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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Interactive microbial distribution analysis using BioAtlas.

Jesper Beltoft Lund¹, Markus List², Jan Baumbach^1,2

¹Department of Mathematics and Computer Science (IMADA), University of Southern Denmark, 5000 Odense, Denmark.

Nucleic Acids Research

|May 2, 2017

Summary

This summary is machine-generated.

BioAtlas is a new web tool for analyzing microbial distribution using 16S rRNA sequencing data. It visualizes microbial communities on maps, integrating public databases and user-uploaded samples for location-specific insights.

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Area of Science:

Microbiology
Bioinformatics
Computational Biology

Background:

Vast amounts of 16S rRNA sequencing data exist in public databases.
Sequences are often tagged with geographical or body-location information.
A user-friendly tool for location-specific microbial distribution analysis is currently lacking.

Purpose of the Study:

To introduce BioAtlas, an interactive web application.
To bridge the gap between sequence databases, taxonomy profiling, and location data.
To enable map-supported browsing and analysis of microbial 16S rRNA data.

Main Methods:

Development of an interactive web application (BioAtlas).
Integration of public 16S rRNA sequence databases (GOLD, SILVA, GG, RDP).
Implementation of visualization tools for global, human body, and custom maps.
Functionality for uploading and mapping user-provided sample data.
Support for user-contributed custom maps for various environments (e.g., plants, animals).

Main Results:

BioAtlas enables browsing of taxonomically annotated sequences on interactive maps.
Users can upload their own data to visualize microbial distribution in specific contexts.
The application facilitates the creation and use of custom maps for diverse ecological niches.
It automates the mapping of taxonomies to location data, simplifying analysis.

Conclusions:

BioAtlas provides a user-friendly platform for location-specific analysis of microbial communities.
It enhances the exploration of public 16S rRNA data and facilitates the analysis of novel datasets.
The tool supports a wide range of applications, from human microbiome studies to environmental microbiology.