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=cvlqk3FLgKyIyK3xkUy2...
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/>
3 weeks, 6 days
NFDI4Microbiota Newsletter 2/2025
by Mueller, Mattea
Newsletter Quarter 2 2025
[https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/eighthnews...]
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
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NFDI4Microbiota Symposium and booth that the VAAM
[https://jekyll.wp.dev.nfdi4microbiota.de/assets/img/newsletter/2025_Q2_ne...]
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
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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
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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
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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_ne...] 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/ninthnewsl...]
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_ne...]
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-coffe...>
Services
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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_str...]
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_ne...]
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
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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/ninthnewsl...]
Previous Training
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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
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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...>
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/>
1 month, 1 week
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=cvlqk3FLgKyIyK3xkUy2...
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/
1 month, 2 weeks
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/
1 month, 3 weeks
