CosmosID team have established optimum read depth ranges for different samples types, using species and strain-level Bioinformatics. Whilst the optimum depth for any given sample will depend on study intent, microbial diversity & expected host DNA contamination, CosmosID offers shallow shotgun sequencing at 3M reads which yields consistent species and strain-level resolution of bacteria.

Shallow Shotgun SequencingIs shallow shotgun right for you?

With Shallow Shotgun Sequencing, researchers can unlock the microbiome with better species level resolution than 16S sequencing whilst also maintaining cost effectiveness, making it a fantastic option for large cohort studies that focus on the gut microbiome where statistical significance is paramount!

Advantages of shallow shotgun sequencing include:

  • Cost-effectiveness
  • Well-suited for biobanking, large cohort & population studies
  • Well-suited for gut microbiome research
  • Well-suited for routine testing, including microbiome-based diagnostics

Shallow Shotgun SequencingSample Processing

CosmosID’s CLIA-certified, GCP compliant facility receives samples from all around the world. Your precious pre-clinical or clinical samples will be barcoded & accessioned into the CosmosID LIMS system for sample tracking and project management.

CosmosID also offers validated DNA extraction protocols which are optimized by sample type, resulting in minimal bias, optimum yield and purity.

Shallow Shotgun SequencingLibrary Preparation & Sequencing

Once DNA QC metrics are established for received or generated DNA samples, these samples then undergo Illumina library preparation and QC prior to sequencing at 3 Million total reads (1X150bp or 2X150).

Shallow Shotgun SequencingBioinformatics & Other Deliverables

In addition to sample processing & sequencing, CosmosID includes, as standard:

  • Multi-kingdom species & strain-level resolution via the CosmosID-Hub
  • Access to AMR & Virulence genes
  • Interactive and user-friendly charts & visualizations with access to comparative analysis features including heat maps, PCA plots, Alpha Diversity & Beta Diversity PCoA
  • Methods & QC data upon request – DNA QC, Library QC & fastQC
  • Fastq/Fasta file transfer via AWS s3 Bucket/Dropbox

Shallow Shotgun SequencingTurnaround Time & Customer Service

CosmosID offers different turnaround time options as fast as 3-5 business days for shotgun sequencing & analysis. Simply let us know about any special requirements and we can tailor our service accordingly.

Once samples have arrived at the lab, our operations team will keep you updated on a weekly basis on the status of your study!

Shallow Shotgun SequencingTypes of Next-Generation Sequencing

CosmosID offers a comprehensive range of next-generation sequencing services tailored to meet diverse research needs. Our advanced sequencing methodologies provide insights into microbial communities at various levels, allowing researchers to choose the most suitable approach based on their specific objectives. 

The following types of next-generation sequencing services are available:

Sequencing Library Preparation

Our sequencing library preparation services ensure the quality and integrity of DNA samples before sequencing. From our impeccable Sample Collection & Logistics service, to our DNA extraction protocols and optional PCR amplification, we ensure that samples are prepared for sequencing in the most efficient and accurate manner.


  • Optimized library preparation techniques for various sample types
  • Minimized bias and maximum yield & purity of DNA
  • Optional PCR amplification to improve sensitivity and detection of low-abundance species

Shallow Shotgun Metagenomic Sequencing

Shallow shotgun metagenomics, as seen on this page, is performed at a read sequencing depth (depending on sample type) typically around 3M reads, is an ideal choice for researchers seeking cost-effective solutions with consistent species and strain-level resolution of bacteria.


  • Cost-effectiveness
  • Well-suited for large cohort studies and population research
  • Excellent for gut microbiome exploration, offering better species-level resolution than 16S sequencing
  • Increased diversity of detection relative to 16S sequencing, including multi-kingdom, functional pathway, and AMR gene characterization

Deep Shotgun Sequencing

For in-depth analysis, deep shotgun sequencing is available to explore microbial communities at a higher read depth. The deep sequencing approach is suitable for investigations requiring extensive coverage and detailed characterization of the microbiome.


  • Comprehensive analysis of microbial diversity
  • Ideal for in-depth research projects and detailed profiling of multi-kingdom microbial communities and functional pathways
  • Provides rich shotgun sequencing data for a thorough understanding of complex microbial ecosystems and increased sensitivity to lower level organisms/genes

Amplicon Sequencing

Amplicon sequencing focuses on specific target genes, such as the 16S rRNA gene, allowing for targeted analysis of microbial diversity. This method is particularly effective for profiling bacterial species and communities.


  • Targeted analysis of specific genomic regions
  • Well-suited for studying microbial composition, especially in 16S rRNA gene-based studies
  • Increased sensitivity to microbial signal in higher non-microbial DNA sample types (skin, blood, etc)
  • Enables efficient and cost-effective exploration of microbial communities

Predictive Functional Profiling

Beyond taxonomic identification, predictive functional profiling allows researchers to infer the functional capabilities of microbial communities. This analysis provides insights into the potential roles and activities of the identified microbial species, which can be useful for applications such as nutrition, immunity, and antimicrobial resistance research.


  • Unveils the functional potential of microbial communities
  • Enables the exploration of metabolic pathways and biological functions to aid human health
  • Enhances the understanding of microbial community dynamics

CosmosID’s expertise, state-of-the-art facilities, and commitment to quality ensure the delivery of reliable and insightful sequencing data for your research endeavors.

Choose the next-generation sequencing approach that aligns with your research goals, whether it’s for cost-effective large cohort studies, in-depth microbial community analysis, or targeted investigations of specific genomic regions.

From general research to clinical trials, our comprehensive suite of next-generation sequencing services extends to a multitude of applications.

By decoding the microbiome, we empower researchers to drive transformative discoveries in the world of human health.

Shallow Shotgun SequencingDownload the Product Sheet - End-to-End Microbiome Analysis via Next Generation Sequencing

Frequently Asked Questions

What is shotgun sequencing?

Shotgun sequencing involves breaking up DNA within a sample into small fragments, which is then subsequently sequenced using next-generation sequencing. In using these DNA fragments, the identification of microorganisms is possible, with resolution down to strain level (depending on sequencing coverage and analysis techniques). 

As a result of sequencing all genomic content within a sample, shotgun sequencing can also leverage gene detection for predictive functional profiling of the microbiota. This method offers a detailed view of the microbiome, surpassing the resolution of 16S sequencing.

How does the 16S rRNA gene sequencing compare with shotgun sequencing data?

While 16S rRNA gene sequencing is a popular method for studying microbial communities, it often lacks the species-level resolution, as well as multi-kingdom characterization, offered by shotgun metagenomics.

Shotgun sequencing data provides a more detailed picture of the microbial community, including strain-level identification and insights into the functional potential of the community, which is not possible with 16S rRNA gene sequencing alone. 

This is due in large part to 16S rRNA sequencing only analyzing the 16S rRNA gene, whereas shotgun sequencing enables the detection and analysis of all genomic regions present within a sample.

How does shallow shotgun metagenomics contribute to the understanding of the human microbiome?

Shallow shotgun metagenomic sequencing offers a cost-effective method to analyze the human microbiome in samples that have a high proportion of microbial genetic content, such as the gut microbiome.

Utilizing shallow shotgun metagenomic sequencing in high microbial content samples is an important variable to consider, as samples with higher non-microbial content (skin, blood, etc) will result in lower microbial signal in the sequenced data, thus decreasing sensitivity to the microbial community within the sample.

By achieving species and even strain-level resolution through this inexpensive whole genome technique, this method can help better detect the diversity and functional potential of microbial communities in the human body. This, in turn, can provide valuable insights into the role of the microbiome in health and disease.

What is the difference between shallow and deep sequencing?

The main difference between shallow and deep sequencing lies in the amount of data generated by each method. Shallow shotgun metagenomics will generate fewer reads, while deep shotgun sequencing will produce more comprehensive data due to greater sequencing depth.

Additionally, deep shotgun sequencing is often used for increased sensitivity to low level organisms and genes present within the sample, while shallow shotgun metagenomics is more appropriate for species/strain level profiling and core functional pathway annotation. While deep shotgun sequencing is more insightful, it is also more expensive than shallow shotgun sequencing.

Thus, depending on the objectives of your research, shallow shotgun metagenomics can be a cost-effective way to achieve high quality microbiome analysis (relative to amplicon results such as 16S), making it a popular choice for large-scale microbiome studies.

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