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Introduction to the NFDI4Microbiota How We Operate


The NFDI4Microbiota ‘How we operate’ repository shall serve as the base for the productive and aligned work within the NFDI4Microbiota consortium. Here, all information, guidelines, SOPs, documents, and links required for the work in the consortium can be found.


Each member of the consortium can contribute to this repository.

Introduction to the Nationale Forschungsdateninfrastruktur (NFDI) e.V. (NFDI association)

  • The National Research Data Infrastructure (NFDI) aims to systematically index, edit, interconnect, and make available the valuable stock of data from science and research. Digital data storage is an indispensable prerequisite for treating new research issues, generating findings, and making innovations. Therefore, the NFDI association was founded in 2020. Further information can be found on their website.
  • NFDI provides a starter guide (German) (internal link), where you can find information on all committees, etc.
  • Many documents addressing the NFDI e.V. and the proposals of most consortia are published on Zenodo.
  • The NFDI e.V. has five sections addressing cross-cutting topics of all consortia.
  • In a 30-minute video, the statute of the NFDI e.V. (German) is explained on their YouTube channel.
  • The Deutsche Forschungsgesellschaft (DFG) funds different NFDI consortia (independently of the NFDI e.V.). Further information and introductory videos can be found on the DFG website.

Introduction to NFDI4Microbiota


Researchers can translate data easily into a deep understanding of microbial organisms and their interactions on a molecular level.


  • Be the central hub in Germany for supporting the microbiology community with data access, analysis services, data/metadata standards, and training.
  • Democratize access to microbiota data and high-end computational analyses.

Code of Conduct

It applies the code of conduct of NFDI e.V..

Key Objectives

NFDI4Microbiota aims to facilitate the digital transformation of the microbiology community to significantly accelerate the generation of new, relevant knowledge. Microbiology is intricately linked to numerous other fields, including medicine, agriculture, biotechnology, and earth science, so the overall social impact of these improvements will be immense. To overcome common obstacles to handling data in the field of microbiology (State-of-the-art and needs analysis) NFDI4Microbiota will take steps to achieve the following key objectives (KO):

KO-1: Generate a broad awareness of the importance of FAIR principles, open science, and reproducible research in the microbiological community and drive a cultural change toward their widespread adaptation.
KO-2: Equip the community with the required skills and literacy for efficient and data-driven microbial research by providing a comprehensive training program.
KO-3: Increase the value of other NFDIs by adding microbial expertise and connecting the national and international microbiology communities.
KO-4: Improve the research process by mobilizing, structuring, and linking available data, information, and knowledge related to microorganisms.
KO-5: Support high-quality research data management by introducing professional data stewards into the microbiological research process.
KO-6: Increase the value of data by standardizing and systematically collecting rich metadata and building tools for querying.
KO-7: Make research more reproducible by standardizing data processing and analysis.
KO-8: Provide computational tools and infrastructure for the translation of data into new knowledge.
KO-9: Provide central information hubs tailored to address the needs of the microbial research community and its subfields.
KO-10: Continuously adapt the solutions provided to meet the future needs of our microbiology community.


See tables at the end of each measure in the proposal.

Key Performance Indicators (KPIs)

a) Completed projects
b) Amount of data collected
c) Database entries added
d) Access to a central information hub
e) Download and usage of application programming interfaces (APIs)
f) User help desk requests
g) # of publications
h) # of training
i) # of ambassadors
j) # of commits to the knowledge base

Governance of NFDI4Microbiota

Governance is the process of making and enforcing decisions within an organization or society. In the following, the governance structure will be introduced, and the governance bodies are defined.

Board of Directors

The Board of Directors (BoD) consists of the consortium’s spokespersons (Konrad Förstner and Alice McHardy). Both of whom will represent NFDI4Microbiota internally and externally. They are responsible for orchestrating the TAs and ensuring the proper connection between participants, Use Cases, and measures. As well as coordinating measures to ensure that milestones are reached and deliverables released on time, they will elaborate solutions with relevant consortium members, should problems arise. They will also be responsible for the dynamic adaptation and growth of the consortium and for the achievement of the overall project aims. Finally, they will monitor NFDI4Microbiota’s compliance with all NFDI requirements and obligations, and handle legal, ethical, and contractual issues. The BoD will communicate/meet at least once a month and will report to the General Assembly (GA) and to the Scientific Advisory Board (SAB). They will also have direct contact with the NFDI Directorate.

Administration Unit

As of January 2023, the Administration Unit (AU) consists of the project managers of the BoD: Barbara Götz, Mattea Müller, and Cordula Hege. This unit will support the BoD with the coordination of the consortium, including internal communication, milestone and deliverable monitoring, reporting, quality assurance, and DFG/NFDI administrative tasks. The AU will communicate/meet on a weekly basis and report to the BoD.

General Assembly

The General Assembly (GA) consists of the ten partner institutions, represented by their respective co-spokespersons named in the proposal (with voting rights), and of spokespersons of the participating institutions (without voting rights). It is the ultimate decision-making body of the consortium in regard to content and organization. The GA will monitor progress toward meeting the requirements of the TAs and measures. The GA will also ensure NFDI4Microbiota forges connections with other NFDI consortia and will communicate with the NFDI committees and the national and international communities. ZB MED is responsible for all budget matters and financial decisions made by the GA and for any alterations made to the Consortium Agreement (CA) in the future. Finally, the GA is in charge of accepting/rejecting new partners and project proposals by participants, and of deciding on the premature completion or termination of the project. The GA members will communicate/meet at least once a year (the agenda must be made available 2 weeks beforehand) and report to the BoD on progress made within the TAs and measures they lead. Should the consortium – and therefore the GA – grow, a steering committee (SC) consisting of the BoD, TA leaders, and/or elected partners will be formed. The SC would take over tasks such as progress monitoring and make strategic decisions.

Scientific Advisory Board

The Scientific Advisory Board (SAB) comprises scientific experts and representatives of professional societies (and as such representatives of the user community) from the fields of microbiology and bioinformatics. The SAB members will be involved in research data infrastructures and international initiatives with direct relevance to NFDI4Microbiota. We favored potential SAB members who work in related international infrastructures or consortia in order to facilitate the exchange of expertise among these entities. The SAB provides strategic input and advises the consortium on:

(1) the research data management strategy,
(2) proposals and plans, and
(3) the needs of the research community.

This body also highlights critical issues and emerging global trends. The SAB thus supports the further development of NFDI4Microbiota (see M1.6 - Sustainability and M5.3 - Dynamic adaptation and growth). SAB members communicate/meet at least annually and suggest strategic planning ideas to the BoD.

Members of the SAB:
Markus Engstler
Curtis Huttenhower
Nikos Kyrpides
Robert Finn
Stanton L. Martin
Thomas Schulz
Sünje Pamp
Claudine Médigue
Nicole Wheeler
Christine Moissel-Eichinger

Project Review Board

The Project Review Board (PRB) is responsible for selecting new projects within the scope of the flexible funding (FlexFunds) and allocation mechanism, thus reacting to new and unforeseen scenarios. It is staffed based on suggestions made by the SAB and decision-making includes a peer review process.

NFDI4Microbiota Policy

The General Assembly adopted the NFDI4Microbiota Policy in 2023, which will be published on the NFDI4Microbiota Zenodoo community soon.

Annual timeline of important dates for the consortium

This timeline gives a rough orientation on the annual tasks, deliverables, meetings, etc. of the administration and the outreach of NFDI4Microbiota.

Month Type Measure Topic
Middle of January Task M5.3 Onboard Flex Funds applicants
End of January Deliverable M1.3 Quarterly NFDI4Microbiota newsletter
Middle of March Meeting TA5 Quarterly coordination coffee
Middle of March Deliverable M3.1 Training and event announcement to the community
April Meeting M5.1 General assembly
End of April Deliverable M1.3 Quarterly newsletter
Middle of May Announcement M5.3 Flex Funds Call Announcement
Middle of June Meeting TA5 Quarterly coordination coffee
Middle of June Announcement M1.3 Training and event announcement
Middle of June Announcement M5.3 Opening of Flex Funds call
End of July Deliverable M1.3 Quarterly newsletter
Middle of August Announcement M5.3 Closing of Flex Funds call
Beginning of September Survey M5.2 Opening of query for direct costs distribution of the following year
Beginning of September Meeting TA5 Quarterly coordination coffee
Middle of September Announcement M1.3 Training and event announcement to the community
Middle of October Survey M5.2 Closing of query for direct costs distribution of the following year
End of October Deliverable M1.3 Quarterly newsletter
Beginning of November Resolution M5.3 Circulation of Flex Funds decision in the consortium (2 weeks)
Beginning of November Meeting M5.1 General Assembly
Middle of November Announcement M1.3 Training and Event announcement
Middle of November Announcement M5.3 Forwarding Flex Funds decision to applicants
December Event TA51 NFDI4Microbiota Annual Conference 2024
December Meeting TA5 Quarterly coordination coffee

Download the actual annual timeline here (internal link).

NFDI4Microbiota Community, Members, Partners, and Participants

NFDI4Microbiota Community

The NFDI4Microbiota community is defined as the group of all researchers working within or with microbiology-related projects and the respective data. This community can be further divided into the following groups: consortium members, participating institutions, ambassadors, and societies. For communication different contact and mailing lists exist. An overview of all communication channels is presented at the end of this file.

NFDI4Microbiota Consortium Members

A member of the NFDI4Microbiota consortium is defined as a person who works at one of the ten partner institutions directly funded by NFDI4Microbiota. Responsibilities, contacts, and involvements in the measures of NFDI4Microbiota are documented here ) (internal link). Each member is responsible to update its data frequently. If a member leaves the consortium, the member or someone from his/her institution needs to make sure to inform the AU, so that he/she can be removed from all mailing lists, Open Project, Rocket Chat, Nextcloud, etc (Detailed list in the Offboarding section). All are members of the mailing list Please find a visual overview here (internal link).

NFDI4Microbiota Partners

The NFDI4Microbiota partners are the co-spokespersons of the consortium. The institution they work for is the partner institution of NFDI4Microbiota.

Partner/Co-spokespersons Institution, location Task area(s) (TA)
Prof. Dr. Alexander Sczyrba & Prof. Dr. Jens Stoye BIBI, Bielefeld TA1, 2, 3, 4
Prof. Dr. Peer Bork EMBL, Heidelberg TA1, 2, 3, 4
Prof. Dr. Manja Marz FSU Jena, Jena TA1, 2, 3
Dr. Ulisses Nunes da Rocha UFZ, Leipzig TA1, 2, 3, 4
Prof. Dr. Alice C. McHardy HZI, Braunschweig TA1, 2, 3, 4, 5
Prof. Dr. Alexander Goesmann JLU Gießen, Gießen TA1, 2, 3, 4, 5
Prof. Dr. Jörg Overmann DSMZ, Braunschweig TA1, 2, 3, 4
Prof. Dr. Anke Becker UMR, Marburg TA1, 2, 3, 4, 5
Prof. Dr. Thomas Clavel RWTH Aachen, Aachen TA1, 2, 3

NFDI4Microbiota Participants and Supporting Societies

Participants are participating institutions with contact person(s) for each institution. The list of all participants and supporting societies and their contact details are found here (internal link). All participants are members of the mailing list

NFDI4Microbiota Ambassadors

Ambassadors are young researchers (PhD students, Post Docs, etc.) of microbiology research groups. They actively registered and are part of the mailing list Details on the ambassador program can be found on the web portal.


Within the consortium, as well as externally, we have several communication possibilities through different channels:

NFDI4Microbiota mailing lists

For the communication with different groups inside and outside the consortium, the following mailing lists are available:

  • (Administration Unit + Outreach Coordination)
  • (Helpdesk team)

Further internally used mailing lists are filed here (internal link).

Rocket Chat

The Rocket Chat instance of NFDI e.V. is used for low-level communication within the different consortia, the sections, the task forces, and channels created by members of the NFDI consortia with specific purposes. It can also be considered as an alternative communication without email overload.

Channels provided by NFDI4Microbiota:

To have your user account created on the Rocket Chat, contact one of the Administration Unit. Afterwards, you can access the rocket chat for NFDI.

NFDI e.V. mailing lists

Via this mailing list, general information on e.g. NFDI talks, coffee sessions, onboarding (quarterly), and statute introduction (semi-annually) are shared. If you are involved in further sections, task forces, or administrative groups (more information on NFDI e.V. work), it would be easiest to create an account to manage the NFDI mailing lists. For some mailing lists, archives of past emails do exist and can be viewed too. Every NFDI4Microbiota member should at least register to ‘nfdi-all’ mailing list. All lists can be accessed via this link.


For the consortium, the information on the annual direct cost distributions and flexible funding are of interest. In general, the Usage Guidelines of the DFG giving a guideline on different financial topics as well, like travel costs, etc. As repetition is not intended, here only consortium-specific topics are addressed.

Direct costs

The direct costs were not distributed within the consortium during the proposal phase. Therefore, each year the direct costs have to be distributed throughout the partner institutions. An annual financial forecast is implemented and described in ….

Flexible funding (Flex Funds)

The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, the development of new training programs, and the improvement of the ability to react to unforeseen technical challenges. Therefore, within the NFDI4Microbiota project work, flexible funding (so-called ‘Flex Funds’) for small projects within the research community is available for the years 2023 to 2026. To implement a dynamic system that stays on track with new trends in the field, the Flex Funds shall support small projects and Use Cases from the community as they arise over time, either directly through NFDI4Microbiota activities or independently. Such a system will guarantee flexibility and allow broadening the scope of activities to an even wider pool of participants, increasing the visibility and, eventually, the added value of the consortium. The latest call is found here.

Strategy Funds

The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, the development of new training programs, and the improvement of the ability to react to unforeseen technical challenges. Therefore, within the NFDI4Microbiota project work, unallocated funds, like remaining direct or personnel costs, annual transfer of funds, unspent budgets of partners, etc. shall be collected in the so-called Strategy Funds. The Strategy Funds shall serve different purposes within the consortium that come up unplanned, urgent, or unexpectedly without financing. Such a system will guarantee flexibility and allow reacting flexibly to unexpected, unplanned, or urgent cases. This can be, for instance, publications, workshops, or other direct costs, but also personnel costs.