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 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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