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. 2017 Jul 3;45(W1):W509-W513.
doi: 10.1093/nar/gkx304.

Interactive microbial distribution analysis using BioAtlas

Jesper Beltoft Lund  1 , Markus List  2 , Jan Baumbach  1   2
Affiliations

Interactive microbial distribution analysis using BioAtlas

Jesper Beltoft Lund et al. Nucleic Acids Res. .

Abstract

Massive amounts of 16S rRNA sequencing data have been stored in publicly accessible databases, such as GOLD, SILVA, GreenGenes (GG), and the Ribosomal Database Project (RDP). Many of these sequences are tagged with geo-locations. Nevertheless, researchers currently lack a user-friendly tool to analyze microbial distribution in a location-specific context. BioAtlas is an interactive web application that closes this gap between sequence databases, taxonomy profiling and geo/body-location information. It enables users to browse taxonomically annotated sequences across (i) the world map, (ii) human body maps and (iii) user-defined maps. It further allows for (iv) uploading of own sample data, which can be placed on existing maps to (v) browse the distribution of the associated taxonomies. Finally, BioAtlas enables users to (vi) contribute custom maps (e.g. for plants or animals) and to map taxonomies to pre-defined map locations. In summary, BioAtlas facilitates map-supported browsing of public 16S rRNA sequence data and analyses of user-provided sequences without requiring manual mapping to taxonomies and existing databases.

Availability: http://bioatlas.compbio.sdu.dk/.

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Figures

Figure 1.
Figure 1.
Work-flow for classification of 16S rRNA sequence from IMG and GOLD using Mothur and the Silva reference database.
Figure 2.
Figure 2.
Hierarchical phylogenetic tree featured on the front end, allowing users to interact with a given map based on specific prokaryota selected.
Figure 3.
Figure 3.
On the world map, each marker represents an individual analysis project imported from the GOLD database.
Figure 4.
Figure 4.
Heat map comparison for prokaryota kingdoms in USA. (A) The archaeal heatmap. (B) The bacterial heatmap. Red: high abundance, green: low abundance
Figure 5.
Figure 5.
The view for the Human Female map. A phylogenetic tree (left) and a list sample locations (right) can be used to filter results.
Figure 6.
Figure 6.
An overview of the processing pipeline to process user-submitted 16S rRNA sequences.
Figure 7.
Figure 7.
Species distribution for 2,000 bacteria sequences with the phylum rank of Actinobacteria.
See this image and copyright information in PMC

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