microbiomemaps.org

People

---

Principal Investigator: Prof. Giri Narasimhan
Principal Architect: Camilo Valdes
Other Contributors: Vitalii Stebliankin, Daniel Ruiz-Perez, Ji In Park, Hajeong Lee

Motivation: Abundance profiles from metagenomic sequencing data synthesize information from billions of sequenced reads from thousands of microbial genomes. Analyzing and understanding these profiles can be a challenge as the data they represent are complex. Particularly challenging is their visualization, as existing techniques are inadequate when the number of taxa number in the thousands. We present a technique for visualizing abundance profiles using a space-filling curve that transforms a profile into an easy-to-interpret 2D image.
Results: Jasper is a tool for visualizing profiles from 16S and whole-genome sequencing, and orders taxa along a space-filling Hilbert curve. The result is a Microbiome Map, where each position in the image represents the abundance of a single taxon from a reference collection. Jasper can order the taxa in two ways, and depending on the ordering, the maps can highlight "hot spots" of microbes that are either common to, or unique to, the biological conditions under study.
We use Jasper to visualize samples from the Human Microbiome Project, and from a Chronic Kidney Disease study, and discuss a variety of ways in which the "microbiome maps" can be an invaluable tool to visualize spatial, temporal, disease, and differential profiles. Our approach can create detailed "microbiome maps" involving tens of thousands of microbial reference genomes with the potential to unravel latent relationships (taxonomic, spatio-temporal, functional, and other) that could remain hidden using traditional visualization techniques. The maps can be converted into animated movies that bring to life the dynamicity of microbiomes.
Availability: Jasper is open source software, available under the GNU General Public License, version 3.
Download Github Site: Jasper
Contact: Prof. Giri Narasimhan

Valdes, Stebliankin, Ruiz-Perez, Park, Lee, and Narasimhan, Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles, Frontiers in Bioinformatics, Vol. 3, 19 June 2023; Also bioRxiv, 2021.

Below are full resolution images of the datasets from the paper: the human microbiome project (HMP) sites, the chronic kidney disease study (CKD), and the infant gut (IG). You can click on any of the thumbnails to bring up a bigger version. JavaScript is required.