- Nfdi4microbiota-announce

Save the date - NFDI4Microbiota Annual Conference 2025: September 30 - October 02 in Cologne

by Paulmann, Carmen

Dear NFDI4Microbiota followers, We are excited to invite you to the NFDI4Microbiota Annual Conference 2025. The conference will take place from 30 September to 2 October 2025 at the ZB MED – Information Centre for Life Sciences in Cologne. The motto of this year's conference is “From Lab to Publication – Bridging the Gap with Best Practices”! You will have the chance to learn how to use our services and to make your data FAIR through dedicated hands-on workshops and with the opportunity to test your newly gained skills with a small training dataset. This year's conference will once again feature inspiring keynotes and interactive poster sessions. Please save the date and stay tuned for more information! We look forward to your participation and to a successful conference! Best regards, The NFDI4Microbiota Conference Team [cid:a51a6d69-b76d-45b9-9635-7070cad8f001] ________________________________ 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/>

9 months, 2 weeks

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NFDI4Microbiota - Bioinformatics Workshop: Introduction to R

by Paulmann, Carmen

Dear NFDI4Microbiota followers, NFDI4Microbiota is pleased to announce our next bioinformatics workshop: “Introduction to R - NFDI4Microbiota and DZIF Training Course 2025”. This workshop will take place on June 23-25, 2025 and will be held online. The workshop’s language is English. The aim of this seminar is to give participants with little or no experience of working with R the opportunity to close their knowledge gaps and determine whether R can be used in their own research. Topics range from the basics for getting started to advanced examples of using R in practical research. This course is suitable for people who are not familiar with R. Further information about the program and registration: https://events.hifis.net/event/2575/ The deadline for applications is June 6. Places are limited - apply soon to avoid disappointment! We look forward to your participation in this exciting workshop and hope to see you soon! Visit our training website<https://nfdi4microbiota.de/services/trainings.html> for more training courses! Best regards, Carmen Paulmann - NFDI4Microbiota administration unit --- Dr. Carmen Paulmann Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ 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 Bildung und Forschung 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/>

9 months, 3 weeks

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NFDI4Microbiota - Reminder: Community Workshop on 15 May 2025, 1:00 - 3:00 pm, online

by Paulmann, Carmen

Dear NFDI4Microbiota followers, This is a friendly reminder of the 7th edition of the NFDI4Microbiota Community Workshop. The NFDI4Microbiota consortium is in process of writing the renewal proposal for the next funding period. Now we need your feedback on our future work program! Topics on which we need your feedback: * How do we best support researchers in efficiently submitting microbiological data with comprehensive metadata into the designated repositories? * How can Electronic Lab Notebooks (ELNs) help to efficiently document your research? * How can experimental workflow become easily reusable and cititable? * Metadata management & Linked Data - What do you need for quick and easy management? * Finding and deciding on which quality approved analysis scripts and packages to use for your own analysis? and other topics and burning questions for which we want to offer solutions in the near and far future. Join us to offer your insights and help shape the future work of NFDI4Microbiota: What are your pain points, have you found solutions and what is still missing? Let's shape the future of the microbiological research landscape together! Feel free to forward the meeting invite to your colleagues. 📝 Agenda: https://nextcloud.nfdi4microbiota.de/s/9Y6NH7JmCA4dy32 📅 Date: 15 May 2025 🕝 Time: 1:00 - 3:00 pm CEST (Berlin time) 🔗 Zoom Link: https://rwth.zoom-x.de/j/69264435862?pwd=7IbTbahRW8dJBC8pAwvRjdU33GrtXJ.1 Meeting ID: 692 6443 5862 Passcode: 604995 Best wishes from Konrad Förstner and Alice McHardy, on behalf of 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 Bildung und Forschung 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/>

9 months, 4 weeks

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Reminder TODAY: Join our Next NFDI4Microbiota Coffee Talk – April 28 on strain-resolved metagenomics

by Mueller, Mattea

Dear microbiome enthusiasts, This is a friendly reminder that our next Coffee Talk is today! Strain tracking across metagenomic samples with SameStr by Daniel Podlesny (EMBL) Abstract: Microbial communities are integral to human health, yet many fundamental questions about their establishment, stability, resilience, and transmission remain unresolved. In this session, Daniel Podlesny will present SameStr, a bioinformatic tool designed for strain-resolved metagenomics. This tool enables precise tracking of microbial strains across metagenomic samples, allowing us to gain insights into microbial transmission, persistence, and competition. Date & Time: 28 April 2025 14:30 - 15:30 CEST Zoom link: https://helmholtz-hzi-de.zoom-x.de/j/68764089023?pwd=cvlqk3FLgKyIyK3xkUy2Lh… Meeting ID: 687 6408 9023 Passcode: 826218 We look forward to your participation and an engaging discussion. Best regards, The AU Team Dr. Mattea Müller Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ 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 Bildung und Forschung 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/>

10 months, 1 week

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NFDI4Microbiota Newsletter 2/2025

by Mueller, Mattea

Newsletter Quarter 2 2025 [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/eighthnewsle…] Dear Reader, With our eleventh NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, services and cooperations. If you can think of other topics that we should cover, please let us know. We are happy to hear from you!<https://jekyll.wp.dev.nfdi4microbiota.de/contact-form.html> And now: Enjoy reading the newsletter! Community Engagement Events and Conferences ________________________________ NFDI4Microbiota Symposium and booth that the VAAM [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/2025_Q2_news…] From 23–26 March, NFDI4Microbiota was present at the VAAM Annual Conference in Bochum with a booth, a poster, and a dedicated symposium. Visitors to our booth and poster learned how our services support microbiologists with FAIR data workflows, strain information, metadata standards, and Electronic Lab Notebooks. On Monday, 24 March, our symposium “From Lab to Publication: NFDI4Microbiota services for research data management” brought together our experts from DSMZ, HZI, UFZ, and ZB MED to present practical tools for better research data management. Thanks to everyone who stopped by and joined the discussion! NFDI4Microbiota at the DFG Interim Symposium in Bonn [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/2025_Q2_news…] NFDI4Microbiota reached an important milestone this February by presenting its three-year progress at the NFDI Interim Symposium 2025. As one of the second-round NFDI consortia, we had the opportunity to showcase our contributions to the DFG reviewers and the broader NFDI community.Our presentation highlighted advances in data standardization, integration of microbiome datasets, and the development of tools and services that support FAIR data practices across microbiology. We were pleased to receive very positive feedback on our work so far, particularly on our collaborative approach and the scientific relevance of our services. A big thanks to our partners across the NFDI network and look forward to continuing this joint effort to build a sustainable Open Science infrastructure for microbiome research. NFDI4Microbiota at the 34th Annual Meeting of the Society for Virology [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/2025_Q2_news…] From 4–7 March, NFDI4Microbiota was present at the 34th Annual Meeting of the Society for Virology (GVF 2025) in Hamburg with a booth highlighting our services for virology and microbial genomics. We showcased the VirJEN database—our curated platform for virus sequence metadata and standards. A big thank-you to everyone who visited, asked questions, and shared insights. We’re excited to keep building better infrastructures for virology research together! Upcoming Events and Conferences ________________________________ From Data to Discovery: Use Case Conference in May Mark your calendars! The NFDI4Microbiota Use Case Conference “From Data to Discovery: Unlocking the Potential of Host-Associated Microbiomes” will take place on 19–20 May 2025 in Siegburg/Bonn, Germany. This two-day event brings together microbiologists, bioinformaticians, and data curators to explore practical approaches for making microbiome data FAIR and reusable. Kicking off with a keynote by Prof. Dr. John Penders, the program highlights real-world Use Cases and services—from metaproteomics workflows and microbial knowledge graphs to bioimage annotation and virus metadata standards.The conference is free of charge, and registration is now open<https://4microbiota-uc1.sciencesconf.org/> until 17 April. Join us to exchange ideas, get inspired, and help shape the future of microbiome research. We need your Feedback! Join the Community Workshop NFDI4Microbiota is excited to announce the 7th edition of its Community Workshop on 15 May 2025 from 1:00 to 3:00 pm CEST. Since its successful launch in October 2021, the consortium has seen a rapid expansion in its technical solutions and trainings for the microbiology community. Now, after three years and seven months of dedicated work, the entire NFDI4Microbiota team invites you to join them in reflecting on past successes and shaping the future of microbiome research. Join online and share the invitation with your colleagues! More info will soon bee announced here<https://nfdi4microbiota.de/newsroom/news.html>. See you in person! [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/2025_Q1_news…] We will attend different events over the next year - find some of them below - and are looking forward to meet you there: * EVC 2025, April 27-30<https://eusv-congress.eu/> * ViBiom 2025, May<https://evbc.uni-jena.de/events/vibiom2025/> * DGHM 2025, September 22 -24<https://dghm-kongress.de/> 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. [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/ninthnewslet…] 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 bioinformatic 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 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. [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/2025_Q1_news…] We will continue our Coffee Talks this year, too. Get your updates and more information on the schedule and registration information here.<https://nfdi4microbiota.de/newsroom/news/2024-04-26-nfdi4microbiota-coffee-…> Services ________________________________ New update from StrainInfo Welcome to the latest update of StrainInfo <https://straininfo.dsmz.de/news> Version 2025.02.1! Our database now features 26,129 new deposits and 23,797 additional strains from top culture collections, enhancing microbial strain resolution. New features include API v2 with updated nomenclature, integrated ROR and ORCID identifiers, and an improved search table with advanced filtering and CSV downloads. [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/Services/SERVICES_strai…] We continue to collect only anonymized data—see our privacy policy for details. As always, your feedback is welcome. Ask your questions to our Helpdesk! support links 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). [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/2025_Q2_news…] Your question will be answered by one of the NFDI4Microbiota experts, including data data stewards, researchers and software developers. You can contact us either by filling in our contact form<https://nfdi4microbiota.de/contact-form/> or by email: helpdesk(a)nfdi4microbiota.de.<mailto:helpdesk@nfdi4microbiota.de> We look forward to hearing from you! Training Announcements ________________________________ We updated the Training section on our website! Now you get a more comfortable view on the interesting trainings, courses, and workshops to come. Check it out!<https://nfdi4microbiota.de/services/trainings.html> Our upcoming trainings include software carpentry and biometadata workshops. [https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/ninthnewslet…] Previous Training ________________________________ Successful Carpentries Python Workshop The Carpentries Python Workshop, held on March 17–18, 2025, at RWTH Aachen University’s IT Center, offered graduate students and researchers an engaging introduction to Python. Led by Jonathan Hartman and NFDI4Microbiota Data Steward Catherine Gonzalez, the event combined hands-on exercises with collaborative learning, emphasizing Python fundamentals from variables and loops to data manipulation with Pandas and visualizations using Matplotlib. Participants also explored broader topics such as Git version control and clean coding practices We also received encouraging feedback from participants: “I learned a lot from this workshop. All the staff were very kind and professional. I’d love to join another Python workshop under your organization. Thanks!” “Good organization, very well-structured content with understandable examples. I liked the combination of presentations and hands-on exercises.” “All instructors were very engaged and enthusiastic. They provided great examples of how best practices help in day-to-day coding.” The enthusiasm from the instructors made it easier to stay engaged in the tasks.” The inclusive atmosphere, guided by the Carpentries code of conduct, ensured a supportive environment where learners not only built practical skills but also gained the confidence to apply them in their research and data analysis projects. Recent Publications ________________________________ Defining Bacterial Genera with Genomic Precision fix link How can we robustly define bacterial genera in the age of big genomic data? A new preprint by Charlie Pauvert, Thomas Hitch, and Tom Clavel from the University Hospital of RWTH Aachen revisits the Percentage Of Conserved Proteins (POCP) and proposes POCPu—a clearer, more scalable method for genus delineation based on unique protein matches. Read more here https://doi.org/10.1101/2025.03.17.643616, 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 Bildung und Forschung 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/>

10 months, 3 weeks

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Join our Next NFDI4Microbiota Coffee Talk – April 28 on strain-resolved metagenomics

by Mueller, Mattea

Dear Microbiome Researchers, We would like to invite you to the next session of the NFDI4Microbiota Coffee Talk Series on Strain tracking across metagenomic samples with SameStr by Daniel Podlesny (EMBL) Abstract: Microbial communities are integral to human health, yet fundamental questions about their establishment, stability, resilience, and transmission remain incompletely understood. For instance, microbes are passed on to offspring and interconnected through social interactions and food webs, but it remains unclear whether this results in lifelong persistence, adaptation, and stable transmission across generations. Although short-read metagenomics provides cost-effective and high-depth sequencing for studying these questions, it inherently fragments genomes, complicating the reconstruction of microbial genotypes and their tracking across hosts. To address this limitation, we developed SameStr, a bioinformatic program for strain-resolved metagenomics, enabling precise tracking of microbes across metagenomic samples. By leveraging Single Nucleotide Variants (SNVs) within species-specific marker genes, SameStr facilitates the detection and quantification of microbial transmission and persistence, as well as the observation of direct strain competition. To enhance accessibility, we have released SameStr as a Nextflow-based workflow available on GitHub and the NFDI4Microbiota CloWM platform. This allows users to conveniently deploy and execute the SameStr pipeline end-to-end locally, in cloud environments, or through the graphical user interface on CloWM. We have applied the workflow to analyze over 120,000 metagenomic samples, demonstrating its robustness and scalability. SameStr has enabled strain-resolved analysis of microbial dynamics with unprecedented phylogenetic resolution, shedding light on parent-infant microbial transmission in early childhood, longitudinal strain persistence in adults, and strain dynamics during therapeutic interventions, including Fecal Microbiota Transplantation (FMT) and probiotic administration. These analyses have uncovered taxonomic, clinical, and ecological factors critical to microbiome assembly, demonstrating the potential of SameStr to provide deeper insights into microbiome ecology and therapeutic strategies. Date & Time: 28 April 2025 14:30 - 15:30 CEST Zoom link: https://helmholtz-hzi-de.zoom-x.de/j/68764089023?pwd=cvlqk3FLgKyIyK3xkUy2Lh… Meeting ID: 687 6408 9023 Passcode: 826218 We look forward to your participation and an engaging discussion. Best regards, The NFDI4Microbiota Team ________________________________ 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 Bildung und Forschung 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/

11 months

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NFDI4Microbiota - Invitation: Community Workshop on 15 May 2025, 1:00 - 3:00 pm, online

by Paulmann, Carmen

Dear microbiome research enthusiasts, In the past year, you have seen more and more of NFDI4Microbiota’s technical solutions and trainings for the microbiology community in action. Now we need you! Since the successful launch of NFDI4Microbiota in October 2021, we were able to welcome many new participants, we have seen our selection of services and tools grow and become more refined. Now after 3 years and 7 months, it is time to look back at what we have achieved and where our next steps are leading us. We warmly invite you to the 7th edition of our Community workshop to join us and share your ideas, wishes and tools with us. Let's shape the future of the microbiome research landscape together! Feel free to forward the meeting invite to your colleagues. 📝 Agenda: https://nextcloud.nfdi4microbiota.de/s/9Y6NH7JmCA4dy32 📅 Date: 15 May 2025 🕝 Time: 1:00 - 3:00 pm CEST (Berlin time) 🔗 Zoom Link: https://rwth.zoom-x.de/j/69264435862?pwd=7IbTbahRW8dJBC8pAwvRjdU33GrtXJ.1 Meeting ID: 692 6443 5862 Passcode: 604995 Best wishes from Konrad Förstner and Alice McHardy, on behalf of the NFDI4Microbiota consortium. --- Dr. Carmen Paulmann Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ 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 Bildung und Forschung 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/

11 months

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TODAY: ISCBacademy Webinar today with Nico Pfeifer on HIV

by Mueller, Mattea

ISCBacademy<https://www.iscb.org/iscbacademy> Modeling Microbe Evolution Due to Immune System Pressure by Nico Pfeifer (University of Tübingen) Today - February 25, 2025, at 3:00 PM CET Microbes are under constant evolutionary pressure from their environment, with the immune system playing a significant role in shaping their adaptation strategies. Viruses, in particular, must evolve to evade immune responses, enabling them to establish persistent infections. A well-studied example is HIV, where viral adaptation to the host's immune system has been extensively modeled using computational methods. In this talk, Nico Pfeifer will explore the computational approaches developed to model viral adaptation and their implications for understanding microbe evolution under immune pressure. The session will cover: * Early computational models of HIV immune adaptation [1] * Recent advances in Bayesian modeling for predicting viral evolution [2] * The impact of founder effects on adaptation predictions * Applications beyond viruses, including resistance prediction for Mycobacterium tuberculosis These insights not only enhance our understanding of viral evolution but also inform strategies for tackling antimicrobial resistance and improving predictive models for microbial adaptation. [1] Carlson, J., Du, V., Pfeifer, N. et al. Impact of pre-adapted HIV transmission. Nat Med 22, 606–613 (2016). [2] Hake, A., Germann, A., de Beer, C. et al. Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models, PLOS Computational Biology, 19(12): e1010355 (2023). Join the Webinar by logging in to ISCB Nucleus<https://iscb.junolive.co/> ________________________________ Dr. Mattea Müller Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany ________________________________ 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 Bildung und Forschung 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/

1 year

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NFDI4Microbiota Coffee Talk on February 24 on Microbial Protein Prediction

by Mueller, Mattea

Dear Ambassadors, Members, Participants, and Community, We are excited to invite you to our next NFDI4Microbiota Coffee Talk on February 24 at 2:30 PM CET! This session will host Dr. Thomas Hitch (RWTH Aachen University), who will present: Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut Microbes use a range of genetic codes and gene structures, yet these are ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment and limiting our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on taxonomic assignment, removes partial predictions, and optimizes the prediction of small proteins. Applied to 9,634 metagenomes and 3,594 genomes from the human gut, this approach increased the captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimized small protein prediction captured 3,772,658 small protein clusters, many with antimicrobial activity. Integration of these protein sequences and sample metadata into a tool, InvestiGUT, enables the association of protein prevalence with host parameters. Accurate prediction of proteins is critical for understanding microbiome functionality, and this work enhances our mechanistic understanding of microbe-host interactions. When? 📅 Date: Monday, February 24 🕝 Time: 2:30 PM CET Where? 💻 Online on Zoom 🔗 Join the Meeting https://helmholtz-hzi-de.zoom-x.de/j/68764089023?pwd=cvlqk3FLgKyIyK3xkUy2Lh… We look forward to seeing you online for an engaging discussion! Please feel free to share this invitation with colleagues who may be interested. Best regards, Mattea Müller NFDI4Microbiota Team ________________________________ 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 Bildung und Forschung 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/

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NFDI4Microbiota Newsletter 1/2025

by Mueller, Mattea

Newsletter Quarter 1 2025 [https://nfdi4microbiota.de/assets/img/newsletter/eighthnewsletter/icon_news…] Dear Readers, With our tenth NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, services and cooperations. If you can think of other topics that we should cover, please let us know. We are happy to hear from you!<https://nfdi4microbiota.de/contact-form/> And now: Enjoy reading the newsletter! [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/new_yea…] We wish you all a great and healthy start into 2025. Community Engagement Events and Conferences ________________________________ Great experiences at our 3rd Annual Conference [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/annual_…] The NFDI4Microbiota conference was a fantastic opportunity for the NFDI4Microbiota community to meet in person. We presented current development of our services and future plans during the public conference. .It was great to have several representatives from other NFDI consortia and Base4NFDI attend the event, as it provided the chance to exchange updates, discuss upcoming events, and align on shared goals. The keynote and panel talks inspired discussion of the policy, infrastructure, training and support needs of our various user communities. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/panel_a…] The Hands-on Workshops covered a variety of topics and were set in different styles, according to the topics. The Use Case workshop for example was a discussion-style workshop, were the Use Cases VirJenDB and MetaProt were presented and discussed with the participants. The workshop on Research Data Management on the other hand used a LEGO activity that highlighted the importance of metadata in experimental reproducibility. The game was based on a similar exercise by University of Glasgow. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/collage…] The workshop participants were divided into small groups of 2-3 people, each tasked with building a vehicle using at least 10 LEGO pieces within a limited timeframe of 15 minutes. Once the vehicles were built, each group documented their construction process by creating Standard Operating Procedures (SOPs). This documentation was crucial, as it provided detailed instructions on how to reconstruct their creations accurately. The emphasis on thorough SOPs mirrored the nature of scientific documentation, reinforcing its significance in ensuring reproducibility. After the initial LEGO creation and documentation of SOPs, groups switched tables with another team. They then had 15 minutes to rebuild the vehicles based solely on the provided instructions. This phase was not only a test of clarity and precision in documentation but also an opportunity for participants to appreciate how well-structured metadata can aid in replicating complex experiments. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/first_b…] [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/second_…] The LEGO activity served as a playful yet impactful reminder of the vital role that metadata plays in research. Just as accurate instructions can lead to successful LEGO constructions, comprehensive data management is essential for fostering reproducibility and reliability in scientific endeavors. Participants left with a renewed understanding of collaboration and communication's importance in both science and play. Successful first NFDI BioMed Workshop [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/BioMed_…] Several NFDI consortia supporting the work with biomedical and health data came together for a cross-consortium workshop on biomedical research data management (RDM). The event, jointly organized by NFDI4Bioimage, NFDI4Health, NFDI4Immuno, NFDI4Microbiota, and GHGA, successfully brought together experts from different NFDI consortia to share knowledge, discuss challenges, and identify opportunities for collaboration. The workshop provided a unique opportunity for exchange within the NFDI. Participants discussed potential joint use cases , explored areas of synergy for collaborative efforts, and developed pathways for further collaboration in biomedical RDM. This event was an important step in fostering collaboration and advancing research data management to generate solutions for the Germany biomedical research community. Community Engagement Upcoming Events and Conferences ________________________________ Next Community Workshop coming soon! [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/communi…] The upcoming Community Workshop will be held online in spring. We want to get YOUR feedback - straight out of the community. We will discuss how we further can support your microbiological research by providing data management infrastructure. The exact date will be announced soon in the Event section of our website<https://nfdi4microbiota.de/newsroom/events.html>. Stay tuned! Use Case Conference in May 2025 Join the experts and learn more about the NFDI4Microbiota Use Cases at the Use Case Conference on May 19. More information coming soon in the Event section of our website<https://nfdi4microbiota.de/newsroom/events.html>. See you in person! [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/coffee-…] We will attend different events over the next year - find some of them below - and are looking forward to meet you there: * GfV 2025, March 4-7<https://virology-meeting.de/> * VAAM 2025, March 23-26<https://vaam-kongress.de/> * EVC 2025, April 27-30<https://eusv-congress.eu/> * ViBiom 2025, May 13-15<https://evbc.uni-jena.de/events/vibiom2025/> Announcing the next Knowledge Base Sprint [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/KB-spri…] 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. [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/n4m_ambass…] 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 bioinformatic 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 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. We will continue our Coffee Talks this year, too. Get your updates and more information on the schedule and registration information here.<https://nfdi4microbiota.de/newsroom/news/2024-04-26-nfdi4microbiota-coffee-…> [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/coffee_…] Services ________________________________ Foundational Guidelines published To support our community we published NFDI4Microbiota Foundational Guidelines<https://zenodo.org/records/13628175> on Zenodo. The Guidelines shall act as basis for specific policies of all NFDI4Microbiota projects and services and are supposed to help researchers to offer data handling and storage, bioinformatic tools and services as well as training within the scope of a centralized infrastructure to a broad scientific audience. Training Announcements ________________________________ [https://nfdi4microbiota.de/assets/img/newsletter/ninthnewsletter/Isometric_…] We updated the Training section on our website! Now you get a more comfortable view on the interesting trainings, courses and workshops to come. Check it out!<https://nfdi4microbiota.de/services/trainings.html> More courses will be announced soon, e.g. the "Joint NFDI4Microbiota, de.NBI & DZIF Nextflow Metagenomic Training Course 2025", which will take place in person in Brunswick in April, so make sure to check the section regularly. Previous Training ________________________________ Intense 3-day-workshop on 16S Amplicon microbiome experiments [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/group_p…] Evaluating the mountain of 16S rRNA amplicon sequencing data after a successful microbiome experiment can be daunting, especially if you do not know where to start. That is why, as part of an on-going collaboration, de.NBI and NFDI4Microbiota hosted a course on Microbiome Analyses at Justus Liebig University in Gießen at the beginning of October. The aim was to encourage fellow scientists to feel confident enough in their skills to kickstart the analyses of their own data. Over the span of three days, the 17 participants, from PhD student to PI, were first introduced to the basic steps for running amplicon experiment analyses, including the pitfalls and best practices connected to high-throughput computations. The main part of the course was spent with hands-on sessions, assessing the quality of reads, using the tools Qiita and QIIME2 to preprocess the data, and subsequently analysing it. Cooperations ________________________________ Presentation at BY-COVID consortium meeting The final BY-COVID consortium meeting took place in Brussels on September 10 and 11. Noriko Cassman and Kilian Ossetek from VirJenDB attended and Kilian presented his project, which was funded by the open call that VirJenDB was awarded. His project is a submission web tool for the upload of virus sequences to ENA via the VirJenDB as a data broker. The pilot tool is available here<hxxps://www[.]virjendb[.]org/submission>. [https://nfdi4microbiota.de/assets/img/newsletter/2025_Q1_newsletter/BY-COVI…] Recent Publications ________________________________ Memorandum of Understanding on Biodata Interest Group published We intensify the collaboration with the consortia DataPLANT and NFDI4Biodiversity as the Biodata Interest Group. Therefore, our consortia signed a Memorandum of Understanding (MoU) which is now published here<https://zenodo.org/records/13880944>. Our three NFDI-consortia will pool expertise, energies and technologies in order to provide the scientific community with even better support in managing and processing their biological data. The focus of the MoU is on the cross-consortium harmonization of research data management strategies. Lesson plan on data organization Data Steward Justine Vandendorpe and Sophie Boße from ZB MED created a lessons plan and slides on data organization<https://zenodo.org/records/14234219> for an interactive workshop on the same topic. The lessons plan covers topics such as the motivation behind good data organization, file naming, versioning, folder structure and tidy data. Video publications on TIB AV-Portal In addition to the written publications we provide on our website, we proudly present our very own NFDI4Microbiota channel on the TIB AV-Portal.<https://av.tib.eu/publisher/NFDI4Microbiota> There you can find recordings of talks given within the consortium, for example on topics like ELNs, workflows, our Use Cases and, of course, an introduction to NFDI4Microbiota. Some selected video publications you can also find directly in the new media center on our website.<https://nfdi4microbiota.de/newsroom/mediacenter.html> 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 Bildung und Forschung 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/

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