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

Peter E. Larsen, Frank Collart, Folker Meyer, Jack A. Gilbert

2011

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.

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Paper Citation


in Harvard Style

Larsen P., Collart F., Meyer F. and Gilbert J. (2011). PREDICTED RELATIVE METABOLOMIC TURNOVER - Predicting Changes in the Environmental Metabolome from the Metagenome . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: Meta, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 337-345. DOI: 10.5220/0003314803370345


in Bibtex Style

@conference{meta11,
author={Peter E. Larsen and Frank Collart and Folker Meyer and Jack A. Gilbert},
title={PREDICTED RELATIVE METABOLOMIC TURNOVER - Predicting Changes in the Environmental Metabolome from the Metagenome},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: Meta, (BIOSTEC 2011)},
year={2011},
pages={337-345},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003314803370345},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: Meta, (BIOSTEC 2011)
TI - PREDICTED RELATIVE METABOLOMIC TURNOVER - Predicting Changes in the Environmental Metabolome from the Metagenome
SN - 978-989-8425-36-2
AU - Larsen P.
AU - Collart F.
AU - Meyer F.
AU - Gilbert J.
PY - 2011
SP - 337
EP - 345
DO - 10.5220/0003314803370345