The One Codex Blog

We’re excited to announce that the CDC’s Advanced Molecular Detection initiative has named One Codex as the winner of its $200K “No-Petri-Dish” Challenge! We are thrilled to be recognized by a world-leading public health agency and excited to begin offering solutions for next-generation public health and epidemiology.

The “No-Petri-Dish” Diagnostic Test Challenge asked participants to develop a fast “straight-to-strain” method for identifying a type of E. coli known as STEC (a common cause of severe foodborne outbreaks). Current tests available to public health officials fall into two major categories: “culture-based” tests, which require growing a bacterial culture and can take days or weeks to complete; and faster, but significantly less informative tests for specific pathogens or toxins (e.g., PCR-based tests).

There has been a lot of (sometimes heated) discussion over the years about the pros and cons of various normalization approaches for analyzing microbiome samples sequenced to different depths when using 16S sequencing.

There are three main schools of thought when it comes to how to analyze this data: rarefaction, proportional normalization, and doing nothing.

Doing nothing

The fundamental challenge is that when you sequence a sample more deeply, you increase the likelihood of detecting false positive classifications that are purely the result of sequencing error. In other words, spurious errors in the sequencing reads lead to the read looking more similar to the 16S sequence of a near neighbor to the bug that is actually in you sample.