Networking

We are convinced that interrelations with Academia are inevitable to offer state-of-the-art professional solutions in the field of computational microbial identification, also for non-academic users such as diagnostic laboratories and microbial quality control in large-scale industry. 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 maintain and extend our connections to Academia, we permanently embedded subjects of our R&D into selected projects (see Permanent Co-operations below). This mutualistic relationship has turned into a fruitful win-win situation over the last decade.

In consequence, by representing a unique bridge between (i) the latest status of microbial systematics and (ii) industrial requirements, Ribocon is able to provide common tools and resources on a highly professional level, by combining academic and commercial expertise.
This is exemplified by our GMP-validated dblast 16S rRNA reference data set, reflecting nearly all publicly available valid bacterial species.

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 by SILVA, e.g. the unification of the Eukaryotic microbial taxonomy.

The project follows a dual licensing model: SILVA is free for Academic users whereas Commercial users require a fee-based license to exploit the data sets.

As partner of the SILVA project, Ribocon supports the maintenance and advancement of the databases and services, and issues the SILVA Commercial Licenses. In addition, subsets of the SILVA databases are further refined by Ribocon to make them fit for use in commercial products and industrial processeses. Finally, extended professional support related to the SILVA project is provided by Ribocon on request.

List of prokaryotic names with standing in nomenclature (LPSN)

LPSN (www.bacterio.net) was established in 1997 by Jean P. Euzéby and is now continued by Aidan C. Parte. It has since provided accurate information about the current status of prokaryotic names, synonyms, and other related information, and solves the problem that names of prokaryotic taxa are assigned and change continuously, and that keeping up with these changes is always challenging.

LPSN includes, alphabetically and chronologically, the nomenclature of prokaryotes and the nomenclatural changes as cited in the Approved Lists of Bacterial Names or validly published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), formerly International Journal of Systematic Bacteriology (IJSB). A classification is proposed for all taxa (except tribes), and a hierarchical classification of prokaryotes is available in the file Classification of domains and phyla - Hierarchical classification of prokaryotes. As far as possible, also the public accession numbers for the 16S rRNA gene sequences of the type strains are available.

Because of the outstanding importance of a central resource providing the current status of prokaryotic nomenclature in an accessible manner, Ribocon supports the maintenance of the LPSN data set by allocating advanced computational solutions in order to foster sustainability of the project.

Focus: Standardized Data Analysis & Software Development
Status: Project ongoing (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 ongoing (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). They gained more than 8,600 citations with a median of 495 per paper (status of April, 2017), reflecting the scientific impact of our activities.

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

Lloyd K.G., L. Schreiber, D.G. Petersen, K.U. Kjeldsen, M.A. Lever, A.D. Steen, et al.
Predominant archaea in marine sediments degrade detrital proteins.
Nature, 2013, 496:215-218
doi:10.1038/nature12033

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