Our Methods

We have a range of short read sequencing methods available to meet all your research needs. These range from the traditional and widely used 16s rRNA amplicon sequencing to shotgun sequencing at varying depths. We pride ourselves on working with our partners to select the best approach for them on a case-by-case basis. We also offer long read sequencing when applicable.

Shallow Shotgun

Ideally suited for representative analysis of microbial communities including bacteria, yeast, viruses and fungi. Achieving sub-species or strain resolution. Generating insights into genes present and their functions. Premium consumer products, pilot clinical trials and academic studies.

At a Glance

  • All DNA extracted from a sample is broken into small sections at random
  • Multiple samples are uniquely barcoded and pooled
  • Quality control checks are conducted
  • Barcoded sections are sequenced – generating unbiased datasets.
  • Sequences are assembled and taxa are assigned

Tech Specs

  • Automated DNA extraction: Promega, Qiagen
  • Automated library preparation: Illumina DNA Prep, NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina
  • Sequencing depth: suggested 2-5 million reads, approx.0.6-1.6 Gb per sample
  • Sequencing platform: Illumina Nextseq 2000
  • Sequencing output: FASTQ
  • QC reports are provided
  • Bioinformatic analysis available please contact us to discuss

Deep Shotgun

Specifically providing detailed analysis of microbial communities including bacteria, yeast, viruses and fungi, our Deep Shotgun method is also ideally suited for discovering novel and difficult to find associations with treatments. Detecting low abundant or new species through advanced bioinformatic techniques. Novel clinical and academic clinical trials of high importance.

At a Glance

  • All DNA extracted from a sample is broken into small sections at random
  • Multiple samples are uniquely barcoded and pooled
  • Quality control checks are conducted
  • Barcoded sections are sequenced – generating unbiased datasets.
  • Sequences are assembled and taxa are assigned

Tech Specs

  • Automated DNA extraction: Promega, Qiagen
  • Automated library preparation: Illumina DNA Prep, NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina
  • Sequencing depth: suggested 10-25 million reads, approx. 3.2-8 Gb per sample
  • Sequencing platform: Illumina Nextseq 2000
  • Sequencing output: FASTQ
  • QC reports are provided
  • Bioinformatic analysis available please contact us to discuss

Metabolomics

Ideally suited for situations where understanding the outcomes of metabolism and providing phenotypic information are more important than understanding which bacteria are present. Detection of metabolic signatures or specific metabolites of interest based on a given treatment. A great partner for another ‘omic’ approach that provides information on the genetic and functional potential of a microbiome.

At a Glance

  • Samples are aliquoted as appropriate and prepared for analysis. This depends on sample type and metabolites of interest.
  • Quality control checks are carried out on the machine and a pooled QC sample.
  • Samples are analysed and metabolites quantified
  • Run Quality control is carried out
  • Metabolites from the same sample but different analysis are combined and analysed

Tech Specs

  • We design targeted metabolomic assays according to the needs of our clients.
  • Our custom assays that are quantitative, where possible, to provide you with the most accurate data.
  • Some example using UHPLC-MS targeted methods include:
    • Bile acids
    • Amino acids
    • Short chain fatty acids

16S

Ideally suited for high level representative analysis of bacterial composition. Achieving genus and sometimes species level depth. Looking for broad differences in treatment groups based on bacterial compositions. Basic consumer product, one-off experiments and a first look at a new system.

At a Glance

  • DNA is extracted and a select portion of the 16s rRNA gene is amplified which includes conserved and highly variable regions.
  • Multiple samples are uniquely barcoded and pooled
  • Quality control checks are conducted
  • Barcoded sections are sequenced – generating 16s datasets.
  • Sequences are matched to databases and taxa are assigned

Tech Specs

  • Automated DNA extraction: Promega, Qiagen
  • Automated library preparation: Nextera XT DNA Library Preparation Kit
  • Sample multiplexing up to 384 samples
  • Sequencing platform: MiSeq
  • Sequencing output: FASTQ
  • QC reports are provided
  • Bioinformatic analysis available please contact us to discuss

qPCR

Ideally suited for investigations into a specific bacteria or specific set of bacteria through targeted panel. Achieving species or strain level depth. Looking for very specific differences between treatments. One-off experiments, targeted academic or clinical trials.

At a Glance

  • DNA is extracted and primers are used to amplify a specific region in a semi-quantitative manner
  • Targets can be carried out in single or multiplex (up to 5 targets in one well)
  • Quality control checks are carried out (extraction and qPCR)
  • Data is reported in a digital first manner that suits you

Tech Specs

  • Automated DNA extraction: Promega, Qiagen, Zybio
  • Automated qPCR prep: Custom or existing panels prepared using MANTIS
  • Multiplex up to 5 targets
  • qPCR platform: BioRad CFX-Opus, qTOWER
  • qPCR output: Ct values available in all formats e.g. machine output, excel, JSON.
  • QC reports are provided