RESEARCH GROUP Computational Metagenomics > Projects

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

FAIRagro

The FAIRagro consortium with more than 25 partners is building a FAIR (Findable, Accessible, Interoperable, Reusable) research data management system for the agrosystems research community. We are developing the right tools and workflows to lay the foundations for sustainable crop production – now and in the future.

We establish an interoperable and scalable RDI by connecting available repositories to make research data FAIR. We facilitate combined data analyses and establish a multilevel support system by setting up a Data Steward Service Center. We provide guidelines and information material, and focus on knowledge transfer for agrosystem researchers. FAIRagro addresses quality and legal security challenges beyond the FAIR principles.

Our aims are accomplished by close collaboration with other NFDI consortia and the national and international community. We advance NFDI ambitions with expertise and approaches for legal data security challenges, stakeholder involvement and RDIs for highly interdisciplinary and multi-scale research in a field of high societal relevance.

funding organisation DFG

Base4NFDI

Today, research data is often stored in many different places, difficult to find and only available for a limited time. The NFDI aims towards better findability, accessibility and reusability of research data. Base4NFDI integrates and establishes basic services as common, interoperable solutions. Already existing services are adapted or extended to be usable for researchers from other disciplines. This way, parallel developments are avoided - since many scientific fields have similar requirements for a number of research data management services.

All institutions in the scientific community (and beyond) can actively participate in the development and implementation of these services and submit proposals via the sections of the German National Research Data Infrastructure (NFDI). A panel of experts selects the proposals of the development teams for Base4NFDI, which then receive funding from the German Research Foundation (DFG). These teams also receive support and guidance in areas such as development, implementation, and training. After development, the NFDI basic services will be offered permanently to the scientific community. Base4NFDI thus actively contributes to the systematic opening and networking of the German science system.

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

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