Marine Microbial Biodiversity, Bioinformatics and Biotechnology

Result description

Six meta-genomic libraries were functionally screened and selected for different enzymatic activities (dioxygenases and oxygenases, lipases, cellulases, phosphatases and phytases).

Result type

* exploitable scientific result

Link to result

https://www.microb3.eu/sites/default/files/deliverables/MB3_D7_5_PU.pdf

References

Result description

The prokaryotic strain Cycloclasticus zancles, with exceptional functional capabilities for degradation of polyaromatic compounds and for sulfidogenic oxidation of acetate, has been isolated and its whole genome has been characterised.

Result type

* data

Link to result

http://dx.doi.org/10.1371/journal.pone.0121178

References

Mathew, D. C., Ho, Y.-N., Gicana, R. G., et al. (2015) PLOS One Accession number: NC_021917

Result description

The M2B3 Reporting Standard describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories.

Result type

* guidelines/standards

Link to result

http://dx.doi.org/10.1186/s40793-015-0001-5

References

Result description

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

Result type

* guidelines/standards

Link to result

http://mibig.secondarymetabolites.org/

References

Result description

Repository for all Ocean Sampling Day (OSD) related source code with information on how-to access OSD data.

Result type

* data

Link to result

https://github.com/MicroB3-IS/osd-analysis

References

Result description

an in silico screening has been developed for the identification of interesting bacterial groups harbouring Polyketide Synthases (PKS) gene cluster matching to a specific consensus sequence. This model can be used as a compass for selection of the best candidates for drug discovery.

Result type

* other

Link to result

References

Result description

Consultancy for ABS legislation by user and provider states. Knowledge on Access to (marine) microorganisms and Benefit-Sharing obtained can be used for providing consultancy concerning new ABS legislation, drafting ABS guidance for research funding organisations and for universities.

Result type

* other

Link to result

References

Result description

The Multivariate Analysis Applications for Microbial Ecology (MASAME) suite provides users with a means to perform multivariate analysis techniques through easy-to-use web applications.

Result type

* software/modelling tools

Link to result

http://mb3is.megx.net/masame/

References

Result description

Easy to use widget for displaying and interacting with geographic maps from the Genes Mapserver.

Result type

* software/modelling tools

Link to result

https://colab.mpi-bremen.de/wiki/display/microb3/MegxMapWidget

References

Result description

The prokaryotic strain Halanaeroarchaeum sulfurireducens, with exceptional functional capabilities for degradation of polyaromatic compounds and for sulfidogenic oxidation of acetate, has been isolated and its whole genome has been characterised.

Result type

* exploitable scientific result

Link to result

References

Accession number: CP008874

Result description

15 phytases (myo-inositol hexakisphosphate phosphohydrolase) identified in metagenomic libraries. Relevant phytase clone selected, with most robust activity at hard operating conditions (high temperature and low pH). Clone shows high thermostability and high transformation useful in reducing phosphate excretion in animals when supplied in animal feedstuff.

Result type

* exploitable scientific result

Link to result

https://www.microb3.eu/sites/default/files/deliverables/MB3_D7_5_PU.pdf

References

Result description

MICRO B3 Model Agreement on Access to (marine) microorganisms and Benefit-Sharing; a free contribution to biological Resrach and Development (R&D) infrastructure. It can be used by other R&D projects, and its proprietary option can also be adopted by private companies.

Result type

* Report

Link to result

https://www.microb3.eu/sites/default/files/pdf/MICRO_B3_ABS_model_agreement_17122013%20explanatory%20notes.pdf

References

Result description

3DM information systems (a platform that collect, combine and integrate protein-related data) have been developed, for seven protein super-families.

Result type

* data

Link to result

References

Result description

Best practice guide and standard operating procedure for large scale sampling of microbial biodiversity.

Result type

* guidelines/standards

Link to result

https://www.microb3.eu/sites/default/files/osd/OSD_Handbook_June_2015.pdf

References

Result description

MiMeT DB contains a pre-calculated set of metagenomic traits described in Barberan et al. 2012 "Exploration of community traits as ecological markers in microbial metagenomes" for a large variety of public metagenomes. The traits included in the statistical analyses range from GC content to functional diversity, and deliver a valuable set of ecological markers in order to discriminate between habitats,geographic locations, or temporal samples. Furthermore, inter-trait relationships can be used as habitat descriptors or indicators of artifacts during sample processing.

Result type

* data

Link to result

http://mb3is.megx.net/mg-traits

References

Result description

Gene MapServer is a database for geo-referencing DNA sequences and relating them to environmental data.

Result type

* software/modelling tools

Link to result

http://blast2.mpi-bremen.de/gms

References

Result description

Ocean Sampling Day (OSD) Registry. The database and web sites for the registration of OSD participants and public access to sampling site data.

Result type

* data

Link to result

http://mb3is.megx.net/osd-registry/; http://www.gigasciencejournal.com/content/4/1/27

References

Result description

Ocean Sampling Day Smartphone App developed and tested. The OSD App provides the opportunity to enter environmental parameters plus an illustrative photo in an electronic “log sheet” which are sent to the OSD server. It is available for Android and iPhone.

Result type

* multimedia

Link to result

www.microb3.eu/myosd/osd-citizen-app

References

Result description

A novel antibiotic, termed ‘Subtilomycin’ was purified which shows bioactivity against a broad range of pathogens including multidrug resistant pathogens.

Result type

* product

Link to result

References

Phelan, R. W., Barret, M., Colter, P. D. et al. (2013) Marine Drugs, 11(6), 1878-1898. DOI: 10.3390/md11061878

Result description

79 phosphatases identified and clone selected for enzyme with best, most robust activity at high temperature and low Ph. They have been immobilized for further studies.

Result type

* exploitable scientific result

Link to result

https://www.microb3.eu/sites/default/files/deliverables/MB3_D7_5_PU.pdf

References

Result description

eleven expression and four metagenomic libraries established and tested on their potential to express oxygenases, esterases, meta-cleavage and glycosyl-hydrolases and glycosyltrans-ferases now available.

Result type

* exploitable scientific result

Link to result

References

Alcaide, M., Tchigvintsev, A., Martinez-Martinez, M., et al. (2015) Applied and Environmental Microbiology, doi: 10.1128/AEM.03387-14; Yakimov, M. M., La Cono, V., Spada, G. L., et al. (2015) Environmental Microbiology, 17(2), 364-382, doi: 10.1111/1462-2920.12587; Alcadie, M., Stogios, P. J., Lafraya, A., et al. (2015) Environ. Microbiol., 17(2), 332-345, doi: 10.1111/1462-2920.12660; Yakimov, M. M., La Cono, V., Smedile, F., et al., (2014) Environmental Microbiology reports, 6(6), 709-722, doi: 10.1111/1758-2229.12192; Sorokin, D. Y., Kublanov, I. V., Gavrilov, S. N., et al. (2015) ISME Journa, doi: 10.1038/ismej.2015.79

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