Computational Metagenomics (IBG-5)

The German Competence Center Cloud Technologies for Data Management and Processing (de.KCD) focuses on teaching how to handle data using cloud technologies. In the current phase of digital transformation, scientific and economic success depends on structured data collection, innovative tools and reliable infrastructure. de.KCD meets these challenges by bundling and communicating knowledge about cloud computing and providing the corresponding cloud infrastructure, storage space, standardized data analyses and training. Access to this is facilitated by virtual environments. In addition, de.KCD aims to promote collaboration and knowledge sharing by setting up a networked data space for national and international research projects.

Funding organization: BMBF

Website de.KCD

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 easily translate research data into a deep understanding of microbial species and their interactions at the molecular level.

The objective of the NFDI4Microbiota consortium is to be the central hub in Germany for supporting the microbiology research community with access to data, analysis services, data/metadata standards and training.

Bielefeld University leads Task Area 4 (Technical Infrastructure), which creates the technical basis for the NFDI4Microbiota platform that provides computing and storage resources for the microbiology community.

Funding organisation: DFG

Website NFDI4 Microbiota

Marine microbiomes make up 90 % of the total living marine biomass, but only a small proportion of them can be cultivated. For this reason, they are an under-researched source of bioactive compounds, carbohydrate polymers and proteins, among others. New approaches are needed to overcome the limitations in the study of marine microbial communities and their sustainable use.

Bluetools will unlock the potential of marine microbiomes for healthier oceans and the blue bioeconomy by integrating different disciplines to develop innovative tools that support rapid, efficient and sustainable exploration and utilization of microbiomes and avoid the drawbacks of traditional biosystems discovery methods.

Bluetools' expected results include the discovery of several hundred enzymes, rhodopsins, resistance genes, antimicrobials and antifouling agents thanks to a hybrid workflow of in silico and microfluidics-based function discovery.

Bluetools brings together five leading European companies, eight academic teams and a private registered educational institution that have pioneered the fields of functional metagenomics, microfluidics, microbial ecology and synthetic biology.

The Center for Biotechnology at Bielefeld University is contributing to the project by providing state-of-the-art sequencing technologies and bioinformatics approaches for data analysis.

Funding organization: EU, Horizon Europe

Website Bluetools

In just over a decade, metagenomics has become a powerful and productive method in microbiology and microbial ecology. The ability to extract and organize portions of genomic DNA from any natural context has opened a window into the vast universe of uncultured microbes. Tremendous progress has been made in computational approaches to interpreting this sequence data, but none can fully recover the complex information encoded in metagenomes.

Several challenges stand in the way of this. Simplifying assumptions are necessary and lead to severe limitations and potential inaccuracies in practice. A critical point to note is that methodological improvements are difficult to assess as there is no general standard for comparison. For developers, it requires considerable effort to evaluate existing approaches individually, which consumes time and computational resources and can lead to unintended biases. The Critical Assessment of Metagenome Interpretation (CAMI) is a new community-driven initiative that aims to help address these issues by providing an independent, comprehensive and unbiased assessment of methods.

Link to publication in nature

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

Website Base4NFDI

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.

Website FAIRagro

SIMBA (Sustainable Innovation of Microbiome Applications in the Food System) is a European innovation project funded under the EU Horizon 2020 funding program that provides a holistic and innovative approach to the development of microbial solutions to improve food and nutrition security.

The project aims to use microbiomes to create a better EU agri-aqua-food system that is resource-efficient, climate-resilient, sustainable and consumer-centric. To achieve this, SIMBA will explore and utilize microbiomes from land and sea over the four-year project period to develop numerous innovative solutions to the identified key challenges.

Funding organization: EU, Horizon 2020

Website SIMBA

Despite their biotechnological potential, there are considerable gaps in knowledge and many fundamental scientific questions about the group of anaerobic fungi, which hinder methodological progress in the detection and especially in the maintenance of long-term cultures.

Therefore, the HiPoAF project focuses on the fundamental questions of anaerobic fungi research to better understand their diversity, metabolic needs and syntrophic microbial interactions by focusing on work packages such as standardization, diversity and cultivation, detection and classification, and semi-continuous cultivation.

Funding organisation: DFG D-A-CH

Website HiPoAF

Nowhere is biological sequence diversity more evident than in the vast sequence space of viral genomes. The VIRUS-X project specifically explores the outer reaches of this diversity by targeting the viral sphere of selected microbial ecosystems and investigating the encoded functional diversity of viral gene products. The project is driven by the expected high innovation value and unique properties of viral proteins already demonstrated by the many virus-derived DNA- and RNA-processing enzymes used in biotechnology.

At the same time, the project will improve our understanding of important aspects of ecology in relation to viral diversity, ecosystem dynamics and virus-host interactions. Not least because of the inherent challenges in gene annotation, functional mapping and other virus-specific technical obstacles of viral metagenomics, the Virus X project specifically addresses these challenges by applying innovative measures in all parts of the discovery and analysis pipeline, from sampling in difficult extreme biotopes to sequencing, innovative bioinformatics and efficient production of enzymes for molecular biotechnology.

Funding organization EU, Horizon 2020

Cordis project website