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This article is part of the supplement: Selected articles from The 8th Annual Biotechnology and Bioinformatics Symposium (BIOT-2011)

Open Access Research

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences

Kevin Riehle1, Cristian Coarfa1, Andrew Jackson1, Jun Ma2, Arpit Tandon1, Sameer Paithankar1, Sriram Raghuraman1, Toni-Ann Mistretta3, Delphine Saulnier4, Sabeen Raza3, Maria Alejandra Diaz3, Robert Shulman5, Kjersti Aagaard2, James Versalovic3 and Aleksandar Milosavljevic1*

  • * Corresponding author: Aleksandar Milosavljevic amilosav@bcm.edu

  • † Equal contributors

Author Affiliations

1 Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

2 Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA

3 Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA

4 Nizo Food Research, Ede, 6710 BA, The Netherlands

5 Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA

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BMC Bioinformatics 2012, 13(Suppl 13):S11  doi:10.1186/1471-2105-13-S13-S11

Published: 24 August 2012

Abstract

Background

Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings.

Methods

To address this need we have integrated a rich collection of microbiome analysis tools into the Genboree Microbiome Toolset and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis. The Toolset drives hypothesis generation by providing a wide range of analyses including alpha diversity and beta diversity, phylogenetic profiling, supervised machine learning, and feature selection.

Results

We validate the Toolset in two studies of the gut microbiota, one involving obese and lean twins, and the other involving children suffering from the irritable bowel syndrome.

Conclusions

By lowering the barrier to performing a comprehensive set of microbiome analyses, the Toolset empowers investigators to translate high-volume sequencing data into valuable biomedical discoveries.