Newsletter Quarter 3 2025

Mattea Mueller Newsletter 2025-07-01

Dear Reader,

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

Community engagement – calls, events and conferences

The 2026 Flex Funds call is open

The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, development of new training programs, and 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 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 Flex Funds call for 2026 project proposals is now open. Detailed information on eligibility criteria, funding requirements, and the application process is available on our web portal.

Register for the NFDI4Microbiota Annual Conference 2025

We’re excited to announce that the NFDI4Microbiota Annual Conference “From Lab to Publication – Bridging the Gap with Best Practices” will take place in Cologne from 30 September to 2 October 2025. This free, open-to-all event will feature hands-on workshop sessions covering everything from microbiome analysis without coding skills to best practices in research data management, alongside scientific talks that explore the latest tools and FAIR data practices. Whether you’re working at the bench as a wet-lab scientist, developing pipelines as a bioinformatician, or ensuring FAIR compliance as a data steward, you’ll find practical training, inspiring presentations, and ample networking opportunities. Program details and registration information can be found here.

International Virus Bioinformatics Meeting (ViBioM), 13–15 May 2025, Lisbon, Portugal

NFDI4Microbiota was represented at the international ViBioM, Virus Bioinformatics Meeting, in Lisbon. Many members of this vibrant microbial sub-community were very interested in the general infrastructure services, RDM training, and especially databases like VirJenDB. We also strengthened our existing connections to our international partner consortia at GSC, NMDC, and ICTV. Our consortium presented posters that sparked engaging discussions around data management best practices and microbial data integration. Additionally, an outlook talk highlighted our strategic vision for advancing FAIR principles and enhancing data interoperability within microbiome research. We also had a outlook talk by Noriko Cassman from the Friedrich-Schiller-University Jena at the RdRp summit, the satellite event of ViBiom about sharing best practices on RdRp-based virus discovery.

NFDI4Microbiota booth at ViBioM 2025: Clemens Thölken, Paul Klemm and Marlina Indrayani from Philipps-Universität Marburg.

Recap on the 7th NFDI4Microbiota Community Workshop

The 7th edition of the NFDI4Microbiota Community Workshop took place in May, offering an important opportunity for exchange as the consortium prepares its renewal proposal for the next funding phase. The workshop focused on gathering direct feedback from the community to help align future work with actual needs. Key discussion points revealed a strong demand for improved communication, targeted training, and better support for workflow development. Participants emphasized the need for real-time communication platforms to strengthen collaboration and knowledge sharing. There was a clear call for more accessible, self-paced training materials—particularly on FAIR data management practices. Wet-lab researchers highlighted the need for hands-on support in implementing FAIR protocols, suggesting initiatives like “Do-a-thons” and the use of standardized templates via platforms such as protocols.io. Infrastructure developments like ARUNA are progressing, yet participants noted that improved interoperability and alignment on metadata standards across systems are essential. Additionally, community-driven development of analysis pipelines (e.g., via nf-core) and the use of flexible platforms like Galaxy were seen as key opportunities to better support research workflows. Looking ahead, NFDI4Microbiota will further explore real-time communication tools, expand training offerings, and continue to engage with the community to identify priorities. Community members are warmly invited to share ideas, feedback, and needs to help shape the next phase of NFDI4Microbiota’s journey.

Upcoming Events

We will attend different events this year - find some of them below - and are looking forward to meet you there:


Join the ambassador meetings

Do you know our Ambassador Program? The mission of the NFDI4Microbiota consortium is to serve as the central hub in Germany, providing essential support to the microbiology community by facilitating access to data, analysis services, data/meta-data standards, and training. To fulfill this mission, we are running the NFDI4Microbiota Ambassador Program, dedicated to connecting and training (early career) researchers within the microbiology community. As part of our commitment, we aim to assist young scientists in expanding their research networks and disseminating knowledge on data handling, metadata standards, standardized bioinformatics workflows and further related topics. Join us in our Ambassador Program for networking and spreading FAIR principles and openness in microbiome research! For our Ambassadors, we host bimonthly Ambassador meetings with interesting topics. The next meeting will be announced soon! Get your updates and more information on the program here.

Take a break and join our Coffee Talks

The Coffee Talk 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. Get your updates and more information on the schedule and registration information here.

Services

Ask your questions to our Helpdesk!

The NFDI4Microbiota Helpdesk is the point of contact for the microbiology research community for all questions related to microbial (omics) data and associated metadata. We welcome questions from anyone - students, researchers, data stewards and more - working with this type of data, regardless of organism (bacteria, archaea, eukaryotic microorganisms, viruses), environment (e.g. soil, plants, host-associated and water) or data type (e.g. nucleic acid sequences, functional genomics, image data). You can contact us either by filling in our contact form or by email: helpdesk@nfdi4microbiota.de.

Training announcements

We updated the Training section on our website! Now you get a more comfortable view on the interesting training events, courses and workshops to come. Check it out!

The next courses are

Recent Publications

Advances in Anaerobic Cultivation for Functional Microbiome Research

This perspective highlights cutting-edge biotechnological advances that usher in a new era of anaerobic cultivation and propel functional microbiome research forward. It covers high-throughput isolation and characterization methods, genetic engineering approaches, parallel continuous culture systems, and multiplex molecular profiling techniques. The focus is on gut microbial communities dominated by strict anaerobes that play crucial roles in human health. Technical and infrastructural challenges involved in deploying these advanced cultivation workflows are also discussed. DOI: 10.1038/s41587-025-02660-6

The Human Intestinal Bacteria Collection (HiBC)

Introducing HiBC: a publicly accessible library of 340 bacterial strains isolated from the human gut. This collection spans 198 species across seven phyla and includes 29 newly described and named taxa. The study also sheds light on plasmid prevalence and diversity within the gut microbiome as nearly half (46 %) of the strains harbor plasmids, including common pBAC elements and large “megaplasmids” such as pMMCAT. Additionally, butyrate production was profiled across various Faecalibacterium strains, revealing substantial strain-specific variation. DOI: 10.1038/s41467-025-59229-9

The CAMI Benchmarking Portal for Metagenomic Software

Choosing the right tools and their optimal settings for shotgun metagenome analysis is critical but often daunting. Since 2015, the community-driven Critical Assessment of Metagenome Interpretation (CAMI) initiative has set standards, provided gold-standard datasets, and organized benchmarking challenges. Until now, however, evaluations were performed offline, demanding significant time, expertise, and leaving gaps between challenge rounds.

The new CAMI Benchmarking Portal has been launched, a web-based, FAIR-compliant repository and evaluation server. Users can upload assembly, binning, or taxonomic profiling results and instantly compare them against 28,675 existing submissions including a live demo on the marine dataset from the CAMI II challenge using rich metrics and interactive visualizations. This streamlined platform democratizes benchmarking, accelerates best-practice adoption, and keeps metagenomic tool development moving forward. DOI: 10.1093/nar/gkaf369

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