Expanding Visualization and Analysis Tools for Comparative Microbial Ecology

Marine Biological Laboratory, Woods Hole MA

Investigators

Abstract

The Marine Biological Laboratory (MBL) is awarded a grant to improve and develop database-driven web-based tools for analysis and comparison of microbial communities for microbial ecologists. Next-generation DNA sequencing technologies allow ecologists to explore microbial communities at depths much greater than ever before uncovering new organisms faster than names can be given and accepted. The alternative taxonomic-independent approach of clustering similar DNA sequences using regions of the SSU rRNA gene is now standard for microbial ecology. The website will provide a variety of tools to allow researchers to upload and cluster massively-parallel tag sequence data and will provide a new clustering algorithm incorporating known information about sequencing error rates, rates of evolution, and information about community structure. Specifically, it will offer: (i) direct import of massively-parallel sequences of any targeted gene and taxonomic identification of sequences from any region of the ribosomal small-subunit gene; (ii) dynamic sequence-based clustering using a variety of methods, including a new method to be developed incorporating experimental and biological variables that does not inflate diversity values; and (iii) improved tools for comparing microbial communities that links sequence-based clusters to taxonomy and metadata. The website will be freely available, and all software will be open source and, to the extent possible, platform independent. Next-generation sequencing provides far more data than many researchers have the bioinformatics capacity to handle. The VAMPS website (vamps.mbl.edu) has already proven invaluable in aiding research teams from around the world, including NSF-funded research projects, by providing the bioinformatics support, database engine, and computational resources needed to analyze these very large and growing datasets, and by providing the only publicly-available interface for visually comparing microbial community information derived from environmental sequencing. In collaboration with the MBL's graduate and postdoctoral level Microbial Diversity summer course and undergraduate Semester in Environmental Science, this project will provide unique educational opportunities through its combination of data from a variety of environments, metadata associated with the International Census of Marine Microbes datasets, its integration of sequence cluster-based and taxonomy-based analytical and visualization tools, and the instruction provided by project developers.