- Nfdi4microbiota-announce

NFDI4Microbiota Coffee Tandem Talk - Bas E. Dutilh & Noriko Cassman

by Magel, Maja

Dear virology & microbiology enthusiasts, we warmly invite you to our next Tandem Coffee Talk, where NFDI4Microbiota aims to connect current microbiome research practices with research data management (RDM) services in a practical and accessible way. This time with insights into Viral Ecology and Omics research with our guest speaker Prof. Dr. Bas E. Dutilh (University of Jena, Excellence Cluster "Balance of the Microverse") and Dr. Noriko Cassman (NFDI4Microbiota's VirJenDB, University of Jena). 🕒 Time: Monday, February 23rd, 14:00 – 15:00 CET/ CEST (Berlin time) 💻 Join here via Zoom<https://rwth.zoom-x.de/j/69637480434?pwd=aq6VlWq8JB8w3W4OJ3P3pI7aQcRahP.1> Meeting ID: 696 3748 0434 Passcode: 760425 In this talk, Prof. Dr. Bas E. Dutilh will show how curated big data enables us to learn phage–host interactions at scale to answer fundamental questions in viral ecology and microbiome research. His work highlights how interoperable data resources can transform metagenomics from descriptive cataloguing into predictive, system-level insight. High-throughput sequencing has generated an unprecedented volume of data — but researcher-submitted datasets in public repositories require extensive curation and quality control before they can be reliably reused. Addressing this challenge, VirJenDB - presented by Dr. Noriko Cassman - offers a user-friendly platform for versioned, community-driven curation and ontology development. Virus sequences were ingested from 16 sources, integrating ~200 metadata fields covering taxonomy, sample, and host information, with curated metadata now linked to 15.4 million virus sequences. We warmly invite PIs and researchers interested in interdisciplinary, data-driven research to join the discussion and explore how curated big data can accelerate discoveries in phage–host biology. [Find more information on our <b>Coffee Talk series</b> here.] ________________________________ ☕ Grab your coffee and join us online! We look forward to learning state-of-the art research and exchanging ideas how good scientific data practices can empower the virology research community. The NFDI4Microbiota Outreach Team Carmen (Paulmann), Lina (Junctorius) und Maja (Magel) Interested in more talks? Join our NFDI4Microbiota Coffee Talk series 2026!<https://nfdi4microbiota.de/community/coffee_talk_series/> Website<https://nfdi4microbiota.de/> | Helpdesk <https://nfdi4microbiota.de/de/support/helpdesk/> | LinkedIn<http://www.linkedin.com/company/nfdi4microbiota>| GitHub<https://ddei5-0-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2…> | Mastodon<https://nfdi.social/@NFDI4Microbiota> | BlueSky<https://bsky.app/profile/nfdi4microbiota.bsky.social> You want to stop receiving NFDI4Microbiota's e-mails? Please write to contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> to unsubscribe from the mailing list.

2 weeks, 4 days

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NFDI4Microbiota Newsletter Quarter 1/2026

by Paulmann, Carmen

[cid:image005.png@01DC7F10.51AF4EC0] View the optimized display by clicking here<https://nfdi4microbiota.de/newsroom/newsletters/2026-q1/>. Newsletter Quarter 1 2026 2025-01-06 [Example Image] Dear Reader, With our 14th 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!<https://wp-dev.nfdi4microbiota.de/support/helpdesk/> And now: Enjoy reading the newsletter! Consortium News ________________________________ A foreword from the NFDI4Microbiota Board of Directors [cid:image008.png@01DC7F10.51AF4EC0]As we begin 2026, we take a moment to look back on a remarkable year for NFDI4Microbiota. The year 2025 was marked by several achievements, and we are deeply grateful for the contributions by the supporting scholarly societies, participants and partners, which made it all possible. Reflecting on the past year, we are especially proud to have passed our mid-term evaluation in January 2025 with flying colors, earning high praise from the reviewers. This milestone set the tone for a [NFDI4Microbiota Board of Directors: Prof. Alice McHardy (right) and Prof. Konrad Förstner (left).] year of continued success. Our key services, launched as part of our program, not only met but exceeded expectations, attracting impressive user numbers throughout 2025. These services are now established as supporting tools for FAIR and open research in microbiology in Germany, Europe and beyond. Alongside them, our training and outreach activities, the service helpdesk, the knowledge base, and our use cases have all flourished - with even further developments on the horizon for the final year of our first funding period. We also strengthened our collaborations with other NFDI consortia in the life sciences and expanded our activities within the BioMed and Biodata interest groups, to generate solutions for the broader scientific community. Furthermore, we contributed in the discussions regarding the future structure and governance of NFDI always with the vision of “One NFDI” in mind. A particular highlight was our annual conference in Cologne, which brought together numerous community members for learning, networking, and meaningful exchange. As we look ahead, we are awaiting the outcome of our second proposal, hoping to continue our mission into the future. Until then, we wish you all a year filled with success, health, and happiness in 2026! Defense of the NFDI4Microbiota second funding phase proposal [cid:image013.jpg@01DC7F10.51AF4EC0] [NFDI4Microbiota partners presented our working progam for the next funding phase to the DFG reviewers: Prof. Alexander Goesmann (JLU), Prof. Alexander Sczyrba (Bielefeld University), Prof. Manja Marz (FSU Jena), Prof. Konrad Förstner (ZB MED), Prof. York Sure-Vetter (NFDI e.V.) and Prof. Alice McHardy (HZI).] After successfully submitting our renewal proposal for the second funding phase, we presented and defended it before the DFG reviewers in October 2025. The discussion was highly constructive and offered valuable insights into both our past achievements and our plans for the coming years. If the evaluation is positive, our work will continue from October 2026 onward. The consortium sincerely thanks the reviewers and the DFG for their time and thoughtful feedback, as well as NFDI e.V. for its continuous support. We are excited about the road ahead! BioMed Interest Group strengthens collaboration on the path to One NFDI [Example Image]The NFDI BioMed interest group – jointly formed by GHGA, NFDI4BIOIMAGE, NFDI4Health, NFDI4Immuno and NFDI4Microbiota – aims at advancing biomedical data management across NFDI. The workshop was held from December 2-4, 2025 at ZB MED Cologne to define next steps for continued collaboration. During the strategy workshop, the consortium speakers explored how BioMed can contribute to a more unified structure within the broader NFDI, and developed a shared definition of services. In the outreach session, several action points for future [Prof. Konrad Förstner (NFDI4Microbiota) and Prof. Juliane Fluck (NFDI4Health) at the workshop of the NFDI BioMed interest group.] collaboration were refined. The existing services and training catalogs are being consolidated to identify overlaps and synergies. Additionally, the user’s need for a shared metadata platform is being assessed through a survey. Finally, existing offers for helpdesk and websites are being enhanced by referring to the other consortia. The workshop further strengthened connections within the BioMed interest group and was a step towards the vision of One NFDI. Community engagement – calls, events and conferences ________________________________ Joint NFDI4Microbiota Annual Conference 2026 [Example Image] Save the date for the 5th NFDI4Microbiota Annual Conference on September 15 -17, 2026! This year, the conference will be a joint event organized together with other life science consortia of the NFDI biodata interest group, highlighting the full spectrum of NFDI biodata services. Stay tuned—more details will be announced soon! Meet us at the VAAM and DGE 2026 We are excited to meet our research community in March 2026 at the Annual Conference of the Association for General and Applied Microbiology<https://vaam-kongress.de/> (VAAM) and at the Conference of the German Nutrition Society<https://www.dge.de/veranstaltungen/kongresse/63-wissenschaftlicher-kongress/> (DGE), which will focus on nutrition and the microbiome this year. NFDI4Microbiota will have a booth at both events and will also host a lunch symposium at the VAAM 2026. Join us to learn more about FAIR-compliant research data management and analysis in microbiology! Impressions from the NFDI4Microbiota Annual Conference 2025 [Example Image]The fourth NFDI4Microbiota Annual Conference took place from September 30 to October 2, 2026, at ZB MED in Cologne. We were delighted to welcome around 50 external participants from our community, including PIs, data stewards, bioinformaticians, and early career researchers. Several attendees also joined our Ambassador Program, which aims to connect and train scientists across the microbiology community. [Group picture of all attendees at the NFDI4Microbiota Annual Conference.] [Example Image]Across nine hands-on workshops, we taught FAIR research data management and microbiological data analysis and discussed how participants can apply these principles in their daily work. Many attendees highlighted that they especially appreciated the introductory, easy-to-follow workshop formats, the hands-on elements, and the opportunity to reflect on their own research practices. The poster session proved to be a lively networking space, and the diversity of topics and participants (from wet lab to dry lab to data stewardship) was frequently mentioned as a major strength of the event. [Lively and friendly mood at the poster session.] [Example Image]Our three keynote speakers — Samantha Pearman-Kanza, Alexandre Smirnov, and Ruth Schmitz-Streit — provided inspiring insights into implementing Electronic Lab Notebooks, practical, real-world examples of FAIR implementation, and current trends in microbiology research. A panel discussion on the intersection of AI and wet-lab science also drew great interest. Overall, the conference was described as “refreshing,” “friendly,” and “inspiring,” with participants emphasizing the importance of discussing FAIR practices across all career stages, from students to PIs. We [Dr. Alexandre Smirnov (University of Strasbourg) shared inspiring insights into how he set up a FAIR lab.] thank everyone for their contributions, ideas, and enthusiasm, and we look forward to continuing this journey together. [Example Image] [Panelists of the discussion “Wet-Lab Meets AI – How and Where?” moderated by Dr. Ulisses Nunes da Rocha: Dr.. Alexandre Smirnov (University of Strasbourg), Prof. Alice McHardy (HZI), Dr. Lorenz Reimer (DSMZ), and Dr. Ines Krohn (University of Hamburg).] Recap on recent workshops and conferences The 4th biannual NFDI4Microbiota Knowledge Base Sprint was held as a lunch-to-lunch hybrid event, based in Jena, on November 24-25, 2025. There were 15 participants across the two days, whose contributions resulted in 48 git commits and 29 files updated. We had nice discussions and coffee breaks together online, and in person shared a tour around the new office building in Jena. The knowledge base<https://knowledgebase.nfdi4microbiota.de/> 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. On October 7, 2025, researchers met at the Center for Molecular Biosciences in Kiel for the Biometadata-05 Workshop<https://events.hifis.net/event/2672/overview>, “How to describe biological data? A primer to a FAIR approach for now and the future.” Organized by NFDI4Microbiota and hosted by miTarget<https://www.mitarget.org/>, the workshop provided a practical introduction to creating FAIR-compliant microbiome metadata. Participants learned how to use controlled vocabularies and ontologies to describe biological datasets, practiced annotating metadata for their own projects, and discussed common challenges such as mapping experimental details to standard fields or documenting missing information. Well-structured metadata is essential for reproducible and reusable microbiome research, and the workshop helped equip attendees with the skills needed to prepare and share high-quality metadata. Looking ahead, participants are encouraged to apply these practices in their ongoing projects and future data submissions. Find more impressions from the workshop here<https://www.mitarget.org/2025/10/bringing-fair-metadata-to-life-in-microbio…>. [cid:image026.jpg@01DC70E7.B2F550D0] Biometada Workshop at the Center for Molecular Biosciences in Kiel. SFBs and research institutes interested in FAIR biometadata training in 2026 are welcome to contact us via the NFDI4Microbiota helpdesk<https://nfdi4microbiota.de/support/helpdesk/>. Refinement of the NFDI4Microbiota Ambassador Program [Example Image]The NFDI4Microbiota Ambassador Program<https://nfdi4microbiota.de/community/ambassador/> helps us establish direct connections with local institutes and research initiatives within the microbial research community. This network is essential for driving the cultural change in microbial research data management, as our Ambassadors actively promote our mission and inform their local communities about our services including training opportunities and individual support via our helpdesk. At the same time, we greatly benefit from the valuable feedback they provide, which helps us continuously improve our services. To further strengthen our collaboration, we will restructure our bi-monthly Ambassador meetings to foster a more interactive and [Survey-based overview (July/August 2025) of the functional roles of NFDI4Microbiota Ambassadors.] informal environment and to address topics relevant to the different user personas illustrated in the graphic and described on our website<https://nfdi4microbiota.de/community/personas/>. You can find more information about the Ambassador Program on our website<https://nfdi4microbiota.de/community/ambassador/> or register directly here<https://survey.nfdi4microbiota.de/index.php/158936?lang=en>. Take a break and join our Coffee Talks [Example Image]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<https://wp-dev.nfdi4microbiota.de/community/coffee_talk_series/>. Services ________________________________ To support the microbial research community in data management and analysis, the NFDI4Microbiota consortium has established a range of dedicated services. Visit our persona<https://nfdi4microbiota.de/community/personas/> webpage to explore which services are available for you as a wet-lab scientist, bioinformatician, data steward, or PI, or find an overview of all our services here<https://nfdi4microbiota.de/services/>. Protologger is back online Protologger<https://protologger.bi.denbi.de/> — a central tool of the NFDI4Microbiota use case “TAXA”<https://nfdi4microbiota.de/usecases/taxa> that automates bacterial protologue generation to ensure standardized taxonomic descriptions — is now fully accessible again. We apologize for any inconveniences this has caused! Due to recent technical issues, users will need to create a new account to continue using the service. The issue has been resolved, and new monitoring measures are in place to prevent similar downtime in the future. Give it a try and let us know if you encounter any problems! Two NFDI4Microbiota co-funded services recognized as official de.NBI services We are pleased to announce that two services co-funded by NFDI4Microbiota have recently been acknowledged as official services within the de.NBI network: CloWM<https://clowm.bi.denbi.de/> and the MdoA tool box<https://mdoa-tools.bi.denbi.de/home>. This recognition is an important milestone. Inclusion in the de.NBI service portfolio is not automatic, it follows a strict evaluation process designed to ensure that all services meet high scientific, technical, and community standards. According to de.NBI’s assessment principles<https://www.denbi.de/images/Service/deNBI_ELIXIR_DE_Guidelines_ServiceSelec…>, services must remain dynamic, relevant, up-to-date, and aligned with the evolving needs of life science researchers. Continuous evaluation and maintenance ensure optimal performance and adherence to rigorous scientific criteria. Ask your questions to our Helpdesk! [Example Image] 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<https://wp-dev.nfdi4microbiota.de/support/helpdesk/> or by email: helpdesk(a)nfdi4microbiota.de<mailto:helpdesk@nfdi4microbiota.de>. Training announcements ________________________________ [Example Image]Education and training are key goals within NFDI4Microbiota. To support our community, the consortium offers training opportunities on a variety of topics and across different disciplines. Explore our training offers here<https://nfdi4microbiota.de/services/trainings/>. If you like to stay up to date on training opportunities in research data management for the life sciences, we recommend to subscribe to this mailing list<https://lists.nfdi.de/postorius/lists/training4lifescience.lists.nfdi.de/> offered by NFDI and designed to keep professionals, students, and researchers in the biosciences regularly informed about upcoming training sessions, workshops, and continuing education opportunities. Publications ________________________________ StrainInfo—the central database for linked microbial strain identifiers In microbiology, the communication and comparison of research findings and data is often complicated by the existence of a number of different designations and identifiers for the same strain. StrainInfo is a service developed by NFDI4Microbiota to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and deposition data. An article has been recently published and discusses the new StrainInfo database<https://straininfo.dsmz.de/>, developed to address the challenges of microbial strain identifiers across scientific literature and databases. By consolidating and standardizing strain data from multiple sources, StrainInfo improves the findability, reusability, and integration of published information related to strains. DOI: 10.1093/database/baaf059<https://doi.org/10.1093/database/baaf059> . Metalog: curated and harmonised contextual data for global metagenomics samples [Example Image]Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ [Graphical Abstract from Nucleic Acids Res, gkaf1118. © The Author(s) 2025. Published by Oxford University Press.] observations impedes cross-study comparisons and metaanalyses. The authors of this article therefore created the Metalog database<https://metalog.embl.de/>, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. DOI: 10.1093/nar/gkaf1118<https://doi.org/10.1093/nar/gkaf1118> . Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu) Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. In this study, the authors evaluated the commonly used Percentage of Conserved Proteins (POCP) and an improved version, POCPu which considers unique matches only, across 2.3 million proteome comparisons from 4,767 genomes. Using DIAMOND, POCPu run 20× faster than BLASTP and differentiates better within-genus from between-genera values than POCP, which improves bacterial genus assignment. DOI: 10.7717/peerj.20259<https://doi.org/10.7717/peerj.20259> . metaTraits: a large-scale integration of microbial phenotypic trait information [Example Image]We are excited to announce the release of metaTraits, now published in Nucleic Acids Research. metaTraits harmonizes microbial phenotypic trait data, summarizing more than 140 traits across 2.2 million genomes in a single unified resource. By combining culturebased evidence with genome-based predictions, it integrates data silos and fills [Graphical Abstract from Nucleic Acids Res, gkaf1241. © The Author(s) 2025. Published by Oxford University Press.] critical gaps for uncultured lineages. Initiated through an NFDI4Microbiota Flex Fund, metaTraits was developed by Daniel Podlesny and Chan Yeong Kim et al. from the Bork Group at EMBL Heidelberg, in collaboration with Lorenz Reimer and colleagues from the Leibniz Institute DSMZ. metaTraits provides workflows for annotating user-submitted genomes/MAGs and metagenomic profiles, and can be interactively explored at metaTraits<https://metatraits.embl.de>. DOI: 10.1093/nar/gkaf1241<https://doi.org/10.1093/nar/gkaf1241> . This newsletter is brought to you by NFDI4Microbiota [cid:image070.png@01DC7F02.E7A3DC10]<https://nfdi.social/@NFDI4Microbiota> [cid:image071.png@01DC7F02.E7A3DC10] <https://bsky.app/profile/nfdi4microbiota.bsky.social> [cid:image072.png@01DC7F02.E7A3DC10] <https://www.linkedin.com/company/98488870/admin/feed/posts/> [cid:image073.png@01DC7F02.E7A3DC10] <http://www.nfdi4microbiota.de/> Mail: contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> If you no longer wish to receive this newsletter, click here to unsubscribe.<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Forschung, Technologie und Raumfahrt Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/ <https://www.helmholtz-hzi.de/de/service/datenschutz/>

1 month, 3 weeks

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Season’s Greetings from NFDI4Microbiota & Save the Date 2026

by Paulmann, Carmen

[cid:image001.png@01DC6E7A.7D8A18A0] Dear Microbiology community, Looking back, 2025 was a highly successful year for NFDI4Microbiota. We paved the way for our future work by submitting and defending our renewal proposal for the next funding phase starting in October 2026. We passed our mid-term evaluation with flying colors, launched widely used FAIR research services, expanded our training and outreach activities, and strengthened collaborations across NFDI life-science consortia. A major highlight was our Annual Conference in Cologne, which brought the community together for exchange and networking. Please also save the date for our upcoming Annual Conference, 15–17 September 2026, which we will co-organize with other NFDI consortia of the Biodata Interest Group. Mark your calendars and stay tuned, more information coming soon! We wish you a peaceful Christmas, relaxing holidays, and a great start to a healthy and successful 2026. Best regards, The NFDI4Microbiota Consortium ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Forschung, Technologie und Raumfahrt Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/ <https://www.helmholtz-hzi.de/de/service/datenschutz/>

2 months, 2 weeks

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NFDI4Microbiota Coffee Talk: Access Control, Data Protection & Security in Digital Microbiology Research

by Magel, Maja

Dear microbiome researchers, data stewards, and digital microbiology enthusiasts, How can we make microbiology research both open and secure? Join us for our final NFDI4Microbiota Coffee Talk of the year to explore practical strategies for data protection, access control, and secure data management in microbiome research. This session, led by Justine, will provide real-world guidance drawn from current best practices and community standards — helping you understand how to manage and share your research data responsibly while staying FAIR-compliant. ________________________________ 📢 Talk: Access Control, Data Protection & Security in Digital Microbiology Research presented by Justine Vandendorpe (ZB MED - Information Centre for Life Sciences) 📅 Date: Monday, 15 December 2025 🕒 Time: 14:30 – 15:30 CET (Berlin time) 💻 Join here via Zoom<https://rwth.zoom-x.de/j/69637480434?pwd=aq6VlWq8JB8w3W4OJ3P3pI7aQcRahP.1> Meeting ID: 696 3748 0434 Passcode: 760425 ________________________________ Target audience * Wet-lab and bioinformatic microbiologists aiming to improve how they handle, share, and secure research data. * Data stewards and NFDI4Microbiota ambassadors seeking practical examples of policy implementation and secure data workflows. ________________________________ ☕ Grab your coffee and join us online! We look forward to seeing you and discussing how secure, FAIR data practices empower the microbiome community. The NFDI4Microbiota Outreach Team Carmen (Paulmann), Lina (Junctorius) und Maja (Magel) https://nfdi4microbiota.de

2 months, 2 weeks

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[Dec 15th] NFDI4Microbiota Coffee Talk: Access Control, Data Protection & Security in Digital Microbiology Research

by Magel, Maja

Thank you for sharing the event with your colleagues! Dear microbiome researchers, data stewards, and digital microbiology enthusiasts, How can we make microbiology research both open and secure? Join us for our final NFDI4Microbiota Coffee Talk of the year to explore practical strategies for data protection, access control, and secure data management in microbiome research. This session, led by Justine, will provide real-world guidance drawn from current best practices and community standards — helping you understand how to manage and share your research data responsibly while staying FAIR-compliant. ________________________________ 📢 Talk: Access Control, Data Protection & Security in Digital Microbiology Research presented by Justine Vandendorpe (ZB MED - Information Centre for Life Sciences) 📅 Date: Monday, 15 December 2025 🕒 Time: 14:30 – 15:30 CET (Berlin time) 💻 Join here via Zoom<https://rwth.zoom-x.de/j/69637480434?pwd=aq6VlWq8JB8w3W4OJ3P3pI7aQcRahP.1> Meeting ID: 696 3748 0434 Passcode: 760425 ________________________________ Target audience * Wet-lab and bioinformatic microbiologists aiming to improve how they handle, share, and secure research data. * Data stewards and NFDI4Microbiota ambassadors seeking practical examples of policy implementation and secure data workflows. ________________________________ ☕ Grab your coffee and join us online! We look forward to seeing you and discussing how secure, FAIR data practices empower the microbiome community. The NFDI4Microbiota Outreach Team Carmen (Paulmann), Lina (Junctorius) und Maja (Magel) Warm regards, Maja (Magel) The NFDI4Microbiota Outreach Team Carmen Paulmann, Lina Junctorius, Maja Magel Website<https://nfdi4microbiota.de/> | Helpdesk <https://nfdi4microbiota.de/de/support/helpdesk/> | LinkedIn<http://www.linkedin.com/company/nfdi4microbiota>| GitHub<https://ddei5-0-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2…> | Mastodon<https://nfdi.social/@NFDI4Microbiota> | BlueSky<https://bsky.app/profile/nfdi4microbiota.bsky.social> You want to stop receiving these e-mails? Please write to contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> to unsubscribe from the mailing list. _ _ _ Maja Magel https://nfdi4microbiota.de/ Project coordination NFDI4Microbiota Institute for Medical Microbiology Research Group Functional Microbiome ________________________________________ Tel.: +49 (0) 241 80-38117 E-Mail: mmagel(a)ukaachen.de<mailto:mmagel@ukaachen.de> Elevator D4, Floor 5, Room 34 Universitätsklinikum Aachen Pauwelsstraße 30 52074 Aachen Germany

2 months, 4 weeks

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BacDive online workshop | 24th November 2025

by Isabel Schober

Dear colleagues and Bac/Dive/ users, we would like to invite you to this year's *Bac**/Dive/**workshop*, which will take place on *24th November 2025, 3 - 5 PM CET, online*. This workshop will give a short introduction to *the new **Bac/Dive/ website <https://beta.bacdive.dsmz.de>* and a first look at the soon-to-be-introduced *genome browser*. We are especially looking forward to the opportunity to answer your questions, discuss Bac/Dive/ with you, and hear your feedback and ideas. *No registration is needed!* Just join us on Zoom. *https://dsmz-de.zoom-x.de/j/66404609966?pwd=rTDkdH7W85eOWfOvFqYwNiGHIUvzgG.1* <https://dsmz-de.zoom-x.de/j/66404609966?pwd=rTDkdH7W85eOWfOvFqYwNiGHIUvzgG.1> *Meeting-ID: 664 0460 9966** * *Kenncode: 912611 * Feel free to forward this invitation to interested colleagues. We are looking forward to seeing you there! Team Bac/Dive/ -- Dr. Isabel Schober DSMZ Digital Diversity - Team BacDive Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstr. 7 B 38124 Braunschweig Germany Tel. +49531-2616-423 Fax +49531-2616-418 www.dsmz.de Management: Prof. Dr. Yvonne Mast (Interim Director), Bettina Fischer Local court: Braunschweig HRB 2570 Chairman of the management board: MR Dr. David Schnieders DSMZ - A member of the Leibniz Association www.leibniz-gemeinschaft.de

3 months, 3 weeks

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[24-25th November] NFDI4Microbiota Knowledge Base Content & Coding Sprint

by Magel, Maja

Dear microbiome research enthusiasts, Data Stewards and RDM Service providers, we warmly invite you to join our NFDI4Microbiota’s hybrid Knowledge Base and Coding Sprint on November 24-25th, 2025 online or in-person in Jena. The Knowledge Base<https://knowledgebase.nfdi4microbiota.de/> 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, improving the code or by suggesting new content and features<https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/issues>. Some ideas: You can add highly relevant tools to our bio.tools domain, add to our growing list of community-suggested Standard Operating Procedures or share how you apply RDM to your microbiology research. Requirements: * GitHub account & own laptop. * Charger and eduroam credentials are needed for the in-person attendance. GitHub newbies are welcome! We suggest to start with our "good first issues"! Register here and add your name to over 30 contributors!<https://forms.gle/aSgjhNyoUyxFysLTA> *************************** Monday, November 24th 12:00 - 13:00 Arrival 13:00 - 14:00 Welcome & Introduction 14:00 - 17:00 Coding & Content Sprint, coffee & snack breaks throughout (provided) 17:00 - 18:00 Day wrap-up 18:00 - 20:00 Walk and dinner at restaurant (self-paid) Tuesday, November 25th 09:00 - 09:30 Coffee & rolls (provided) 09:30 - 11:00 Coding & Content Sprint 11:00 - 12:00 KB Sprint wrap-up On behalf of the Sprint organizer Noriko Cassman (VirjenDB<https://www.virjendb.org/> & University Jena) Kind regards and see you at the sprint! Maja Magel https://nfdi4microbiota.de/ Projektkoordination NFDI4Microbiota Institut für Medizinische Mikrobiologie Research Group Functional Microbiome [cid:image001.png@01D7E834.38ACC870] ________________________________________ Tel.: +49 (0) 241 80-38117 E-Mail: mmagel(a)ukaachen.de<mailto:mmagel@ukaachen.de> Aufzug D4, Etage 5, Raum 34 Universitätsklinikum Aachen Pauwelsstraße 30 52074 Aachen

3 months, 3 weeks

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NFDI4Microbiota Coffee Talk

by Magel, Maja

Event reminder >>> Feel free to share this with your peers! 📢 NFDI4Microbiota Coffee Talk: Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible presented by Daniel Straub (QBiC Tübingen) 📅 Date: Monday, 27th October2025 🕒 Time: 14:30-15:30 CET (Berlin time) https://rwth.zoom-x.de/j/69637480434?pwd=aq6VlWq8JB8w3W4OJ3P3pI7aQcRahP.1 📍 Zoom Meeting ID: 696 3748 0434 🔒 Passcode: 760425 Dear microbiome research enthusiasts and bioinformatics aficionados, curious about smoother microbiome research? Grab your coffee and join us online! Reproducible, easily shareable workflows are essential for bioinformatics. This holds true for all areas of bioinformatics research, including microbiome research. To facilitate the centralized collection of high-quality Nextflow workflows, nf-core was established with strong involvement from the Quantitative Biology Center (QBiC) core facility. These workflows are used, extended, and improved by a large community in a standardized manner, making a wide range of bioinformatics analyses more accessible and easier to execute than ever before. This presentation will introduce QBiC, discuss some challenges faced, and present examples of solutions, with a focus on data analysis. PS: Struggling with nextflow and nf-core? Daniel will be offering a weekly drop-in session and offer consultation on a first come - first serve basis. More information here: Weekly Drop-in session for bioinformatics analysis with nextflow and nf-core<https://nfdi4microbiota.de/newsroom/news/2025-10-10-weekly-consultation-nex…> PPS: 📢 A new mailinglist: Offering Life Science training events beyond the microbiome universe The Life Science associated NFDIs have joined efforts in gathering and promoting relevant Life Science training events for you. 📍 If mailinglists are how you stay updated, then don't forget to subscribe! Mailing-List: training4lifescience(a)lists.nfdi.de<mailto:training4lifescience@lists.nfdi.de> Join via mail to: training4lifescience-join(a)lists.nfdi.de<mailto:training4lifescience-join@lists.nfdi.de> or subscribe with your existing Postorius-Account via: https://lists.nfdi.de/postorius/lists/training4lifescience.lists.nfdi.de/ Looking forward to Monday! Kind regards Maja (Magel) on behalf of NFDI4Microbiota's Outreach team Carmen (Paulmann), Lina (Junctorius), Mattea (Müller), Maja (Magel) https://nfdi4microbiota.de/

4 months, 1 week

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[27th October] NFDI4Microbiota Coffee Talk: Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible

by Magel, Maja

Dear microbiome research enthusiasts and bioinformatics aficionados, curious about smoother microbiome research? Grab your coffee and join us online! Reproducible, easily shareable workflows are essential for bioinformatics. This holds true for all areas of bioinformatics research, including microbiome research. To facilitate the centralized collection of high-quality Nextflow workflows, nf-core was established with strong involvement from the Quantitative Biology Center (QBiC) core facility. These workflows are used, extended, and improved by a large community in a standardized manner, making a wide range of bioinformatics analyses more accessible and easier to execute than ever before. This presentation will introduce QBiC, discuss some challenges faced, and present examples of solutions, with a focus on data analysis. 📢 NFDI4Microbiota Coffee Talk: Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible presented by Daniel Straub (QBiC Tübingen) 📅 Date: Monday, 27th October2025 🕒 Time: 14:30-15:30 CET (Berlin time) https://rwth.zoom-x.de/j/69637480434?pwd=aq6VlWq8JB8w3W4OJ3P3pI7aQcRahP.1 📍 Zoom Meeting ID: 696 3748 0434 🔒 Passcode: 760425 >>> Feel free to share this with your peers! PS: Struggling with nextflow and nf-core? Daniel will be offering a weekly drop-in session and offer consultation on a first come - first serve basis. ______________________________________________________________ ______________________________________________________________ 📢 A new mailinglist: Offering Life Science training events beyond the microbiome universe The Life Science associated NFDIs have joined efforts in gathering and promoting relevant Life Science training events for you. 📍 If mailinglists are how you stay updated, then don't forget to subscribe! Mailing-List: training4lifescience(a)lists.nfdi.de<mailto:training4lifescience@lists.nfdi.de> Join via mail to: training4lifescience-join(a)lists.nfdi.de<mailto:training4lifescience-join@lists.nfdi.de> or subscribe with your existing Postorius-Account via: https://lists.nfdi.de/postorius/lists/training4lifescience.lists.nfdi.de/ A teaser on what you can look forward to: 1. NFDI4Earth Academy Coffee lecture - "Machine Learning Fundamentals with Application Examples" (Sonja Hänzelmann & Susana Simancas Giraldo, AWI) 📅October 15th, register here<https://gfz-de.zoom.us/meeting/register/Lu8vWZhtQA2MBPLS8Wxwtg#/registration>. Content: Introduction to Machine Learning, Supervised vs. Unsupervised Learning – key concepts and use cases, Unsupervised Learning – Finding patterns in data (Clustering, Dimensionality Reduction) and Supervised Learning – Prediction models (Classification, Regression). Level: Beginner-friendly, perfect for anyone looking to better understand and apply ML methods. 1. in German: GFBio Data Submission und Brokerage Service<https://submissions.gfbio.org/> für biologische, ökologische und Biodiversitätsdaten (Dr. Ivaylo Kostadinov, Gesellschaft für Biologische Daten (GFBio e.V.) 📅October 21st, 11:00 -12:00, register here<https://www.nfdi4biodiversity.org/de/events/biodiversitea-17/>. Looking forward to Monday! Kind regards Maja (Magel) on behalf of NFDI4Microbiota's Outreach team Carmen (Paulmann), Lina (Junctorius), Mattea (Müller), Maja (Magel) https://nfdi4microbiota.de/ Maja Magel https://nfdi4microbiota.de/ Projektkoordination NFDI4Microbiota Institut für Medizinische Mikrobiologie Research Group Functional Microbiome [cid:image001.png@01D7E834.38ACC870] ________________________________________ Tel.: +49 (0) 241 80-38117 E-Mail: mmagel(a)ukaachen.de<mailto:mmagel@ukaachen.de> Aufzug D4, Etage 5, Raum 34 Universitätsklinikum Aachen Pauwelsstraße 30 52074 Aachen

4 months, 3 weeks

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NFDI4Microbiota Newsletter Quarter 4 2025

by Mueller, Mattea

Newsletter Quarter 4 2025 2025-10-02 [https://nfdi4microbiota.de/img/newsletter/fifthnewsletter/img1.png] Dear Reader, With our 13th 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!<https://nfdi4microbiota.de/support/helpdesk/> And now: Enjoy reading the newsletter! Consortium News Submission of the NFDI4Microbiota second funding phase proposal The NFDI4Microbiota consortium has submitted its renewal proposal for the second funding phase, which is scheduled to begin in October 2026, to the DFG. Building on our successful first funding phase, our aim is to expand NFDI4Microbiota’s efforts in the next phase to enhance data accessibility and reuse while enabling AI applications. Our achievements and infrastructure from the first funding period provide a solid foundation for achieving an even greater impact across the microbiology research community and fostering a seamless flow of data. We want to strengthen collaboration with existing stakeholders while actively reaching out to previously underrepresented groups, specifically researchers working on eukaryotic microbes such as fungi and protists, and we will work more closely with data-generating facilities to capture rich metadata early on. In addition, we aim to further strengthen our portfolio of services, databases, and analytical tools, ensuring that they are robust, interoperable, and tailored to evolving community needs. These enhancements will support a more comprehensive and inclusive data infrastructure for microbiological research. To help realise the One NFDI and EOSC vision of a coherent, sustainable, and collaborative research data ecosystem across all disciplines, NFDI4Microbiota will actively engage in cross-consortial initiatives, foster interoperability, and apply the unique perspectives of microbiological science to help shape the broader NFDI landscape. The consortium thanks all those who have committed to supporting the work of NFDI4Microbiota in the next funding phase as participants. ________________________________ Community engagement – calls, events and conferences Recap on recent workshops and conferences NFDI4Microbiota contributed to the 17th Seeon conference of the DGHM specialist group ‘Microbiota-Probiotics-Host’<https://www.dghm.org/seeon/> with an oral presentation and a booth. The event was marked by good food, lively discussions, and a relaxed atmosphere. Some participants even enjoyed a refreshing swim in the lake. Our surprise boxes filled with NFDI4Microbiota merchandise were especially popular – they went like hotcakes! [https://nfdi4microbiota.de/img/newsletter/2025-Q4-newsletter/Seeon.jpg] NFDI4Microbiota at the 17th Seeon Conference: Booth and oral presentation by Mattea Müller from the Helmholtz Centre for Infection Research. [Example Image] NFDI4Microbiota at the ISHPSSB: Charlie Pauvert from the Uniklinik RWTH Aachen (second from left) as invited speaker to a round-table. The ISHPSSB is one of the largest biology conference without biologists as it stands for the International Society for the History, Philosophy, and Social Studies of Biology. Nonetheless, like a few other scientists, Charlie Pauvert, member of the NFDI4Microbiota Consortium, attended the 2025 edition in Porto (PT) as an invited speaker to a round-table on how multifaceted sources of knowledge (i.e., epistemic pluralism) could improve microbiome research. Together with an historian, philosophers of biology and the audience, they reflected on, for instance, what is measurable in microbiome research and how and why do we try to do it; about the microbiome researchers’ impatience to get to causal claims when our field history tells us that it takes time. Whilst microbiology is being more discussed at the IHSPSSB (e.g., healthy microbiome concepts, AMR), another personal highlight was a rethinking of replication in biology, and how scientists are actually performing micro-replication more often than they think as part of trust-establishing practices. The NFDI4Microbiota was represented not only with merchandising, but with the well-received idea to support and guide scientists towards more reproducible research in this data-centric era. On July 1st, 2025, the Biometadata Workshop at the TUM School of Life Sciences, Freising, introduced researchers to the essentials of FAIR metadata. Through short lectures, hands-on exercises, and live demos, participants learned how to describe datasets with standardized vocabularies, validate them with the DataHarmonizer tool, and select suitable repositories for submission. Feedback emphasized the value of the practical, interactive format, particularly the individualized support and deep dive into ontologies. Organized by RWTH Aachen’s Functional Microbiome Research Group in cooperation with NFDI4Microbiota, the workshop highlighted why good metadata is the key to reproducible research. The next Biometadata Workshop will take place on October 7th, 2025, at the University of Kiel. Interested in hosting a workshop at your institution? Contact the NFDI4Microbiota Helpdesk<https://nfdi4microbiota.de/support/helpdesk/>. [https://nfdi4microbiota.de/img/newsletter/2025_Q3_newsletter/ambassador_pic…] 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<https://nfdi4microbiota.de/community/ambassador/>. Take a break and join our Coffee Talks [https://nfdi4microbiota.de/img/newsletter/ninthnewsletter/coffee_talk_800px…] 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<https://nfdi4microbiota.de/newsroom/news/2025-02-04-nfdi4microbiota-coffee-…>. Services To support the microbial community the NFDI4Microbiota consortium established different services. The provided services align with the aims and objectives and cover different topics. Find an overview here<https://nfdi4microbiota.de/services/>. Ask your questions to our Helpdesk! [https://nfdi4microbiota.de/img/newsletter/2025_Q2_newsletter/Support_orange…] 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<https://nfdi4microbiota.de/support/helpdesk/> or by email: helpdesk(a)nfdi4microbiota.de<mailto: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<https://nfdi4microbiota.de/services/trainings/>! [https://nfdi4microbiota.de/img/newsletter/ninthnewsletter/Isometric_Trainin…] The next courses are * Hands-on Biometadata: How to describe biological data? Primer to a FAIR approach for now and future<https://nfdi4microbiota.de/services/training_view/?docid=67dd67f7e68a14a121…> (University Kiel, Oct 07, 2025) * Build a nextflow based custom pipeline<https://nfdi4microbiota.de/services/training_view/?docid=6894a31e110180b6cb…> (online, Oct 09, 2025) * NFDI4Microbiota and de.NBI 16S amplicon training course<https://www.uni-giessen.de/de/fbz/fb08/Inst/algorithm-bioinformatik/teachin…> (Justus-Liebig-University Giessen, Oct 22-24, 2025) * Data Visualization for Biological Sciences<https://events.hifis.net/event/3045/> (online, Nov 18-20, 2025) * Web-based Bioinformatics & Research Data Management<https://pretix.eu/synmikro/tecmeth-bioinfo/> (Philipps-Universität Marburg, Dec 08-12, 2025) * RNA Bioinformatics<https://pretix.eu/synmikro/tecmeth-rna/> (Philipps-Universität Marburg, Feb 09-11, 2026) * RNA-Seq Data Processing<https://pretix.eu/synmikro/tecmeth-rnaseq/> (Philipps-Universität Marburg, Mar 09-13, 2026) If you like to stay up to date on training opportunities in research data management for the life sciences, we recommend to subscribe to this mailing list<https://lists.nfdi.de/postorius/lists/training4lifescience.lists.nfdi.de/> offered by NFDI and designed to keep professionals, students, and researchers in the biosciences regularly informed about upcoming training sessions, workshops, and continuing education opportunities. Social Links and Contact ________________________________ This newsletter is brought to you by NFDI4Microbiota Mail: contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> Web: www.nfdi4microbiota.de<https://www.nfdi4microbiota.de/> If you no longer wish to receive this newsletter, click here to unsubscribe.<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> Follow us Mastodon<https://nfdi.social/@NFDI4Microbiota> LinkedIn<https://www.linkedin.com/company/98488870/admin/feed/posts/> BlueSky<https://bsky.app/profile/nfdi4microbiota.bsky.social> GitHub<https://github.com/NFDI4Microbiota> ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Forschung, Technologie und Raumfahrt Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/ <https://www.helmholtz-hzi.de/de/service/datenschutz/>

5 months

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2026

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Nfdi4microbiota-announce