- Nfdi4microbiota-announce

[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

5 months, 1 week

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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/

6 months

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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

6 months, 2 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/>

6 months, 3 weeks

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Save the date | 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 and a first look at the soon-to-be-introduced genome browser. Participants will have the opportunity to ask questions, give feedback, and contribute ideas. The workshop will be held online, via Zoom. Further information and login details will be sent out in November through the same mailing lists. We look forward to discussing Bac/Dive/ with you! 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

7 months, 2 weeks

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Registration for the NFDI4Microbiota Annual Conference 2025 extended – register until September 11!

by Paulmann, Carmen

Dear NFDI4Microbiota Followers, Good news: You still have time to register for the NFDI4Microbiota Annual Conference 2025 in Cologne! The registration deadline has been extended until September 11. Conference at a glance: * When: September 30 – October 2, 2025 * Where: ZB MED – Information Centre for Life Sciences, Cologne, Germany * Registration Period: June 30 – September 11, 2025 (midnight CEST) 🔗 Infos, Program and Registration: <https://events.hifis.net/event/2654/registrations/> https://events.hifis.net/e/NFDI4Microbiota_annual_conference_2025 This event is the central meeting point for everyone involved in microbiome research or data management within the NFDI4Microbiota community and beyond. Whether you're a researcher, data steward, developer, or simply interested in microbiota data infrastructures, this conference offers a unique opportunity to engage, learn, and collaborate. Highlights include: * Keynote speeches on microbiome research and FAIR labs (Ruth Schmitz-Streit, Alexandre Smirnov, Samantha Pearman-Kanza) * Hands-on Workshop<https://events.hifis.net/event/2654/page/819-workshops> Tracks: * From Bench to Browser: Microbiome Analysis Without Coding Skills * From Lab Bench to Data Bench: Practical Research Data Management for Scientists * From Pipelines to Portals: Next-Generation Tools for Microbiome Analysis * Opportunities for networking and community building across disciplines Participation in the conference is free of charge. Become an NFDI4Microbiota Ambassador and we will cover your hotel and travel expenses when you present a poster. Learn more about the Ambassador program here: https://nfdi4microbiota.de/community/ambassador.html If you have any questions, please contact us at contact(a)nfdi4microbiota.de. We look forward to welcoming you in Cologne! Best regards, The NFDI4Microbiota Conference Team [cid:b84910b0-41af-495e-bd33-3adbe774da5c] ________________________________ 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/>

7 months, 3 weeks

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[25th August] NFDI4Microbiota Coffee Talk: Getting Your Microbiome Research on the Road – Managing Your Data using Qiita

by Magel, Maja

Dear microbiome research enthusiasts, curious about smoother microbiome research? Grab your coffee and join us online! After planning your experiment, collecting samples, and sequencing them, analysing your microbiome data can seem like a daunting next step. After all, there are many steps to consider! Join us for a relaxed coffee talk where we’ll walk you through a typical workflow with our wetlab partners and introduce Qiita—a user-friendly, browser-based platform for managing amplicon sequencing files and metadata. Learn how to use pre-defined or custom workflows and even publish your data to ENA! Target audience: Wetlab and non-computational scientists responsible for their own data analysis and data deposition. 📢 NFDI4Microbiota Coffee Talk: Getting Your Microbiome Research on the Road – Managing Your Data using Qiita presented by Stefan Janssen and Anna Rehm (JLU Gießen) 📅 Date: Monday, 25th August 2025 🕒 Time: 14:30-15:30 CEST/ 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: Interested in hands-on experience? There’s also the opportunity to join our practical data processing and analysis workshop based on this session in Gießen, October 22nd-24th. Find out more about the training course here: Workshop details<https://nfdi4microbiota.de/services/training_view.html?docid=687f570de793b2…> 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/

8 months, 2 weeks

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REMINDER: Registration for the NFDI4Microbiota Annual Conference 2025 in Cologne is still open!

by Paulmann, Carmen

Dear NFDI4Microbiota followers, We warmly invite you to the <https://events.hifis.net/e/NFDI4Microbiota_annual_conference_2025> NFDI4Microbiota Annual Conference 2025—“From Lab to Publication: Bridging the Gap with Best Practices"! Conference at a glance: * When: September 30 – October 2, 2025 * Where: ZB MED – Information Centre for Life Sciences, Cologne, Germany * Registration Period: June 30 – August 31, 2025 (midnight CEST) 🔗 Infos, Program and Registration: <https://events.hifis.net/event/2654/registrations/> https://events.hifis.net/e/NFDI4Microbiota_annual_conference_2025 This event is the central meeting point for everyone involved in microbiome research or data management within the NFDI4Microbiota community and beyond. Whether you're a researcher, data steward, developer, or simply interested in microbiota data infrastructures, this conference offers a unique opportunity to engage, learn, and collaborate. Highlights include: * Keynote speeches on microbiome research and FAIR labs (Ruth Schmitz-Streit, Alexandre Smirnov, Samantha Pearman-Kanza) * Hands-on Workshop<https://events.hifis.net/event/2654/page/819-workshops> Tracks: * From Bench to Browser: Microbiome Analysis Without Coding Skills * From Lab Bench to Data Bench: Practical Research Data Management for Scientists * From Pipelines to Portals: Next-Generation Tools for Microbiome Analysis * Opportunities for networking and community building across disciplines Participation in the conference is free of charge. Become an NFDI4Microbiota Ambassador and we will cover your hotel and travel expenses when you present a poster. Learn more about the Ambassador program here: https://nfdi4microbiota.de/community/ambassador.html If you have any questions, please contact us at contact(a)nfdi4microbiota.de. We look forward to welcoming you in Cologne! Best regards, The NFDI4Microbiota Conference Team [cid:703fe221-7298-4f46-aa2c-d0da0dbeed5b] ________________________________ 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/>

8 months, 3 weeks

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This Monday: FAQ session for the Flex Fund Call Application by NFDI4Microbiota

by Magel, Maja

Dear microbiology research enthusiasts, next Monday, we will be presenting and discussing funding opportunities for your project ideas that are aligned with NFDI4Microbiota's vision of supporting the microbiology community with access to data, analysis services, data/metadata standards and training. More information below! 📢 FAQ session for the Flex Fund Call Application – We Want to Fund Your Project! 📅 Date: Monday, July 28th 2025 ⏰ Time: 14:30-15:30 CEST/ CET (Berlin time) https://rwth.zoom-x.de/j/66301103523?pwd=iUU3vLtvvWwlZGMapBtmvzOKXa1QIG.1 📍 Zoom Meeting ID: 663 0110 3523 🔒 Passcode: 166876 >>> Feel free to share with your peers! These past few weeks have been excitingly intense for our NFDI4Microbiota partners. All our service developers have spent their time extensively fine-tuning our current selection of core services and are now taking a well-deserved vacation in preparation for our Annual Conference "<https://events.hifis.net/event/2654/>From Lab to Publication – Bridging the Gap with Best Practices<https://events.hifis.net/event/2654/>”<https://events.hifis.net/event/2654/> taking place from 30 September to 2 October 2025 in Cologne. It will be fun, don't forget to register! Speaking of funding opportunities: Do you have a great idea or project that could advance microbiology research infrastructure or data management? The NFDI4Microbiota Flex Funds Call 2026 is now open until August 11, 2025—offering flexible funding for small projects and community-driven Use Cases. Whether you’re working on data brokerage, workflow development, storage solutions, training, community outreach, or innovative tools for the microbiology field, this is your opportunity to secure support! Join our FAQ session to learn all about eligibility requirements and how your project can contribute to NFDI4Microbiota’s mission of promoting FAIR principles (Findable, Accessible, Interoperable, Reusable) and open science. We’ll walk you through eligible topics such as establishing data broker functionalities, developing Nextflow workflows for CloWM integration, supporting metadata standards, implementing electronic lab notebooks (ELNs), or enhancing research data curation. Target Audience: Microbiology researchers and teams with funding needs for their infrastructure or services, academic researchers or institutions based in Germany, NFDI4Microbiota's participants or willing to become participant. >>>> The Flex Funds Call is open until August 11th 2025 and you can find preliminary information and submission documents on our webportal<https://nfdi4microbiota.de/newsroom/flexfunds.html>. Bring your questions—our team will be ready to help you navigate the application process and maximize your chances! Don’t miss out on this chance to get your project funded and make a real impact in the microbiology community. 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 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 Maja Magel 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

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NFDI4Microbiota Newsletter 03/2025

by Mueller, Mattea

[https://nfdi4microbiota.de/assets/img/newsletter/fifthnewsletter/img1.png] 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!<https://nfdi4microbiota.de/contact-form.html> 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.<https://nfdi4microbiota.de/newsroom/flexfunds.html> Register for the NFDI4Microbiota Annual Conference 2025 [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q3_newsletter/save_th…] 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<https://events.hifis.net/event/2654>. 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. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q3_newsletter/VBiom_b…] 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<https://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: [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q3_newsletter/confere…] * Conference on Research Data Infrastructure (CoRDI) 2025, 26-28 August in Aachen * GMDS 2025, 7-11 September in Jena<https://gmds2025.de/> * DGHM 2025, 22 -24 September in Jena<https://dghm-kongress.de/en/> * 4th Annual NFDI4Microbiota Conference, 30 Sep - 2 Oct in Cologne<https://events.hifis.net/event/2654> [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q3_newsletter/ambassa…] 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.html>. Take a break and join our Coffee Talks [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/coffee_tal…] 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 ________________________________ Ask your questions to our Helpdesk! [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q2_newsletter/Support…] 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/contact-form.html> 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.html>! [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/Isometric_…] The next courses are * Microbiota profiling by 16S rRNA gene amplicon sequencing: Data analysis Workshop<https://nfdi4microbiota.de/services/training_view.html?docid=682f050c08a308…> * Hands-on Biometadata: How to describe biological data? Primer to a FAIR approach for now and future<https://nfdi4microbiota.de/services/training_view.html?docid=67dd67f7e68a14…> 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. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q3_newsletter/CAMI_Be…] The new CAMI Benchmarking Portal<https://cami-challenge.org/> 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 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/>

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