Showing papers by "Jeroen Raes published in 2008"

Molecular eco-systems biology: towards an understanding of community function.

Abstract: Systems-biology approaches, which are driven by genome sequencing and high-throughput functional genomics data, are revolutionizing single-cell-organism biology. With the advent of various high-throughput techniques that aim to characterize complete microbial ecosystems (metagenomics, meta-transcriptomics and meta-metabolomics), we propose that the time is ripe to consider molecular systems biology at the ecosystem level (eco-systems biology). Here, we discuss the necessary data types that are required to unite molecular microbiology and ecology to develop an understanding of community function and discuss the potential shortcomings of these approaches.

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.

Abstract: To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino-acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community.

A nitrile hydratase in the eukaryote Monosiga brevicollis.

Abstract: Bacterial nitrile hydratase (NHases) are important industrial catalysts and waste water remediation tools. In a global computational screening of conventional and metagenomic sequence data for NHases, we detected the two usually separated NHase subunits fused in one protein of the choanoflagellate Monosiga brevicollis, a recently sequenced unicellular model organism from the closest sister group of Metazoa. This is the first time that an NHase is found in eukaryotes and the first time it is observed as a fusion protein. The presence of an intron, subunit fusion and expressed sequence tags covering parts of the gene exclude contamination and suggest a functional gene. Phylogenetic analyses and genomic context imply a probable ancient horizontal gene transfer (HGT) from proteobacteria. The newly discovered NHase might open biotechnological routes due to its unconventional structure, its new type of host and its apparent integration into eukaryotic protein networks.

Quantitative phylogenetic assessment of microbial communities in diverse environments

Abstract: Quantitative phylogenetic assessment of microbial communities in diverse environments von Mering C 1,4 , Hugenholtz P 2 , Raes J 1 , Tringe SG 2 , Doerks T 1 , Jensen LJ 1 , Ward N 3 , Bork P 1 . European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA The Institute for Genomic Research, Rockville, MD 20850, USA present address: University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large- scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.