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

How does shallow shotgun compare to amplicon for both output and cost?

Shallow shotgun sequencing will enable deeper resolution in taxonomic identification, relative to 16S sequencing. It is expected that shallow shotgun sequencing will typically yield much more consistent species level ID’s and, with the CosmosID bioinformatics tool, strain level calls as well. For human samples, it is not uncommon to see most of the alpha diversity captured of the sample and so depending on your research question, shallow shotgun sequencing can be a very useful tool for general surveillance and profiling of the microbiome. It is also possible to retrieve the most abundant functional genes within a sample.

The other main advantage is that shallow shotgun data is significantly less error-prone and doesn’t suffer the amplification bias that 16S amplicon sequencing will yield. Prices for shallow shotgun are affordable, including bioinformatic analysis, making the two methods equally accessible to researchers.

What sample types can be utilized for shallow shotgun?

Samples with high biomass and high diversity are very suitable for shallow shotgun sequencing, making it particularly effective for gut microbiome research in both human and non-human samples. So if you’re running a highly powered microbiome study and need high-throughput processing of samples and want to balance the cost-benefit ratio of your project, shallow shotgun sequencing is great for you! Shallow shotgun sequencing can also make a profound impact in preclinical in vivo or in vitro studies, infant microbiome studies, controlled fermentation samples and others where the overall diversity of these samples is typically lower than an adult human microbiome.

Is there evidence that shallow shotgun has adequate coverage for analyses?

Yes – CosmosID has undertaken in-house benchmarking to review the effectiveness of shallow shotgun (Please enquire for more information). There are also a considerable number of publications now utilising the shallow shotgun approach as a cost effective method of analysing the microbiome, notably in gut microbiome research. Below are a couple of examples in publically available literature:

A New Strain of Christensenella minuta as a Potential Biotherapy for Obesity and Associated Metabolic Diseases

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

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