Networking

We are convinced that interrelations with the scientific sector are inevitable to offer state-of-the-art professional solutions in the field of computational microbial identification for also non-academic users such as industrial quality control and diagnostic laboratories. This is because current standards and references in microbial systematics are fully led by the scientific community and represented by public databases, culture collections, and academic boards.

To build and maintain our connection to the scientific sector, we constantly partnering up with selected public infrastructures and research projects (see Permanent Co-operations and Collaborative Projects below). This mutualistic relationship has turned into a fruitful win-win situation over the last decade.

In consequence, by representing a unique bridge between

  • the latest status of microbial systematics and
  • the specific requirements of non-academic users,
Ribocon is able to provide solutions on a highly professional level, realized by the combination of broad expertise in both fields.

The SILVA rRNA Database Project

SILVA (www.arb-silva.de) represents the world's leading public database for ribosomal RNA (rRNA) gene sequences and provides comprehensive, quality checked, and regularly updated data sets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) sequences for all three domains of life (Bacteria, Archaea, and Eukarya). This service also includes an integrated and constantly maintained microbial taxonomy, representing the current reference in environmental microbiology.

The SILVA web system offers a variety of online services such as sequence alignment and classification, probe and primer evaluation, as well as amplicon data set (NGS) analysis. Moreover, a number of complementary projects have been initiated with support and involvement of SILVA, e.g. the unification of the Eukaryotic microbial taxonomy (UniEuk).

The SILVA data and services are offered for free to academic and non-academic users under a Create Commons Attribution 4.0 (CC-BY 4.0) license.

In 2019, SILVA has received the status of an ELIXIR Core Data Resource, a set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe with the goal to coordinate these so that they form a single infrastructure.

As partner of the SILVA project, Ribocon actively assists the maintenance and advancement of the databases, mainly by supporting curation of the SILVA taxonomy. In addition, subsets of the SILVA databases are further refined by Ribocon on a commercial basis in order to make them accessible for use in specific e.g. industrial and clinical processes. Finally, extended professional support related to the SILVA project is provided by Ribocon on request.

Focus: Standardized Data Analysis & Software Development
Status: Project finished (2015-2019)
More: AtlantOS official

The overarching goal of the EU Horizon 2020 project AtlantOS (Optimising and Enhancing the Integrated Atlantic Ocean Observing Systems) is to deliver an advanced framework for the development of an integrated Atlantic Ocean Observing System that goes beyond the state-of-the-art, and leaves a legacy of sustainability after project lifetime. Together with partner AWI in Bremerhaven (Germany), Ribocon is covering the aspect of standardized genetic ("-omics") observations (rRNA gene-based community profiling of microbes and selected genetic functions) and also develops software products for on site/on board genetic monitoring. The project is funded with EUR 20.65 million and brings together 62 partners from 18 European and American countries.

Focus: Data Analysis & Alternative Marker Genes
Status: Project finished (2013-2018)
More: Aquavalens official

Objective of the EU Seventh Framework Programme (FP7) project Aquavalens is protecting the health of European citizens by improving methods for the detection of pathogens in drinking water and water used in food preparation. Mainly in collaboration with partner HZI in Braunschweig (Germany), Ribocon for the main part explores the prospects of next generation sequencing (rRNA gene-based) in the context of the project objectives. Furthermore, a prototype data set of an alternative marker gene (gyrB gene) is build and applied for advanced identification of target pathogens. The project brings together 39 partners from 13 European countries, including 17 SMEs.

Focus: Software/Web Server Development & Taxonomic Genome Databases
Status: Project finished (2012-2016)
More: MaCuMBA official

As a partner of the project MaCuMBA (Marine Microorganisms: Cultivation Methods for Improving their Biotechnological Applications), Ribocon mainly is developing bioinformatics infrastructure related to the taxonomic assignment of new prokaryotic cultures on species level based on their complete genomic information. Particularly, the public JSpeciesWS web server for the quick and easy online identification/comparison of prokaryotic genome sequences has been set up, based on a reference data set of >60k publicly available genomes. The MaCuMBA consortium is funded by the Seventh Framework Programme (FP7) of the European Commission and brings together 23 partners from 11 European countries, including 9 SMEs.

Focus: Training
Status: Project finished (2012-2015)
More: Micro B3 official

Within the project Micro B3 (Biodiversity, Bioinformatics, Biotechnology), funded by the Seventh Framework Programme (FP7) of the European Commission, Ribocon has organised and operated training courses in bioinformatics for academic and SME partners of the consortium and external participants. These activities were based on a long-term training experience as documented by recurring workshops conducted for the 'Marine Genomics Europe - Network of Excellence', funded under the FP6 of the European Commission.

We continuously collaborate with Academia on scientific and infrastructure projects as documented by our peer-reviewed publications.
Below you find a list of the ten most cited papers with a Ribocon co-author since 2007 (ordered by year of publication). Together they gained more than 20,200 citations with a median of 1,015 per paper (status of February, 2020), reflecting the scientific impact of our activities.

Richter M., R. Rossello-Mora, F.O. Glöckner, and J. Peplies
JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison.
Bioinformatics, 2016, 32:929-931
doi: 10.1093/bioinformatics/btv681

Yarza P., P. Yilmaz, E. Pruesse, F.O. Glöckner, W. Ludwig, K.-H. Schleifer, et al.
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.
Nature Reviews Microbiology, 2014, 12:635-645
doi: 10.1038/nrmicro3330

Quast C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F.O. Glöckner
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Nucleic Acids Research, 2012, 1-7 [gks1219]
doi: 10.1093/nar/gks1219

Pruesse E., J. Peplies, and F.O. Glöckner
SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes.
Bioinformatics, 2012, 28:1823-1829
doi: 10.1093/bioinformatics/bts252

Klindworth A., E. Pruesse, T. Schweer, J. Peplies, C. Quast, M. Horn, and F.O. Glöckner
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.
Nucleic Acids Research, 2012, 1-11 [gks808]
doi: 10.1093/nar/gks808

Bulgarelli D., M. Rott, K. Schlaeppi, E. van Themaat, A. Ahmadinejad, F. Assenza, et al.
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.
Nature, 2012, 488:91-95
doi: 10.1038/nature11336

Teeling H., B.M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C.M. Bennke, et al.
Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom.
Science, 2012, 336:608-611
doi: 10.1126/science.1218344

Yilmaz P., R. Kottmann, D. Field, R. Knight, J.R. Cole, L. Amaral-Zettler, et al.
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Nature Biotechnology, 2011, 29:415-420
doi: 10.1038/nbt.1823

Yarza P., M. Richter, J. Peplies, J. Euzeby, R. Amann, K. H. Schleifer, W. Ludwig, F.O. Glöckner, and R. Rossello-Mora
The All-Species Living Tree Project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.
Systematic and Applied Microbiology, 2008, 31:241-50
doi: 10.1016/j.syapm.2008.07.001

Pruesse E., C. Quast, K. Knittel, B. Fuchs, W. Ludwig, J. Peplies, and F.O. Glöckner
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.
Nucleic Acids Research, 2007, 35:7188-96
doi: 10.1093/nar/gkm864