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.
grant supported the Visualization and Analysis of Microbial Population Structures (VAMPS) website (http://vamps.mbl.edu). VAMPS helps researchers to better understand bacterial, archaeal, and fungal communities within the context of environmental and human health and broader ecological systems. Specifically the VAMPS website is an interface for analyzing microbial communities based on next-generation DNA sequencing of the small subunit ribosomal RNA gene of the bacterial and archaeal genomes or the internal transcribed spacer region of the fungal genome. With the advent of next-generation sequencing, the study of microbial ecology has expanded dramatically, uncovering great diversity and functional importance that had previously been drastically underestimated. With this new depth of information comes many challenges, including the capacity to handle "big data", the need to identify and remove low-quality data, and analyze the rest. To make matters more complicated, we are discovering new microbes faster than taxonomists can give them official names. VAMPS provides the necessary computer resources, informatics processing, and methods for assigning taxonomic names to the microbes in a sample where we can, or creating "operational taxonomic units", OTUs, based solely on their DNA similarity using sequence clustering methods. As biological research becomes more dependent on exponentially increasing amounts of digital information, ecological and health science researchers become more dependent upon computational biologists to process and analyze data. Ecologists and clinicians, however, still need to explore their results to best understand how to interpret them and what they mean in a broad context. VAMPS helps to bridge the gap between field ecologists, clinicians, and other microbial researchers and the complex analysis of their data. Researchers can upload their data to the VAMPS website and select their preferred methods for quality control, taxonomic assignment, and sequence clustering, without having to have their own hardware, software, or specific expertise. Once their data is in the system, they can select datasets from their own projects and from a wide range of publically available datasets to analyze. Not only are the common tools and approaches built into the system, the interface allows the non-computational researchers to see their results, and interact with them in real time by making new selections and changing the parameters of the analyses or adding new analyses on the fly. VAMPS includes tools for subselecting and aggregating populations within the microbial community of interest, tables describing the community membership, heatmaps comparing similarities between samples, bar graphs and pie charts of relative abundance within the communities, interactive diagrams of different taxonomic levels (e.g., phylum, family, genus), dendrograms (relational trees) showing the relationships between samples, principle coordinate analyses, as well as calculations of diversity and richness. VAMPS now has over 1,500 users, and over 1,000 unique projects. There are more than 25,000 microbial samples taken from all over the world, and the site holds close to half a billion DNA sequences. VAMPS has contributed to the knowledge and understanding of microbial ecology through its use in research in oceans, deep sea vents, glaciers, streams, lakes, and marshes, soils, and air. Microbes are crucial symbionts in most plants and animals. VAMPS has been used to study the microbiomes of humans, mice, chickens, cattle, wildlife, leeches, plants, sponges, and coral. More broadly these projects have contributed to our understanding and protection of environmental and human health through projects involved with sewage treatment, septic tanks, public water supplies, oil spills, and the effects of antibiotics in mice and humans, inflammatory bowel disease, pouchitis, obesity, lung development, and cystic fibrosis to name a few. VAMPS has also been a central database for analyzing and sharing data for the International Census of Marine Microbes, Microbiology of the Built Environment, and the Census of Deep Life. Anyone can use the VAMPS website (http://vamps.mbl.edu) using a variety of public data and the guest account log in, or read our publication describing the project "VAMPS: a website for visualization and analysis of microbial population structures" [Huse et al. 2014. BMC Bioinformatics, www.biomedcentral.com/1471-2105/15/41].
