The One Codex Blog

We teased a few months (blogs) back that we were working on fungal data. We are excited to finally announce the addition of reference-quality genomes from our mycology collection to the ATCC Genome Portal.

The addition of fungal genomes to the ATCC Genome Portal was a significant step for us. Extracting high-quality, concentrated gDNA from fungi is often more complicated than extracting similar quality gDNA from bacteria or viruses. Significantly larger genomes are less compatible with higher throughput sequencing technologies than the smaller viral genomes. Nevertheless, we are excited to provide researchers with our small but growing collection of ATCC mycology genomes.

The microbial communities that inhabit our bodies can be thought of as unique fingerprints that both reflect and help determine many aspects of our health. Currently, metagenomic sequencing offers the best window we have into our microbiomes, which are primarily composed of uncultivated organisms. However, despite important insights gained from 20+ years of sequencing human microbiomes, it is estimated that 40-50% of species in the human gut microbiome lack reference genomes (Nayfach et al, 2019, Nature). Science is still trying to answer the question of who lives in our guts, what differences exist between people, and the underlying mechanisms behind these differences.

At One Codex our mission is to support and advance microbiome discovery through accurate, scalable, and easy-to-use software. By giving scientists better leverage over their genomics data, we’ve helped to accelerate programs in basic and translational research, infectious disease diagnostics, and therapeutics development.

I’m thrilled to announce that One Codex has been acquired by Invitae, where our full team will continue our work to make microbiome data more reproducible, more accessible, and ultimately translatable to clinical practice.

Today, we’re very excited to launch a brand new feature on One Codex that lets you analyze your microbiome data in all new and exciting ways! Custom Plots is a powerful new application for interactively comparing and visualizing your microbiome data across cohorts of many samples.

With Custom Plots, you can explore a variety of different microbiome metrics and plots that were previously only accessible through our Notebooks. This includes taxonomic bar charts (like our current “Quick Compare” tool), alpha diversity plots, and beta diversity plots like heatmaps or Principal Coordinate Analyses (PCoA).

When you’re planning a new study, there are a lot of factors to consider. These can include:

• What population should I target?
• How should I collect and store the samples?
• What analyte do I want to study, and how should I extract it from the samples?
• What kind of technology should I use, PCR, arrays, or sequencing?
• What sequencing approach should I use, amplicon or whole shotgun metagenome?
• How deeply should I sequence?

These are some common questions researchers ask, and your research goals will drive the decisions you make when setting up your study. But there is a commonly underappreciated question, and one that we at One Codex are often asked: how do I know if I have enough samples?