RESEARCH GROUP Computational Metagenomics > Projects
Projects
de.NBI - German Network for Bioinformatics Infrastructure
The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The de.NBI network consists of the eight interconnected centers including more than 40 research, service and infrastructure groups with about 150 bioinformaticians.
The Bielefeld-Gießen (BiGi) Bioinformatics Resource Center combines bioinformatics expertise and facilities at Bielefeld University and Justus-Liebig-University Gießen providing bioinformatics support, compute resources and software tools for the field of microbial genome research. In 2016, the center was extended by the partner project MetaProtServ at the Otto-von-Guericke-University Magdeburg complementing the microbial genome analysis portfolio for metaproteome data analysis.
Developments at the center particularly address large-scale genomics and post-genomics data integration and exploration. A central objective is the development and provision of a repository of reusable workflows allowing to replicate the analyses of former projects on same or additional data, or to recycle tried-and-tested workflows as a starting point for adaptation and enhancement in new projects.
funding organisation BMBF
ELIXIR Hybrid Cloud
The task of the ELIXIR Hybrid Cloud is to coordinate technical, operational and funding aspects of cloud, data and compute services across Europe for the ELIXIR and larger Life Science community within a seamless hybrid cloud ecosystem (EOSC) and to demonstrate the usability of the task's proposal to set up the cloud ecosystem by running hybrid cloud pilot projects.
This hybrid cloud ecosystem will be accessible to researchers spanning from local and private clouds (e.g. EMBL-EBI Embassy) to National community clouds (e.g. cPouta, MetaCentrum cloud, de.NBI) as well as European research and innovation oriented clouds (e.g. EOSC) or rather Public/commercial compliant clouds (e.g. Google, Azure, AWS).
funding organisation ELIXIR
NFDI4Microbiota
NFDI4Microbiota is a consortium that is part of the German NFDI (National research Data Infrastructure). The vision of the NFDI4Microbiota consortium is that researchers in microbiology (including bacteriology, virology, protistology, mycology and parasitology) can translate research data easily into a deep understanding of microbial species and their interactions on a molecular level.
The mission of the NFDI4Microbiota consortium is to be the central hub in Germany for supporting the microbiology community with access to data, analysis services, data/metadata standards and training.
Bielefeld University leads Task Area 4 (Technical Infrastructure), dedicated to providing the technical foundations for the NFDI4Microbiota platform on which compute and storage resources for the microbiology community will be offered.
funding organisation DFG
Bluetools
Marine microbiomes represent 90% of the total living marine biomass but only a small fraction of them can be cultivated. For this reason, they are an underexplored source of bioactive compounds, carbohydrate polymers and proteins, among others. New approaches are necessary to overcome the limitations for the study of marine microbial communities and their “econological use”. Bluetools will unravel the potential of marine microbiomes for healthier oceans and the Blue Bioeconomy through integration of different fields to develop cutting-edge tools that support fast, efficient and sustainable exploration and exploitation of microbiomes, avoiding the drawbacks of conventional biodiscovery practices.
The expected results of Bluetools include discovering several hundreds of enzymes, rhodopsins, resistance genes, antimicrobials and anti- microfouling agents, thanks to a hybrid workflow of in silico and microfluidics-based functional discovery.
Bluetools assembles 5 leading European companies, 8 academic teams and 1 private registered training organization that have pioneered approaches in functional metagenomics, microfluidics, microbial ecology and synthetic biology.
Bielefeld University´s Center for Biotechnology contributes in the project by providing state-of-the-art sequencing technologies and bioinformatics approaches for data analysis.
funding organisation EU, Horizon Europe
CAMI - Critical Assessment of Metagenome Interpretation
In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to interpret this sequence data but none can completely recover the complex information encoded in metagenomes. A number of challenges stand in the way. Simplifying assumptions are needed and lead to strong limitations and potential inaccuracies in practice. Critically, methodological improvements are difficult to gauge due to the lack of a general standard for comparison. Developers face a substantial burden to individually evaluate existing approaches, which consumes time and computational resources, and may introduce unintended biases. The Critical Assessment of Metagenome Interpretation (CAMI) is a new community-led initiative designed to help tackle these problems by aiming for an independent, comprehensive and bias-free evaluation of methods.
SIMBA - Sustainable Innovation of Microbiome Applications in the Food System
SIMBA (Sustainable Innovation of Microbiome Applications in the Food System) is a European innovation project, funded under the EU’s Horizon 2020 Funding Programme, which provides a holistic and innovative approach to the development of microbial solutions to increase food and nutrition security. The project envisions to create a better EU Agro-Aqua-Food system using microbiomes that is resource efficient, climate resilient, sustainable and consumer centred. To do this, over the four-year project, SIMBA will explore and utilise microbiomes from the land and sea to develop numerous innovative solutions to address key challenges identified.
funding organisation EU, Horizon 2020
HiPoAF: Unleashing the hidden potential of the anaerobic fungi
Despite their biotechnological potential, there are significant knowledge gaps and many fundamental scientific questions on the group of anaerobic fungi, impeding methodological progress for the detection and especially maintenance of long-term cultures. Thus, the HiPoAF project focuses on the basic issues in anaerobic fungi research in order to better understand their diversity, metabolic requirements and syntrophic microbial interactions by the focusing on work packages such as standardization, diversity and cultivation, detection and classification and semi-continuous cultivation.
funding organisation DFG D-A-CH
Project Archive
VIRUS-X
Biological sequence diversity is nowhere as apparent as in the vast sequence space of viral genomes. The VIRUS-X project explores specifically the outer realms of this diversity by targeting the virosphere of selected microbial ecosystems and investigate the encoded functional variety of viral gene products. The project is driven by the expected large innovation value and unique properties of viral proteins, previously demonstrated by the many virally derived DNA and RNA processing enzymes used in biotechnology. Concomitantly, the project will advance our understanding of important aspects of ecology in terms of viral diversity, ecosystem dynamics and virus-host interplay. Last but not least, due to the inherent challenges in gene annotation, functional assignments and other virus-specific technical obstacles of viral metagenomics, the Virus-X project specifically addresses these challenges using innovative measures in all parts of the discovery and analysis pipeline, from sampling difficult extreme biotopes, through sequencing and innovative bioinformatics to efficient production of enzymes for molecular biotechnology.
funding organisation EU, Horizon 2020