Our process for gut microbiome sequencing

With highly automated sample prep and integrated controls, our lab process accurately captures the microbial diversity of your samples. Combined with fast turnaround time and our world-class reference database, we set your microbiome research up for success.

Step 1

Sample handling and shipping

We include One Codex Sample Kits in every order to ensure reproducibility and traceability for every sample from your lab through to analysis results on our platform. In addition to packaging and return shipping labels, Sample Kits include One Codex Reformat Tubes for samples not collected in OMNIgene·GUT® collection devices. These Reformat Tubes feature globally unique, etched barcodes, a stabilization buffer, and are compatible with a variety of sample collection methods. Using our tubes avoids sample mislabeling, ensures sample stability during shipping, and allows us to get started on your samples right away without hands on manipulation.

Step 2

Sample Preparation

Because DNA extraction is often the primary source of bias in microbiome workflows, we carefully optimized and fully automated this step. Poor lysis can result in underrepresentation of DNA from gram positive and other difficult to lyse organisms. On the other hand, overly aggressive lysis can lead to DNA degradation. Finally, stool contains many inhibitors that can interfere with downstream enzymatic reactions. With these parameters in mind, we developed a robust process for reproducible extraction of inhibitor-free, high molecular weight genomic DNA that captures the true microbial diversity of stool samples.

After DNA extraction and QC, genomic DNA is ready to be converted into sequencing libraries. This library preparation process can also be a significant source of bias in metagenomics analysis. Thus, we selected a library prep method with minimal GC bias. We also use unique dual indexed (UDI) adapters to ensure reads and/or organisms are not misassigned to the wrong sample due to index hopping.

Step 3

Shotgun whole genome sequencing

After QC, the libraries are sequenced to a depth of 2 million 2x150 bp read pairs. This shallow shotgun sequencing depth enables species and strain level taxonomic resolution without making large projects cost prohibitive.

Step 4

Bioinformatics Analysis

Sequencing data is automatically uploaded to One Codex and analyzed against our One Codex Database, consisting of more than 115k whole microbial reference genomes. A rapid, highly sensitive k-mer classification algorithm maps sequencing reads back to the reference genomes.

The raw classification results are filtered through several statistical post-processing steps designed to eliminate false positive results caused by contamination or sequencing artifacts. The One Codex analysis provides a detailed, highly accurate picture of the composition of your samples, giving you complete confidence in your results.

Sounds interesting?

Start your microbiome sequencing project

Get a quote for sample prep, sequencing, and bioinformatics from One Codex. From sample handling to analysis, our process is designed for microbial samples, so you get the reproducible, reliable data you need.

If still in doubt you can talk to our Sales team.