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Microbiome maps: Hilbert curve visualizations of metagenomic profiles

Abundance profiles from metagenomic sequencing data synthesize information from billions of sequenced reads coming from thousands of microbial genomes. Analyzing and understanding these profiles can be a challenge since the data they represent are complex. Particularly challenging is their visualiza...

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Autores principales: Valdes, Camilo, Stebliankin, Vitalii, Ruiz-Perez, Daniel, Park, Ji In, Lee, Hajeong, Narasimhan, Giri
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10317073/
https://www.ncbi.nlm.nih.gov/pubmed/37405310
http://dx.doi.org/10.3389/fbinf.2023.1154588
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author Valdes, Camilo
Stebliankin, Vitalii
Ruiz-Perez, Daniel
Park, Ji In
Lee, Hajeong
Narasimhan, Giri
author_facet Valdes, Camilo
Stebliankin, Vitalii
Ruiz-Perez, Daniel
Park, Ji In
Lee, Hajeong
Narasimhan, Giri
author_sort Valdes, Camilo
collection PubMed
description Abundance profiles from metagenomic sequencing data synthesize information from billions of sequenced reads coming from thousands of microbial genomes. Analyzing and understanding these profiles can be a challenge since the data they represent are complex. Particularly challenging is their visualization, as existing techniques are inadequate when the taxa number is in the thousands. We present a technique, and accompanying software, for the visualization of metagenomic abundance profiles using a space-filling curve that transforms a profile into an interactive 2D image. We created Jasper, an easy to use tool for the visualization and exploration of metagenomic profiles from DNA sequencing data. It orders taxa using a space-filling Hilbert curve, and creates a “Microbiome Map”, where each position in the image represents the abundance of a single taxon from a reference collection. Jasper can order taxa in multiple ways, and the resulting microbiome maps can highlight “hot spots” of microbes that are dominant in taxonomic clades or biological conditions. We use Jasper to visualize samples from a variety of microbiome studies, and discuss ways in which microbiome maps can be an invaluable tool to visualize spatial, temporal, disease, and differential profiles. Our approach can create detailed microbiome maps involving hundreds 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 also be converted into animated movies that bring to life the dynamicity of microbiomes.
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spelling pubmed-103170732023-07-04 Microbiome maps: Hilbert curve visualizations of metagenomic profiles Valdes, Camilo Stebliankin, Vitalii Ruiz-Perez, Daniel Park, Ji In Lee, Hajeong Narasimhan, Giri Front Bioinform Bioinformatics Abundance profiles from metagenomic sequencing data synthesize information from billions of sequenced reads coming from thousands of microbial genomes. Analyzing and understanding these profiles can be a challenge since the data they represent are complex. Particularly challenging is their visualization, as existing techniques are inadequate when the taxa number is in the thousands. We present a technique, and accompanying software, for the visualization of metagenomic abundance profiles using a space-filling curve that transforms a profile into an interactive 2D image. We created Jasper, an easy to use tool for the visualization and exploration of metagenomic profiles from DNA sequencing data. It orders taxa using a space-filling Hilbert curve, and creates a “Microbiome Map”, where each position in the image represents the abundance of a single taxon from a reference collection. Jasper can order taxa in multiple ways, and the resulting microbiome maps can highlight “hot spots” of microbes that are dominant in taxonomic clades or biological conditions. We use Jasper to visualize samples from a variety of microbiome studies, and discuss ways in which microbiome maps can be an invaluable tool to visualize spatial, temporal, disease, and differential profiles. Our approach can create detailed microbiome maps involving hundreds 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 also be converted into animated movies that bring to life the dynamicity of microbiomes. Frontiers Media S.A. 2023-06-19 /pmc/articles/PMC10317073/ /pubmed/37405310 http://dx.doi.org/10.3389/fbinf.2023.1154588 Text en Copyright © 2023 Valdes, Stebliankin, Ruiz-Perez, Park, Lee and Narasimhan. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioinformatics
Valdes, Camilo
Stebliankin, Vitalii
Ruiz-Perez, Daniel
Park, Ji In
Lee, Hajeong
Narasimhan, Giri
Microbiome maps: Hilbert curve visualizations of metagenomic profiles
title Microbiome maps: Hilbert curve visualizations of metagenomic profiles
title_full Microbiome maps: Hilbert curve visualizations of metagenomic profiles
title_fullStr Microbiome maps: Hilbert curve visualizations of metagenomic profiles
title_full_unstemmed Microbiome maps: Hilbert curve visualizations of metagenomic profiles
title_short Microbiome maps: Hilbert curve visualizations of metagenomic profiles
title_sort microbiome maps: hilbert curve visualizations of metagenomic profiles
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10317073/
https://www.ncbi.nlm.nih.gov/pubmed/37405310
http://dx.doi.org/10.3389/fbinf.2023.1154588
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