Use Case

MULTI: Integration of multi-omics data of microbial species

Abstract: Antimicrobial resistance is a large issue in food production, especially regarding the microbe Listeria monocytogenes, whose different strains are reported to be resistant to a variety of antimicrobial substances. Using multi-omics integration, we can investigate the functional response of a microbial cell to an antimicrobial substance to understand how antimicrobial resistance enables the cell to survive with such compounds in the environment.

Aim: We want to combine genomic, transcriptomic, and proteomic data to investigate the cellular response of Listeria monocytogenes strains on sub-lethal concentrations of a biocide commonly used in meat production factories.

Keywords: Genome Assembly, Transcriptomics, Genome-scale Metabolic Reconstruction, Proteomics

Author: Ulisses Nunes da Rocha and Stefania Magnusdottir from the Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ.

Community Involvement: The data collected and all analysis pipelines will be made publicly available. The genome assembly, annotation, and classification pipeline will be made available separately from the database, meaning that users can test it and help us improve the tool for more diverse uses. The users of the database can contribute with their feedback on the interface, metadata included, or new data sets not yet included in the database. The NFDI4Microbiota community could use our framework to carry out data analyses of their own using our available data, as many studies and analyses can be performed on such a large data set.

Related Documents:

AmpliBench: Replacement or Extension: Systematic Assessment of Differences in Taxonomic Profiling Between Amplicon Sequencing Variants and Operational Taxonomic Units

Abstract: More information will follow soon.

Aim: More information will follow soon.

Keywords: Amplicon Analyses, Targeted Metagenomics, Microbiomics, OTUs, ASVs, Benchmark

Author: Alexander Sczyrba and Sebastian Jünemann from Bielefeld Institute for Bioinformatic Infrastructure, Faculty of Technology, Bielefeld University

Community Involvement: More information will follow soon

MetaProt: Functional profiling and routine diagnosis of humane microbiomes by metaproteomics

Abstract: More information will follow soon.

Aim: More information will follow soon.

Keywords: Metaproteomics, Gut Microbiome, Health Care, Routine Diagnosis, Systems Biology

Author: Dirk Benndorf and Robert Heyer from Bioprocess Engineering, Otto von Guericke University Magdeburg and from Leibniz Institute for Analytical Sciences – ISAS, Multidimensional omics analysis group, respectively.

Community Involvement: More information will follow soon.

Strain-ID: Collecting and matching microbial strain identifiers

Abstract: More information will follow soon.

Aim: More information will follow soon.

Keywords: Persistent Identifiers, Microbial Identity, Reproducibility

Author: Lorenz Reimer and Jörg Overmann from Bioinformatics & Databases, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen

Community Involvement: More information will follow soon.

GUT: Crowd-sourcing high-quality descriptions of novel taxa

Abstract: As a substantial fraction of gut microbiomes is still uncharacterized, there is a dire need to implement innovative approaches to study the wealth of microbial diversity detected by shotgun metagenomics at the strain level. This requires a plethora of wet lab and in silico skills as well as an appropriate analysis pipeline which will allow for a standardized functional and taxonomic description of novel species, a so called ‘protologue’.

Aim: The first instance of this Use Case focuses on the generation of standardized protologues for 10,000 uncultured species from the human gut microbiome using an integrated analysis pipeline. A database displaying the generated output will be made available for the whole microbiome research community and user input will be required to engage with the data, ideally with template edits and revision suggestions. The second instance of this Use Case will be reaching out to research experts of different microbiome communities such as soil and marine microbiomes to expand on the output of the analysis pipeline.

Keywords: Automated Analysis, Protologue, Ecological and Functional Description, Novel Bacteria

Author: Thomas Hitch and Thomas Clavel from the Institute of Medical Microbiology, Functional Microbiome Research Group, University Hospital of RWTH Aachen.

Community Involvement: The long-term aim is to work with experts from different environments (e.g. gut, soil, marine expertise) and identify as well as extract MAGs and SAGs from isolates that are suitable to be analyzed by Protologger. If suitability is confirmed the analysis can be run to create protologues and submit the data to repositories. In order to validly name bacteria, the help from the community is needed. The main focus is currently to collect input from ecological experts who know about existing isolates instead of using ANI-values to categorize species. Community outreach will be conducted via training videos and seminars, to ensure community members can contribute to the description of novel taxa. To validly name an isolate it has to be deposited in two culture collections for the analysis tools to access the sequences. To increase Protologger‘s accessibility to the community a curated database is needed and long-term deposition which will require the technical consultation of the NFDI4Microbiota community.

Related Documents:

MetaProv: Provenance and usage of metagenome data

Abstract: More information will follow soon.

Aim: More information will follow soon.

Keywords: Sequence Analysis, Computational Biology, Function Analysis, Biological Databases, Phylogenomics, Metagenomics, Microbiology, Microbial Ecology, Human Disease, Terrestrial Metagenome, Marine Metagenome, Biogeochemistry, Genetic Potential, Metadata Standards

Author: Ulisses Nunes da Rocha and Stefania Magnusdottir from the Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ.

Community Involvement: More information will follow soon.


The mission of NFDI4Microbiota is to facilitate and stimulate data sharing according to FAIR principles to ensure easy and open access to microbial data and their associated metadata. An important means to achieve this goal is to implement Use Cases (UCs). UCs are real scientific projects in the broad field of microbiome research that are performed at partner institutions with the involvement of a few to multiple additional stakeholders (e.g. research consortia, societies).The intentions are to:

  1. combine the expertise of all stakeholders involved in NFDI4Microbiota, microbiology associated communities and NFDI consortia
  2. benefit from NFDI4Microbiota by implementing measures provided by the consortium to boost the outcome of the UCs; and
  3. nurture ideas for the consortium to implement additional measures, but also act as a platform for community feedback to improve the already existing measures.

Community involvement in Use Cases is highly appreciated and supported by NFDI4Microbiota. The involvement possibilities differ from UC to UC and can be in the form of e.g. UC-specific workshops, trainings, discussions, data submissions, etc.

If you want to participate in one of the active Use Cases, use our contact form with the issue type “Use Cases” to get in touch."

As a selected UC, you have the following benefits

  • Access and support from the NFDI4Microbiota community concerning services, trainings, technical infrastructure, etc. targeted to your Use Case application
  • Participation in workshops to present and discuss
  • Networking and connecting with the community
  • Possibility to apply to NFDI4Microbiota’s project funding (Flex Funds)

By submitting a UC, you commit to the following points

  • Contributing to UC workshops
  • Actively contributing to the Use Case
  • Working with NFDI4Microbiota to ensure smooth integration with our offered services
  • active communication with NFDI4Microbiota

Use Cases can be submitted by

  • NFDI4Microbiota partners
  • NFDI4Microbiota participants and their ambassadors
  • externals with a relation to the topics research data management and microbiome research.

The next round of submissions will open in 2023. The submission will take place via a form and upload function on the web portal. Stay tuned for more information.

Let us know via Contact.