Join our NFDI4Microbiota Symposium at the Annual VAAM & DGHM conference in Würzburg!

On Wednesday, June 5th, we will give an overview of our latest services, databases and workflows for the microbiology community. Have a look at our program!

NFDI4Microbiota Symposium: Public Infrastructure for Making Your Research Data Open and FAIR

  • Welcome and Introduction by Konrad Förstner (ZB MED)

  • Developing and Maintaining Best-Practice Workflows and Services for Processing Microbiological Research Data by Hesham Almessady (HZI)

  • Use Case Metaprot: Standardization and Metadata in Microbial Community Proteomics by Kay Schaller (ISAS)

  • StrainInfo: A Central Database for Resolving Microbial Strain Identifiers by Lorenz Reimer (DSMZ)

  • VirJenDB: Toward a Community-Curated and Open-Source Virus Meta(data) Analysis Platform by Noriko Cassman (University Jena)

When and Where? On 5 June 12:45 to 14:00 CEST in Raum 13!

Visit us also at our NFDI4Microbiota Booth to learn more about new services, training and Use Cases from our NFDI4Microbiota team. See you there!

Open this in new tab

This year we have launched the NFDI4Microbiota Coffee Talk Series! These meetings provide an opportunity to learn more about NFDI4Microbiota’s services and mission from within and around the NFD4Microbiota community. These bimonthly meetings take place online and are open to all who are interested in staying informed about current developments and topics related to data in microbiology research.

Please join us online at 2:30 PM - 3:30 PM CEST in Zoom

  • Meeting-ID: 633 6649 6382
  • Password: 490003.

Timeline for 2024

Date Name Topic Institution (TA)
29. April Isabel Schober StrainInfo - A central database for resolving microbial strain identifiers Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
24. June Sandra Triebel/Sharam Sagha TBA Friedrich Schiller University Jena
26. August Thomas Clavel TBA
RWTH University Hospital Aachen
28. October Ulisses da Rocha Metadata standards in connection with data quality Helmholtz Centre for Environmental Research
16. December TBA TBA TBA
Open this in new tab

Remember the Use Case submission call? We have good news! 3 new topics will help us and YOU to

  1. create knowledge graphs for linked microbial data – MicroBioKG by Vanessa Scharf and Konrad Förstner
  2. solve collection & extraction for image metadata – LichenMetaImage by Stephanie Weidtkamp-Peters and Björn Usadel
  3. use & contribute to a curated database for viral sequences – VirJenDB by Noriko Cassman and Manja Marz

Join the Use Case presentations on Tuesday, 2023-03-26 at 1:00-2:30 PM CET

Zoom-Meeting: 630 7779 8681 Passcode: 973383

Open this in new tab

Did you know that NFDI4Microbiota also helps shaping NFDI? For example, our speaker, Konrad Förstner is also part of the Scientific Senate of NFDI. In this way we are involved in the strategic orientation of the NFDI in general. The Scientific Senate is the substantive and strategic body of the NFDI. The main tasks include the consolidation of project progresses of the consortia, decision making regarding interdisciplinary standards and metadata standards and the decision on integration of new services into NFDI. The Scientific Senate is chaired by the Director of the Association, Prof. Dr York Sure-Vetter, and consists of twelve other experts.

Learn more about NFDI here

Learn more about Konrad Förstner here

Open this in new tab

Do you want to know more about Electronic Lab Notebooks for your research projects? Join our first NFDI4Microbiota Coffe Talk on 26th February from 15:30 - 16:00 with Justine Vandendorpe discussing the benefits and key features of Electronic Lab Notebooks for FAIR research.

Join the meeting on 26th February at 15:30 and log in here: Zoom Meeting-ID: 647 3481 9818 Passcode:269915 

Open this in new tab

Update: You can still join the Knowledge Base Content & Coding Sprint online!

Are you a microbiology researcher, research data management enthusiast or developer? We need your help! Join the NFDI4Microbiota Knowledge Sprint on February 15-16, 2024 online. Find out more about the program!

Join the meeting and log in here: Zoom Meeting ID 889 8299 1488 Passcode:033653 

The Knowledge base offers extensive information about research data management, software development and much more. And you can help us to make this even better! By contributing to the content or improving the code.

Open this in new tab

Are you a microbiology researcher, research data management enthusiast or developer? We need your help! Join the #NFDI4Microbiota Knowledge Sprint on February 15-16, 2024 online or on site in Cologne.  

The Knowledge base offers extensive information about research data management, software development and much more. And you can help us to make this even better! By contributing to the content or improving the code.

If you would like to help the community, join us and register here by January 31: Registration page

Open this in new tab

There are new NFDI4Microbiota services online! We are introducing them in our online Community workshop on February 5, 2024, 10-12:00. Join us and log in here: Meeting ID 687 5464 7684, Passcode: 363736

We will talk about the knowledge base, which provides information about research data management, software development and much more. For more info, check the Knowledge base

Learn how you can use the ARUNA storage to store your (meta-)data according to FAIR principles. For more info about ARUNA, check here: ARUNA Object Storage

And discover StrainInfo, providing microbial strain identifiers, and the new virus database VirJen.

We look forward to an exciting event. See you there!

Open this in new tab

We are happy to announce the open call for the NFDI4Microbiota Use Cases for 2024!
More details, the application guideline and all application documents can be found on the Use Case submission subpage.

The call is open from 2023-12-18 until 2023-01-31. Applications can be submitted to by the end of then.

What are Use Cases and why should you be interested in submitting yours?

In a nutshell, Use Cases will help us to test and fine-tune solutions developed within NFDI4Microbiota based on ongoing scientific projects and generate scientific results or reusable tools. Share your ideas with the consortium to identify new needs or provide new solutions to implement.
At the end, the Use Case outcomes will benefit the broad microbiology research community.

Your Use Case ideas, issues and solutions can range from - but are not limited to topics on research data management, databases, standardizing data and metadata, enhancing and supporting reusability in your field.

Be part of a FAIR solution in microbiology research!

Open this in new tab

Between the 5th 6th December, the final presentation of the cross-consotia hackathon were given by the participants. The Cross-consortia Hackathon DataXplorer was co-organized with NFDI4Eearth and NFDI4Biodiversity. The diverse challenges were related to earth system sciences, biodiversity and microbiology. One specific challenge involved the inspection of colour information in scanned raster maps. Another challenge entailed the development of a a web-based question-answering system to help researchers to find answers related to research data management. Additionally, a microbiome-related challenge aimed to develop a user-friendly and feature-rich meta-data annotation tool for metaproteomic experiments. The presentations and results during the presentations were impressive! You can find them here. The hackathon event was held mainly online, the end-presentations were hybrid, with an in-person meeting in Frankfurt. The meeting was combined with a social event: a torchlight tour in the Senckenberg museum. The next cross-consortia hackathon will be held in the beginning of 2025, this time with even more consortia.

Open this in new tab

Interested in metaproteomics and a hands-on training workshop and getting to know the faces behind NFDI4Microbiota’s Use Case MetaProt?

Join the “Applied Metaproteomics workshop Magdeburg 2023” for training on experimental design, sample preparations, LC-MS measurements, data analysis and metadata suggestions based on standards developed by MetaProteomics Initiative and NFDI4Microbiota.


Dirk Benndorf, Patrick Hellwig, Kay Schallert, Robert Heyer, Nico Jehmlich

When and where?

18th to 22nd September
Otto von Guericke University in Magdeburg, Germany


Registration fee: 100 € (incl. coffee and snacks)
Get the agenda and registration information from

Program light

For more information and full agenda, please contact

Monday from 09:00 - 18:00
Tuesday from 08:00 - 16:00
Wednesday from 09:00 - 17:00
Thursday from 09:00 - 17:00
Friday from 08:00 - 13:00

Open this in new tab

We are glad to announce, that the NFDI4Microbiota Flex Funds 2024 call is open now. More details, the application guideline and all application documents can be found on the Flex Funds announcements page.

The call is open from 2023-07-11 until 2023-08-20. Applications can be submitted to by then.

Open this in new tab

As 2023 is themed around community engagement, we will present our services to the public during the first NFDI4Microbiota online Lecture Talks on April 24 from 11:00-12:30 CEST. The talks will last 20 minutes each and will cover the following NFDI4Microbiota services for the community: the NFDI4Microbiota Knowledge Base, Use Cases, Workflows, and Training.

Date and time:


11.00 - 12.30 PM CEST

Webcast via Zoom:

Meeting ID: 857 7139 3336

Passcode: 095511

Open this in new tab

What are ELNs and LIMS? Why should scientists use them and what are the benefits? Besides the introduction to the topic and the tools, this world café aims to identify the needs in the microbiology community. To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we are organizing a world café on 2023-02-24 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Worflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here.

Open this in new tab

During Love Data Week 2023 several NFDI consortia participate in events or training regarding the topic “Data: Agent of Change”. Togetehr with the NFDI consortia DataPLANT, NFDI4Health and NFDI4Biodiversity, NFDI4Microbiota holds a panel discussion ‘Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences’ at the University of Bremen. Data-driven decisions in the life sciences have an immense impact on the well-being of humans and the environment, as well as on the development of research directions. Therefore, using best practice examples, experts from different areas of life sciences will discuss the importance of data-based decisions. Expect an in-depth discussion on the challenges and benefits of cultural change related to research data governance, Open Science and FAIR principles, and their impact on the daily life of every individual.


Prof. Dr. Konrad Förstner (NFDI4Microbiota), Björn Usadel (DataPLANT), Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Dagmar Waltemath (NFDI4Health)


Dr. Kerstin Elbing (VBio)


Universität Bremen, Room NW2 C0290 (Hörsaal 1)

Date and time:

16.02.2023 15.00 - 17.00 PM CEST

Zoom option:

Meeting-ID: 812 3227 9619

Password: 092856

Open this in new tab

NFDI4Microbiota will attend the 1st BioHackathon Germany organized by de.NBI. The workshop ‘Extending the NFDI4Microbiota Knowledge Base’ will be held during the event from 12th to 16th december 2022 in Wittenberg. NFDI4Microbiota has initiated a dedicated Knowledge Base which will contain information on Research Data Management and Reproducible Data Analysis in the broad field of microbiology. The Knowledge Base is developed in an open, collaborative process on GitHub and offered under a permissive license (CC-BY 4.0).

Several NFDI4Microbiota members will participate in the BioHackathon and use that time as a content spring. The BioHackathon will offer a great opportunity to engage in discussions with other participants on various topics such as best practices, bioinformatical tools, Electronic Lab Notebooks and privacy issues.

Free-of-charge registration is open until 25th of November.

Project Lead: Justine Vandendorpe and Kassian Kobert

Open this in new tab

NFDI4Health, GHGA and NFDI4Microbiota particularly welcome the strategic goal of establishing a decentralized, research-compatible, networked and interoperable health data infrastructure with a central health research data portal. The plea of the German Council of Science and Humanities for a data protection compliant facilitation of data access with the possibilities of the opt-out procedure is explicitly supported by the participating NFDI consortia. Additionally, improved possibilities for the linkage of different data sources (record linkage) on a national level are pleaded for.

For “Rückmeldung der lebenswissenschaftlichen Nationalen Forschungsdateninfrastrukturen NFDI4Health, GHGA und NFDI4Microbiota zu den Positionen und Empfehlungen des Wissenschaftsrats” click here.

For the “Positionspapier zur Digitalisierung und Datennutzung für Gesundheitsforschung und Versorgung” click here.

Open this in new tab

NFDI4Microbiota will take part in the panel discussion ‘Everything FAIR and Open? Restrictions on data publications’ at JCDL 2022. The panel discussion will be held during the NFDI Satellite Event @JCDL 2022 on the 23rd of June 2022. We are looking forward to an intense exchange on different data and their handling and restrictions in the fields of Life and Social Sciences with representatives of NFDI4Health, NFDI4Biodiversity, and KonsortSWD. Our consortium will be represented by our consortial speaker Prof. Dr. Konrad Förstner. Further details can be found via this link. Please have a closer look at the different registration options!

Open this in new tab

More than a 1,000 researchers worldwide have already signed the DSI Scientific Network’s Open Letter, calling for open & equitable sharing of genetic sequence data from. You are wondering why this might be important to you?

A short summary by the DSI Scientific Network, orgnaized by Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH:

“In March 2022, negotiations on Digital Sequence Information (DSI) and benefit sharing will resume among Parties to the Convention on Biodiversity as they work to reach agreement on the new Post-2020 Global Biodiversity Framework, which sets new goals and aims to transform society’s relationship with biodiversity. The scientific community is the primary generator and user of DSI. The outcome of these negotiations will therefore shape our ability to use DSI and generate research that helps move forward sustainable development, protect biodiversity and address global health crises. Given the importance of DSI to our work, it is essential that our perspectives, expertise and experience be included in considerations of different approaches to benefit sharing for DSI. DSI is used by researchers in a wide of contexts including for studying and monitoring biodiversity, understanding ecosystem impacts from climate change, improving crops, developing new medicines, and tracking the spread and evolution of new infectious diseases. Access to DSI is therefore crucial to research supporting many of the UN Sustainable Development Goals. A wide range of organizations and experts have called for DSI policy solutions that provide equitable benefit-sharing through multilateral mechanisms that protect open access DSI.” Source and more information

We highly support this initiative and want to invite all researchers to sign the DSI ScientificNetwork’s Open Letter to ensure good research in the future.

Open this in new tab

Become an NFDI4Microbiota ambassador for your institute! You will not only increase your knowledge on topics like research data management, but also have the possibility to network and influence our work as well as getting solutions for your problems. We do adress this program specifically to young researchers like PhD candidates and PostDocs. You can get more information and register here The first Ambassador Coffe Talk will be on the 13th of June, so make sure to register by the 23rd of May, so you will receive an invitation #NFDIrocks

Open this in new tab

We are pleased to announce our next bioinformatics workshop: “Introduction to deep learning with R”, which will take place online on June 13-15, 2022. Deep learning based techniques have shown remarkable results in domains such as speech synthesis, natural language processing and image vision. Recently, these methods have been applied to the bioinformatics domain and have been shown, for example, to achieve an unprecedented level of performance for the protein folding task. In this workshop, we will explore and train deep neural networks using the R programming language on genomic datasets. Interested? Then please find additional information here. We are looking forward to seeing you in the workshop! The link for registration here

Open this in new tab

We are pleased to announce the first bioinformatics workshop: “Introduction to R”, which will take place online from 7th to 9th of March 2022. Increasingly, physicians and biologists are facing largeamounts of data that can no longer be analyzed “by hand”. The R environment offers free software facilities for data manipulation, calculation and graphical display. It thus allows handling of large data amounts, simplifies the interpretation of the data, or enables a deeper analysis Interested? Then register here. We are looking forward to seeing you in the workshop!

Open this in new tab

You are still looking for some fine FAIR data training material for higher education institutions? Our consortium member Justine Vandendorpe recently published together with other FAIR experts a teaching and training handbook. The handbook included 179 pages and is openly available on Zenodo: We wish you happy reading and teaching!

Open this in new tab

The good news does not stop, so better save the date! After NFDI4Microbiota finally started in October 2021, we are glad to announce our 5th Community Workshop. The event will take place (online) on the 18th of March 2022 from 10-12 AM CEST. This great opportunity will be used to kick off our ambassador program to the microbiology community. If you are not hooked yet, wait for more information to come soon.

Open this in new tab

After three months of successfull work within our consortium, the election of the consortial speaker as representative within NFDI e.V. took place at the end of 2021. We congratulate Prof. Dr. Konrad Förstner and Prof. Dr. Alice McHardy as speaker and deputy speaker of the NFDI4Microbiota consortium! We are looking forward to a fruitful cooperation with NFDI e.V. and all its members.

Open this in new tab