Development of Models and Tools for the Exploration of Gut Microbiota as Mediators of Disease

Abstract

The gut microbiota is a mediator of pathogen colonization and persistence in the host. Alterations in the abundance of healthy gut flora affect pathogen colonization and pathogen-associated immune responses. Campylobacter jejuni, a leading cause of bacterial diarrheal illness and acute peripheral neuropathy, stimulates more severe inflammatory responses in murine models with antibiotic depleted or humanized microbiota compared to those with normal murine microbiota. Furthering of our understanding of the microbiotas role in disease is dependent upon a combination of basic research, clinical testing, and robust computational methods. Dahak is a software suite that integrates state-of-the-art open-source tools for metagenomic analyses of microbiomes (https://github.com/dahak-metagenomics/dahak/). The overall goals of the dahak project are to develop, optimize, and deliver open-source tools to identify organisms within metagenomes with high confidence, as well as characterize functional content and allow for the comparative analysis of multiple metagenomic samples. Dahak workflows enable the user to perform taxonomic and functional assignments of sequences from high coverage organisms within the limit of database content. The dahak analytical framework is an automated and containerized workflow system, with far fewer dependency, installation, and execution problems typically associated with other open-source bioinformatics solutions. This maximizes software usability and reproducibility of results.

Speaker Bio

Dr. Phillip Brooks is a co-chair for the NIH DCPPC Interoperability Task Force, Certified Data Carpentry Instructor, former Associate Director of Data Intensive Biology Institute at the University of California, Davis, and member of the American Association for Microbiology (ASM), with years of experience in microbiology, immunology, microbiome analysis, open source project development and cloud computing. Phillip is an experienced developer of genomic and metagenomic analysis pipelines, responsible for project management and data generation, interpretation, and presentation. He earned his PhD in Comparative Medicine and Integrative Biology (CMIB) and Environmental Toxicology from Michigan State University in 2016 and completed his BS in Psychology with a minor in Chemistry from Georgia State University in 2010.