Newsletter Quarter 2 2024


Dear Reader,

With our seventh NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, cooperations and publications. If you can think of other topics that we should cover, please let us know. We are happy to hear from you!
And now: Enjoy reading the newsletter!

Community Engagement

Events and Conferences

NFDI4Microbiota joined the annual meeting of the Research Data Alliance

As a part of NFDI e.V., NFDI4Microbiota is a member of the Research Data Alliance (RDA) Germany. The goals of the RDA, like to improve the social and technical requirements for an increased data exchange and an easier reuse of data, align with ours. Therefor we were happy to represent our fields of expertise at the annual meeting on February 20th and 21st.

Due to the recent entry of NFDI e.V. into the RDA, the presence of NFDI consortia was significantly increased compared to previous years. Alongside NFDI and NFDI4Microbiota, other consortia like NFDI4Earth also showcased their work. In total, there were approximately six posters related to NFDI, our NFDI4Microbiota Poster included.

The meeting proved to be insightful, offering a different perspective on research data management than usual. Notably, several talks delved into the political aspects of research data management. One such talk was delivered by Renate Nikolay, the Deputy Director General for Communications Networks, Content, and Technology at the EU Commission, focusing on “The Cornerstones of the European Data Strategy.”

Successful NFDI4Microbiota Knowledge Base Content and Coding Sprint

The NFDI4Microbiota Knowledge Base is a collection of information and references with relevance for the microbiology community in terms of Research Data Management, Data Analysis, FAIR principles, standards, and much more. Furthermore, information about the NFDI4Microbiota consortium are collected.

To raise awareness of this resource and to further improve it, we planned a comprehensive Knowledge Base Content and Coding Sprint. After having to reschedule the event multiple times, we finally found a time slot in February 2024 to hold the NFDI4Microbiota Knowledge Base Content and Coding Sprint in Cologne.

Roughly 20 participants, mostly, but not exclusively, from NFDI4Microbiota, came together in a 2-day concentrated effort to push the NFDI4Microbiota Knowledge Base forward. Some joined us online, while others met at ZB MED in Cologne. A lot of content was added by individuals and groups focusing on specific topics. Perhaps more importantly, getting so many interested people together has allowed us to have in-depth discussions about issues and strategies related to the Knowledge Base that might not have happened otherwise.

We consider the NFDI4Microbiota Knowledge Base Content and Coding Sprint an overall success. This is not just limited to the two days dedicated to the Sprint. Having people interested in the Knowledge Base and learning about it in preparation for the Sprint already had an impact. Leading up to the Sprint, and especially in the weeks following the Sprint, the Knowledge Base Git repository showed a much higher level of activity than usual.

Given the reception and success of the sprint, we are aiming to have this as a regular recurring event. Specifically, we, and you, can look forward to the next instance of the NFDI4Microbiota Knowledge Base Content and Coding Sprint, planned to be hosted in Marburg on September 11th - 13th, 2024.

Community Engagement

Upcoming Events and Conferences

Meet us in Würzburg on June 2-5, 2024

NFDI4Microbiota is attending the VAAM&DGHM Microbiology & Infection Conference in Würzburg. The conference takes place on June 2-5, 2024.

We look forward to meet you in person, so feel free to step by, if you are attending and learn more about us.

Bimonthly ambassador meetings

On 29th January we restarted the NFDI4Microbiota Ambassador program. During the first meeting, we provided an overview of NFDI4Microbiota in general and discussed the ambassador program. On March 25th, Sarah Schulz from EMBL delivered a talk on “Standards and Policies” related to NFDI4Microbiota.

In July (29th) we will delve into ARUNA Object storage) with detailed insights shared by Frank Förstner. November (25th) Kassian Korbert (BiBI) will tell us about the NFDI4Microbiota Knowledge Base. The topic for September is still to be determined.

Are you a postdoc or a PhD student in the field of microbiology, or are you interested in data management? Or perhaps you know someone who might be interested? We warmly welcome new participants and invite you to join our bimonthly meetings, which are held on the last Monday of each month at 3:30 PM. Learn more about the program and register here.


Involving our community through new Use Cases

Three new Use Cases have been accepted recently and will expand NFDI4Microbiota’s pool of services to create targeted solutions for you and us. Our Use Cases are your explicit invitation to get involved as they offer possibilities to engage with the research community, so take a look at the new Use Cases to see what the future holds:

  1. MicroBioKG will be explore and serve as a blueprint for how knowledge graphs can make microbiological data FAIR, open and sustainably accessible, and how this enables connectivity between resources. This Use Case will follow three real projects with real data. Follow them and you will soon be able to apply the guidelines developed by Vanessa Scharf and Konrad Förstner to your own data.

  2. LichenMetaImage will explore the best of many worlds – namely lichen (fungus and bacterial photosymbiont) and its unique interaction with its microbiome – using a multi-omics (imaging, metagenomics, transcriptomics) approach. This Use Case will also bridge existing imaging metadata collection efforts developed by DataPLANT and NFDI4BIOIMAGE. We are excited to see what Björn Usadel and Stefanie Weidtkamp-Peters’ big picture will look like.

  3. VirJenDB is now also a Use Case as future plans to expand the platform include adding automated and community curated analysis workflows, data, metadata and more (see above). By interacting with this Use Case, e.g. as an interested virologist with data published in ENA, you could be trained in RDM topics and contribute to community curation of the platform and datasets. These and many more interaction opportunities will be offered soon. The faces behind this Use Case are Noriko Cassmann, Manja Marz and Shahram Saghaei.

Collecting publicly available virus resources, metadata and sequences: VirJenDB

We are pleased to announce the beta release of the VirJenDB version 0.1 which is available here. VirJenDB is a comprehensive virus database based in Jena providing user-friendly access to community-curated virus sequences, metadata, visualizations and tools. If you are interested in becoming a beta user, joining the curation community, or helping us to improve the database, please email the VirJenDB team.

Training Announcements

There are several interesting training offers currently open for registration, like:

  • the NFDI4Microbiota and de.NBI 16S amplicon training course (Oct 8th-10th 2024)
  • Microbiota profiling by 16S rRNA gene amplicon sequencing: Data analysis Workshop

And more courses are planned. For example, there will be an “Introduction to R course” in early May, and “Basic statistic with R” at the end of May. In September you can learn about “Linux Basics for Bioinformatics” and in November about “Metagenomics”.

As soon as the registration opens, you will find it on the NFDI4Microbiota website. More courses will be announced soon, so check the website regularly for training opportunities.

Join us for our next Electronic Lab Notebook (ELN) event on June 17, 2024

Our successful ELN events are going into the next round! Join the online seminar on June 17, 2024 from 13:00 - 16:00 CET. The seminar will provide you with an overview of NFDI4Microbiota and ELNs in general, followed by in-depth presentations and discussions on eLabFTW from different perspectives (experienced and new users, developers).

Save the date if you are interested! Registration will start soon and will be announced here.

Previous Training

Joint NFDI & de.NBI Metagenomic Training Course 2023

In early February, de.NBI and NFDI4Microbiota collaborated to host a comprehensive training course on metagenomic data at the University Bielefeld. With that the Task Area 1 of NFDI4Microbiota completed one of its milestones.

The participants, representing over 10 different research institutes from across Germany, were primarily at early to mid-career stages. Spanning three days, the course provided an extensive overview of tools and bioinformatics techniques essential for analyzing next-generation sequence (NGS) data from microbial communities, with ample hands-on training opportunities. The first two days focused on preprocessing, quality assessment, error management, and various genome-related tasks such as assembly, binning, and taxonomic and functional analysis. On the final day, participants learned from experts of the Helmholtz Centre of Infection Research (HZI) how to incoporate metagenomics worklflow in nf-core workflows using Nextflow for automated and reproducible analysis.

In summary, the workshop proved to be both intense and engaging with lots of opportunity to ask questions and network with peers. Special thanks to all the organizers for their efforts in making this event a success!


NFDI4Microbiota joined JourFixe of the FDM initiatives

Most of the German federal states have set up initiatives for research data management (RDM), which network with each other in a regular JourFixe, the Forum of Digital Methods (FDM) initiatives. The aim of these initiatives is to establish recommendations and solutions for RDM processes in the respective federal states and to incorporate these into an overall national strategy as part of the joint JourFixe.

To support those initiatives with their profound knowledge and expertise, the NFDI consortia joined the JourFixe on February 21, 2024.

The NFDI consortia were specifically invited to increase their presence and contribute to the discussions. The main topic of the meeting was “International Outreach and Exchange.” There were 25 attendees, with the majority not from NFDI4-related initiatives. Represented at the meeting were NFDI e.V, NFDI4Objects, NFDI4Ing, Base4NFDI, NFDI4Ing, and NFDI4Microbiota.

The JourFixe provided an opportunity for the exchange of ideas and to plan cooperation on several projects. One of these projects is to write a paper or an abstract about the structures and diversity of Research Data Management (RDM) initiatives and actors in Germany and explain the complexity of the field.

2024 Flex Funds projects

The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, development of new training programs, etc. Therefore, within the NFDI4Microbiota project work, flexible funding (so called ‘Flex Funds’) for small projects within the research community are 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 will support small projects and active Use Cases from the community as they arise over time. The 2024 Flex Funds call resulted in the approval of four new Flex Funds projects funded with an overall budget of approx. 300,000 €.

Short abstracts of them will be published on the web portal in the near future. The project titles are listed below.

  • Piloting the integration of national sequencing centers with NFDI4Microbiota through metadata capture and data submission workflows
  • Prediction of novel gut biotransformation pathways
  • Establishment of guidelines for metaproteomics research data management and quality control
  • Empowering All Microbiome Scientists: Building Bioinformatic Proficiency for Advancing Microbiome Science Worldwide

The projects are funded on an annual basis. The 2025 Flex Funds call will be most likely opened in the mid of June 2024 and can be found on the web portal.

Recent Publications

Best practices on how to share microbiome data

Microbiome data, metadata and analytical workflows have become ‘big’ in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary and multi-omic nature of the field can make resources difficult to identify and use.

Do you want to learn more about sharing of microbiome data and the way it is analyzed? If this is the case, you should check the article “Challenges and opportunities in sharing microbiome data and analyses”, published 2023 in Nature Microbiology. NFDI4Microbiota co-speaker Alice McHardy, together with Curtis Huttenhower and Robert D. Finn, outlines in this article best practices, challenges and opportunities in sharing microbiome data. They are also calling out successful examples to date and suggest steps for future improvements.

NFDI4Microbiota – national research data infrastructure for microbiota research

Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered.

The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data.

Learn more about NFDI4Microbiota and its way to achieve its goal in the article “NFDI4Microbiota – national research data infrastructure for microbiota research” by Konrad U. Förstner, published 2023 in Research Ideas and Outcomes.

Social Links and Contact

NFDI4Microbiota is now part of the BlueSky network

To replace our now deprecated X-account, NFDI4Microbiota started a Bluesky account. Follow us on BlueSky. We are looking forward to get in touch with you there.

This newsletter is brought to you by NFDI4Microbiota



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