The Genboree Microbiome Toolset and the Analysis of 16S rRNA Microbial Sequences
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1 The Genboree Microbiome Toolset and the Analysis of 16S rRNA Microbial Sequences Kevin Riehle* Molecular & Human Genetics Baylor College of Medicine Houston, TX 77030 Email: [email protected]Cristian Coarfa* Molecular & Human Genetics Baylor College of Medicine Houston, TX 77030 Email: [email protected]Andrew Jackson* Molecular & Human Genetics Baylor College of Medicine Houston, TX 77030 Email: [email protected]Jun Ma Obstetrics and Gynecology Baylor College of Medicine Houston, TX 77030 Email: [email protected]Arpit Tandon Molecular & Human Genetics Baylor College of Medicine Houston, TX 77030 Email: [email protected]Sameer Paithankar Molecular & Human Genetics Baylor College of Medicine Houston, TX 77030 Email: [email protected]Sriram Raghuraman Molecular & Human Genetics Baylor College of Medicine Houston, TX 77030 Email:[email protected]Toni-Ann Mistretta Pathology & Immunology Baylor College of Medicine Pathology, Texas Children’s Hospital Houston, TX 77030 Email: [email protected]Delphine Saulnier Nizo Food Research Ede, 6710 BA Email: [email protected]Sabeen Raza Pathology & Immunology Baylor College of Medicine Pathology, Texas Children’s Hospital Houston, TX 77030 Email: [email protected]Maria Alejandra Diaz Pathology & Immunology Baylor College of Medicine Pathology, Texas Children’s Hospital Houston, TX 77030 Email: [email protected]Robert Shulman Department of Pediatrics Baylor College of Medicine Houston, TX 77030 Email: [email protected]Kjersti Aagaard Obstetrics and Gynecology Baylor College of Medicine Houston, TX 77030 Email: [email protected]James Versalovic Pathology & Immunology Baylor College of Medicine Pathology, Texas Children’s Hospital Houston, TX 77030 Email: [email protected]Aleksandar Milosavljevic Molecular & Human Genetics Baylor College of Medicine Houston, TX 77030 Email: [email protected]*These authors contributed equally to the manuscript Abstract—Microbial metagenomic analyses rely on an increasing number of publicly available tools. Many researchers do not have the expertise required to install, integrate and maintain the required tools. 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 both novice and savvy users 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 profiles, supervised machine learning, and feature selection. We validate the Toolset in two studies of the gut microbiota, one involving obese and lean twins, and the other involving children suffering from irritable bowel syndrome. Index Terms—16S rRNA, Human Microbiome, Microbiome, Genboree Microbiome Toolset, Genboree Workbench, Translational studies
