Meta 2011 Abstracts


Full Papers
Paper Nr: 2
Title:

PREDICTED RELATIVE METABOLOMIC TURNOVER - Predicting Changes in the Environmental Metabolome from the Metagenome

Authors:

Peter E. Larsen and Frank Collart

Abstract: Metagenomics, the sequencing and analysis of genomic DNA extracted directly from an environment, can provide insight into taxonomic and functional diversity, but there are few tools for directly comparing metabolomes predicted from metagenomic data sets. We present a new method, Predicted Relative Metabolomic Turnover (PRMT), for comparing the predicted environmental metabolomes encoded in separate metagenomes and identifying those compounds predicted to be differentially metabolized. The PRMT method was validated using three separate sets of ocean metagenomic sequence studies, totaling 15 metagenomic samples, over 4.5 million sequence fragments and over 840 million base pairs. These data sets enable the construction of models representative of the environmental metabolome of the English Channel. Not only did 88% of the predicted metabolic Predicted Metabolic Relative Turnover shows excellent correlation with observed oceanographic parameters, but PRMT derived parameters are shown to generate potentially constructive and testable biological hypotheses that could form the basis for future biological experiments.

Paper Nr: 4
Title:

AUTOMATIC ANNOTATION OF BACTERIAL COMMUNITY SEQUENCES AND APPLICATION TO INFECTIONS DIAGNOSTIC

Authors:

Victor Solovyev, Asaf Salamov and Igor Seledtsov

Abstract: To annotate bacterial sequences from an environmental sample, we have developed an automatic annotation pipeline Fgenesb_annotator that includes self-training of gene-finding parameters, prediction of CDS, RNA genes, operons, promoters and terminators. New version of pipeline includes frame shift corrections and special module with improved prediction accuracy of ribosomal proteins. To analyze next-generation sequencing data we have developed OligiZip assembler and Transomics pipeline that provide solutions to the following tasks: 1) de novo reconstruction of genomic sequence; 2) reconstruction of sequence with a reference genome; 3) SNP discovery; 4) mapping RNA-Seq data to a reference genome, assemble them into alternative transcripts and quantify the abundance of these transcripts. Using the OligoZip assembler and gene Fgenesb pipeline we have developed a novel computational approach of identification toxic and non-toxic bacterial serotypes using next-generation sequencing data. It can be used for detection of bacterial infections in wounds, water or food contamination.

Short Papers
Paper Nr: 5
Title:

INFRASTRUCTURE FOR METAGENOME DATA MANAGEMENT AND ANALYSIS

Authors:

Tatiana Tatusova

Abstract: Metagenome sequencing projects are generating unprecedented amounts of data. Public sequence archive databases are challenged with large-scale data management issues including data storage, quick search and retrieval of the sequence data for further analysis. The sequence data is linked to the rich set of metadata attributes such as geochemical and ecological parameters for environmental projects and clinical patient in-formation for human microbiome studies. That complex collection of heterogeneous information has to be integrated, organized and presented to the users in a meaningful and the most useful way. For the last 20 years The National Center for Biotechnology Information (NCBI) has been developing the infrastructure that allows an easy storage and distribution of various types of bimolecular data as well as data integration and easy navigation in complex information space. Here we describe NCBI resources that are used for me-tagenomics data management.

Paper Nr: 8
Title:

PROPOSAL FOR OPEN DISCUSSION - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments

Authors:

Folker Meyer and Nikos Kyrpides

Abstract: With DNA sequence data production no longer the bottleneck in microbial studies, a rapidly increasing number of researchers from diverse areas of interest can now use metagenomic tools to study their environment of interest. The large quantities of sequence data becoming available are posing significant challenges to the existing analysis tools and indeed to the community providing analysis portals.

Paper Nr: 11
Title:

ANNOTATING UniProt METAGENOMIC AND ENVIRONMENTAL SEQUENCES IN UniMES

Authors:

Samuel Patient and Maria Martin

Abstract: This short paper outlines the mechanisms for the system developed in UniProt for function annotations of UniProt Metagenomic and Environmental Sequences in UniMES.