Metagenomics for bioexploration - Tools and application

    Project: EU research project

    Project Details

    Description

    This proposal will (further) develop and apply metagenomics tools to access the enzymatic potential borne in the cryptic biota of selected natural habitats, in particular target soil-related and aquatic ones. In the light of the environmental relevance of chitins and lignins (as natural compounds recalcitrant to degradation) and halogenated aliphatic and aromatic compounds (anthropogenic recalcitrant compounds), the enzymatic activities that we will target are functions able to degrade these compounds. A database of gene functions will be established and maintained. Next to its great relevance to environmental biotechnology including bioremediation, a spin-off of the work will be the discovery of novel biocatalytic functions of industrial relevance. We will in particular address the catabolic potential that is encoded by the mobilome, the collective pool of mobile genetic elements in the microbiota. We will further apply high-throughput (454-based) sequencing to rapidly unravel the metabolic complement in this mobile gene pool. The project brings together a suite of 15 contractors across Europe, encompassing 21 laboratories spread over 11 copuntries and including 4 SMEs. Most of the partners are renowned laboratories which have vast experience in metagenomics of environmental samples, biotechnology, enzymology, bioinformatics, the mobilome, waste management and bioremediation and enzyme production.
    AcronymMETAEXPLORE
    StatusFinished
    Effective start/end date1/05/0930/04/14

    Research Output

    Fungi found in Mediterranean and North Sea sponges: How specific are they?

    Naim, M. A., Smidt, H. & Sipkema, D., 2017, In : PeerJ. 5, 3722.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
  • 9 Citations (Scopus)

    Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

    Versluis, D., D'Andrea, M. M., Ramiro Garcia, J., Leimena, M. M., Hugenholtz, F., Zhang, J., Öztürk, B., Nylund, L., Sipkema, D., van Schaik, W., de Vos, W. M., Kleerebezem, M., Smidt, H. & van Passel, M. W. J., 2015, In : Scientific Reports. 5, 10 p., 11981.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
  • 27 Citations (Scopus)

    Culture-dependent and independent approaches for identifying novel halogenases encoded by Crambe crambe (marine sponge) microbiota

    Öztürk, B., de Jaeger, L., Smidt, H. & Sipkema, D., 2013, In : Scientific Reports. 3, 2780.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
  • 27 Citations (Scopus)

    Datasets

    Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions

    Versluis, D. (Creator), D'Andrea, M. M. (Creator), Ramiro Garcia, J. (Creator), Leimena, M. M. (Creator), Hugenholtz, F. (Creator), Zhang, J. (Creator), Ozturk, B. (Creator), Nylund, L. (Creator), Sipkema, D. (Creator), van Schaik, W. (Creator), de Vos, W. (Creator), Kleerebezem, M. (Creator), Smidt, H. (Creator) & van Passel, M. W. J. (Creator), Wageningen University, 29 Jan 2016

    Dataset

    Sequencing the bacterial metatranscriptome associated with the marine sponge Crambe crambe

    Versluis, D. (Creator), D'Andrea, M. M. (Creator), Ramiro Garcia, J. (Creator), Leimena, M. M. (Creator), Hugenholtz, F. (Creator), Zhang, J. (Creator), Ozturk, B. (Creator), Nylund, L. (Creator), Sipkema, D. (Creator), van Schaik, W. (Creator), de Vos, W. (Creator), Kleerebezem, M. (Creator), Smidt, H. (Creator) & van Passel, M. W. J. (Creator), Wageningen University, 7 Dec 2015

    Dataset