- Nfdi4microbiota-announce

NFDI4Microbiota - Flex Funds call 2024 now open

by Goetz, Barbara

Dear NFDI4Microbiota community, We are glad to announce that we just opened the NFDI4Microbiota Flex Funds call for 2024. The call is open from 2023-07-11 until 2023-08-20. A brief summary of the call: Aim of the NFDI4Microbiota Flex Funds 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. In the following, a guideline regarding the application and allocation process is provided. Eligible topics Applications must address services to be developed and deployed that are related to the NFDI4Microbiota proposal. This could include, but is not limited to, the following topics · Data Brokerage · Infrastructure/Services · Data storage and workflow execution · Training · Community engagement and outreach · Establishment of local data stewards · Use Case connection or an active Use Case · Generation and/or curation of large, high quality data sets All details, the application guideline and the application forms are accessible here: https://nfdi4microbiota.de/flexfunds/ For further details please read the full guideline on our web portal. Please contact us via contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> if you have further questions. On behalf of the NFDI4Microbiota consortium. Kind regards, The NFDI4Microbiota Administration Unit Barbara Götz, Dr. Carmen Paulmann, Dr. Cordula Hege --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota Part of the Administration Unit of NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

2 years, 11 months

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4th NFDI4Microbiota Newsletter

by Paulmann, Carmen

4th NFDI4Microbiota Newsletter - PDF version in the attachment Dear Reader, With our fourth NFDI4Microbiota newsletter, we would like to share news about conferences and events, the new StrainInfo-Archive and available online videos. If you are interested in other topics we should cover, please let us know. We are happy to <https://nfdi4microbiota.de/contact-form/> hear from you<https://nfdi4microbiota.de/contact-form/>! And now: Enjoy reading the newsletter! Community engagement – events and conferences The second NFDI4Microbiota annual conference was held in April under the theme “Community Engagement” We were glad to meet some of our participants and ambassadors during the second NFDI4Microbiota annual conference in Frankfurt am Main, Germany. Our participants had the opportunity to introduce themselves by giving flash talks and presenting posters and to get insights into the aims and current achievement of our consortium. [cid:ed7b0cab-6e0f-43cc-84ac-0f457fa36069] In addition, we were able to invite two international keynote speakers who reported on their infrastructure projects. First, <https://www.wur.nl/de/Personen/Hauke-prof.dr.-H-Hauke-Smidt.htm> Prof. Dr. Hauke Smidt<https://www.wur.nl/de/Personen/Hauke-prof.dr.-H-Hauke-Smidt.htm><https://www.wur.nl/de/Personen/Hauke-prof.dr.-H-Hauke-Smidt.htm> from Wageningen University, the Netherlands, presented the work and opportunities that the <https://www.wur.nl/en/article/unlock-1.htm> UNLOCK<https://www.wur.nl/en/article/unlock-1.htm><https://www.wur.nl/en/article/unlock-1.htm> project offers to microbiology scientists. The UNLOCK infrastructure is open for exploring new horizons for research on microbial communities. The free service provides the ability to study microbial communities in a variety of environments. Our second keynote speaker, Lee Ann McCue, came all the way from the Pacific Northwest National Laboratory in the US. She is a member of the <https://microbiomedata.org/> National Microbiome Data Collective (NMDC)<https://microbiomedata.org/><https://microbiomedata.org/>. After presenting the work of NMDC, a fruitful discussion and exchange took place with our consortium. Collaboration on similar topics is planned throughout the project. [cid:6b6eed56-4d28-48f0-8b1a-182685738ce2] NFDI4Microbiota will present its work during the Thuringian RDM Days The <https://forschungsdaten-thueringen.de/rdm-days/articles/rdm-days.html> Thuringian RDM Days<https://forschungsdaten-thueringen.de/event/fdm-tage-2023-en.html> are an annual series of events during which the universities in Thuringia offer various lectures and workshops on research data management under a specific motto. These are primarily targeted at researchers in Thuringia, but are also open to researchers and other interested parties! We will present the work of NFDI4Microbiota online on June 21 at the Thuringian RDM Days 2023. ICTV/EVBC Workshop on Automating Virus Taxonomy From July 31 to August 2, 2023, the EVBC (European Virus Bioinformatics Center) and the ICTV (International Committee on Taxonomy of Viruses) are organizing a workshop on “Automating Virus Taxonomy” in Jena, Germany. Prof. Manja Marz, NFDI4Microbiota partner, is part of the organising committee. The workshop will be hybrid and can therefore be attended live or online. On the first day, Prof. Alexander E. Gorbalenya (Leiden University, the Netherlands) and several other virology experts will present on virus taxonomy and the ins and outs of classifying specific viruses. In the morning of the second day, bioinformaticians will explain how they have implemented automated classification methods. In the afternoon, both groups, virology experts and bioinformaticians, will be brought together for discussion sessions with the goal to start or deepen collaborations between participants. In addition to this program, satellite hands-on sessions (August 2, 2023) will be offered focusing on automating bioinformatics workflows (Snakemake) and virus databases (organized by NFDI4Microbiota). For more information and to register click <https://evbc.uni-jena.de/events/virus-taxonomy-workshop/> here<https://evbc.uni-jena.de/events/virus-taxonomy-workshop/>. Second in-person meeting of the NFDI management circle took place in Hamburg A strong network needs good coordination. For this reason, people from the different NFDI consortia met for a second in-person meeting to discuss different management topics at the Deutsches Elektronen-Synchrotron (DESY) in Hamburg. The meeting addressed common challenges and approaches to solutions with a focus on administrative issues. The two days in Hamburg also offered plenty of opportunities for networking and personal exchange. We are glad to be able to work in such a supportive and friendly community. [cid:a2f411ac-e731-4c06-adb2-e9bf3fa0140b] NFDI4Microbiota Services Alpha version of the StrainInfo-Archive is online In microbiology, resolving microbial strain identifiers is an important requirement. Strain identifiers represent a universal language for working with strains and can be found throughout literature, databases and culture collection catalogs. StrainInfo is a service being developed to provide a one-stop shop for strain identity information by storing culture collection numbers, their relations and associated information on taxonomy, sequence accessions and literature to help researchers in their work with microbial strains. StrainInfo was initially created by BCCM/LMG between the years 2005 and 2015 and is currently being developed by the NFDI4Microbiota partner institution DSMZ. The alpha version<https://straininfo.dsmz.de/#><https://straininfo.dsmz.de/#><https://straininfo.dsmz.de/> of StrainInfo is now online and utilizes test data provided by LMG. Media Interview on the importance of research data management in microbiology is online Is scientific work even possible today without dedicated research data management? And what role do infrastructures play in this? Elke Roesner talks about this in the new “ZB MED Nachgefragt” with Barbara Götz, microbiologist and project manager at NFDI4Microbiota, and Prof. Dr. Konrad Förstner, bioinformatician and speaker of our consortium. This <https://www.youtube.com/watch?v=xwmMuPh0LBw> video podcast<https://www.youtube.com/watch?v=xwmMuPh0LBw> (German) explains where NFDI4Microbiota stands today, the challenges to be overcome, future plans and why it is necessary to reach scientists even earlier in their careers to embed awareness of research data management in the scientific communities. [cid:89929157-3a76-48c1-990b-ca45593e0aa6] NFDI4Microbiota contributed to Love Data Week 2023 with a panel discussion on the benefits of data-driven decisions in life sciences – video is now online What needs to happen to establish conscientious research data management in the disciplines of the life sciences? How can researchers be convinced and reservations be overcome? These were the questions addressed in a highly interesting panel discussion on February 16, 2023, jointly organised by the NFDI consortia NFDI4Biodiversity, DataPLANT, NFDI4Health and NFDI4Microbiota. Panelists were Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Konrad Förstner (NFDI4Microbiota), Prof. Dr. Björn Usadel (DataPLANT) and Prof. Dr. Iris Pigeot (NFDI4Health). The discussion was moderated by Dr. Kerstin Elbing (Verband Biologie, Biowissenschaften und Biomedizin in Deutschland e. V. – VBIO). The discussion was introduced by keynote speeches from Dr. Martin Friedrichs-Manthey (NFDI4Biodiversity), Prof. Dr Björn Usadel and Prof. Dr Iris Pigeot. The event was part of the Love Data Week 2023, an international week of action to discuss and reflect on research data together. Under the motto "Data: Agent of Change" the Love Data Week 2023 was celebrated worldwide from February 13-17 with numerous events on a wide range of research data management (RDM) topics. The <https://www.youtube.com/watch?v=3k64WHbwy8I> video<https://www.youtube.com/watch?v=3k64WHbwy8I> of the panel discussion is now online! Short clip: The work of a data steward A Data Steward is, generally said, a person who is responsible for ensuring the quality of data assets, including metadata. However, the tasks of data stewards are very different and fulfill different requirements. This is also the case in the field of research. Good research data management is essential in research. Data stewards play a crucial role here, as they support researchers in this task and take on the role of intermediaries between the different fields of work. Justine Vandendorpe, one of NFDI4Microbiota’s data stewards at <https://www.zbmed.de/kontakt/justine-vandendorpe> ZB MED<https://www.zbmed.de/kontakt/justine-vandendorpe>, explains what her tasks as a data steward look like: “As a data steward within NFDI4Microbiota, I support the curation of microbial omics data and associated metadata. In practice, this means that I train researchers in research data management and reproducible data and software practices. I also advise researchers on the use of electronic lab notebooks and in writing their data management plan.” Learn more about her work in this <https://www.youtube.com/watch?v=LcoNsvfwvts> video<https://www.youtube.com/watch?v=LcoNsvfwvts>. [cid:9eed2032-837e-4e0b-b92d-88dd91632b20] NFDI4Microbiota is now part of the Mastodon network As a decentralised network, Mastodon represents an alternative to well-known social media platforms such as Twitter. Since mid of May, we have a <https://nfdi.social/@NFDI4Microbiota> new Mastodon profile<https://nfdi.social/@NFDI4Microbiota> on the NFDI instance<https://nfdi.social/home>. The instance is designed to be a place where users can share ideas about research data management (RDM) and discuss exciting topics from the NFDI consortia as well as the scientific community. You can also follow us from another server if you look for: @NFDI4Microbiota@nfdi.social Open access research data management training material publication A group of research data management (RDM) experts at our partner institution ZB MED just published an open access RDM training workshop material in Publisso<https://repository.publisso.de/resource/frl:6452660>. The ‚Online Training Workshop on Research Data Management in (Bio-)Medicine‘ is build of three main chapters: 1) General aspects of RDM, 2) Discipline-specific content, and 3) Engagement methods. This material is not only for self-study purpose, but explicitly for training purposes. It is published under the Creative Commons Attribution 4.0 International License. Social links and Contact Follow us on Twitter<https://twitter.com/nfdi4microbiota?lang=en>, <https://nfdi.social/@NFDI4Microbiota> <https://nfdi.social/@NFDI4Microbiota> Mastodon<https://nfdi.social/@NFDI4Microbiota><https://nfdi.social/@NFDI4Microbiota><https://nfdi.social/@NFDI4Microbiota><https://nfdi.social/@NFDI4Microbiota> and <https://github.com/NFDI4Microbiota> GitHub<https://github.com/NFDI4Microbiota>! Questions or suggestions<https://nfdi4microbiota.de/contact-form/>? <https://nfdi4microbiota.de/>Learn more<https://nfdi4microbiota.de/><https://nfdi4microbiota.de/> about NFDI4Microbiota! <https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…>Subscription / Unsubscription<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…><https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…><https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…><https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Dr. h.c. Dirk Heinz - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

3 years

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Update: NFDI4Microbiota - Lecture talks on the 24th of April 2023 11-12:30 CEST + training announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, save the date for our short lecture talks on different services NFDI4Microbiota provides for its community: training, workflows, Use Cases and the NFDI4Microbiota Knowledge Base. The lectures will be webcasted on the 24th of April 2023 11-12:30 CEST. Update: Zoom login details: Meeting ID: 857 7139 3336 Passcode: 095511 We also would like to announce training offers by our partner: · 3-day Workshop on Nanopore Sequencing<https://bic.uni-jena.de/what-we-offer/training/>, 2023-04-26 - 2023-04-28, 09:00 - 16:00 CEST. · Introduction to R<https://docs.google.com/forms/d/e/1FAIpQLSd3U-NmjfZOIORKmhGsd__q1SwtWSvI3dY…>, 2023-05-15 - 2023-05-17, 10:00 - 13:00 CEST. Your NFDI4Microbiota Administration Unit, Barbara Götz, Carmen Paulmann and Cordula Hege --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 2 months

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NFDI4Microbiota - Save the date: Lecture talks on the 24th of April 2023 11-12:30 CEST + training announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, save the date for our short lecture talks on different services NFDI4Microbiota provides for its community: training, workflows, Use Cases and the NFDI4Microbiota Knowledge Base. The lectures will be webcasted on the 24th of April 2023 11-12:30 CEST. The login details will be shared with you soon. We also would like to announce training offers by our partner: · 3-day Workshop on Nanopore Sequencing<https://bic.uni-jena.de/what-we-offer/training/>, 2023-04-26 - 2023-04-28, 09:00 - 16:00 CEST. · Introduction to R<https://docs.google.com/forms/d/e/1FAIpQLSd3U-NmjfZOIORKmhGsd__q1SwtWSvI3dY…>, 2023-05-15 - 2023-05-17, 10:00 - 13:00 CEST. Your NFDI4Microbiota Administration Unit, Barbara Götz, Carmen Paulmann and Cordula Hege --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 2 months

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NFDI4Microbiota Newsletter 01/23

by Paulmann, Carmen

Welcome Dear Reader, With our third NFDI4Microbiota newsletter, we would like to share news about our upcoming conferences and events. In this issue, you can also read about our connecting efforts and we continue presenting recent publications, news and much more. If you are interested in other topics we should cover, please let us know. We are happy to hear from you! And now: Enjoy reading the newsletter! [cid:acbf171d-64b1-4e79-b779-c87d658e74e1] _________________________ Community engagement – events and conferences Save the date for the second NFDI4Microbiota annual conference The theme of this year's NFDI4Microbiota conference is "Community Engagement", as we want to get to know our participants and their needs, and give them an insight into our services. The conference will take place April 24-26, 2023, venue and registration information will follow shortly. On the morning of the first day, we will present our services to the community during NFDI4Microbiota lectures, which will be available online for everyone to attend. The rest of the conference will be reserved for NFDI4Microbiota participants, ambassadors, committees and the NFDI4Microbiota consortium. The first day will be a community day to connect with our participants and ambassadors. The second day will be dedicated to cross-cutting issues such as training and workflows, as well as the General Assembly. The third day will feature inspirational talks from international speakers involved in similar projects, followed by roundtable discussions about our Use Cases and a community workshop. Love is in the air! NFDI4Microbiota contributes to Love Data Week 2023 with a panel discussion on the benefits of data-driven decisions in life sciences During the Love Data Week 2023, several NFDI consortia participate in events or training regarding the topic “Data: Agent of Change”. Together with the NFDI consortia DataPLANT, NFDI4Health and NFDI4Biodiversity, we will host an in-person panel discussion on ‘Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences’ at the University of Bremen. Data-driven decisions in the life sciences have an immense impact on human and environmental well-being, as well as on the development of research directions. Therefore, experts from different areas of the life sciences will discuss the importance of data-driven decisions using best practice examples. Expect an in-depth discussion on the challenges and benefits of cultural change related to research data governance, Open Science and FAIR principles and their impact on the daily life of each individual. * Panelists: Prof. Dr. Konrad Förstner (NFDI4Microbiota), Björn Usadel (DataPLANT), Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Dagmar Waltemath (NFDI4Health) * Moderation: Dr. Kerstin Elbing (VBio) * Location: University of Bremen Bremen, Room NW2 C0290 (Hörsaal 1) * Date and time: 2023/02/16 15.00 - 17.00 PM CEST * Zoom option: Meeting-ID: 812 3227 9619, Password: 092856 [cid:967bf743-0b62-405f-9667-f0b7a6addb88] NFDI4Microbiota World Café on Electronic Lab Notebooks (ELNs) To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we will run a virtual World Café on 2023-02-24, 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Workflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here<https://us02web.zoom.us/meeting/register/tZAqceyppjwpHdRHg7uF7AqPb6Yxq4Phq3…>. NFDI4Microbiota will showcase its activities to the virology and parasitology communities In March, we will present our mission, work progress and services at the 32nd Annual Meeting of the Society for Virology <https://virology-meeting.de/> and the 30th Annual Meeting of the German Society for Parasitology<https://parasitology-meeting.de/>. The NFDI4Microbiota consortium members met at the first NFDI4Microbiota annual conference In November 2022, we met for the first time during the internal NFDI4Microbiota conference in Cologne. Presentations and fruitful discussions took place on our current work in the areas of computational infrastructure, data storage and analysis, data and metadata standards, training and outreach. In addition, our six active Use Cases<https://nfdi4microbiota.de/latest/usecase> were presented and discussed in roundtable sessions. [cid:729f6990-ab4c-44e2-8221-03696c157b63] The NFDI4Microbiota consortium met in Cologne. _________________________ Networking and Collaborations Regular exchange of NFDI4Microbiota and NMDC The National Microbiome Data Collaborative (NMDC) was initiated in July 2019 as the foundation of a community-driven US national effort aimed to develop standards, processes, and infrastructure for an integrated microbiome data ecosystem. The NMDC aims to achieve similar solutions for the US as we at NFID4Microbiota are pursuing for Germany. They are working with the community to develop and lead an integrated, open-source microbiome science gateway that leverages existing resources and enables comprehensive access to multidisciplinary microbiome data and standardized, reproducible data products. Like our NFDI4Microbiota consortium, NMDC is committed to open science and the FAIR principles. Our representatives from NFDI4Microbiota meet regularly with those from NMCD to explore synergies and to determine how best to integrate efforts in all areas, such as standards, analytical workflows, data and results sharing, and training. [cid:fb6eee7e-d580-43c5-9cc4-4fb56ca0ae39] _________________________ Publications Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities – Published in Cell Host & Microbe Microbiome research needs comprehensive repositories of cultured bacteria from the intestine of mammalian hosts. The groups of our NFDI4Microbiota partners, Prof. Thomas Clavel and Prof. Jörg Overmann, both NFDI4Microbiota partners, expanded the mouse intestinal bacterial collection to 212 strains, all publicly available and taxonomically described. This includes strain-level diversity, small-sized bacteria, and previously undescribed taxa (one family, 10 genera, and 39 species). This collection enabled metagenome-educated prediction of synthetic communities (SYNs) that capture key functional differences between microbiomes, notably identifying communities associated with either resistance or susceptibility to dextran sulphate sodium (DSS)-induced colitis. Additionally, nine species were used to amend the Oligo-Mouse Microbiota (OMM)12 model, yielding the OMM19.1 model. The added strains compensated for phenotype differences between OMM12 and specific pathogen-free mice, including body composition and immune cells in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available for future studies. In conclusion, this work improves the knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates. Microbiota research is hampered by the fact that approximately half of complex microbial communities is still unknown. Moreover, there is a lack of cultured isolates publicly available, which prevents functional studies. This published work addresses both issues by making cultured bacteria from the mouse intestine and their metadata available according to FAIR principles. Read more Toward FAIR Representations of Microbial Interactions – Published in mSystems Despite an ever-growing number of datasets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies. Here, Charlie Pauvert from our consortium and the other authors propose guiding principles to make microbial interaction data more findable, accessible, interoperable, and reusable (FAIR). They outline specific use cases for interaction data that span the diverse space of microbiome research, and discuss the untapped potential for new insights that can be fulfilled through broader integration of microbial interaction data. These include, among others, the design of intercompatible synthetic communities for environmental, industrial, or medical applications, and the inference of novel interactions from disparate studies. Lastly, they envision potential trajectories for the deployment of FAIR microbial interaction data based on existing resources, reporting standards, and current momentum within the community. Read more _________________________ Services and Infrastructure The BacDive database of the Leibniz Institute DSMZ has been selected as a Global Core Biodata Resource The Bacterial Diversity Metadatabase (BacDive) of the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH has been selected as a Global Core Biodata Resource by the renowned Global Biodata Coalition. This makes BacDive one of the most important global databases for bacterial research. BacDive is the world’s largest database for standardised bacterial phenotypic data, developed by one of our partners. It aims to mobilise and standardise research data to improve the accessibility and comparability of phenotypic data in microbial research. Read more [cid:7991d46f-b833-4752-b89d-ac3f61cd42b2] _________________________ Media In a recent episode of the Open Science Radio Podcast the director of the NFDI, York Sure-Vetter, gives an overview of the NFDI including the potential and challenges as well as its history and international context. Listen to it. _________________________ Social links and Contact Follow us on Twitter and GitHub! Questions or suggestions? Learn more about NFDI4Microbiota! Subscription / Unsubscription 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. Dr. h.c. Dirk Heinz - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

3 years, 4 months

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NFDI4Microbiota - Happy new year + training and event announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, Happy new year to all of you! We are looking ahead to the year 2023 under the motto "Community Engagement". Today we would like to point out some event and training highlights : · Love Data Week 2023<https://forschungsdaten.info/fdm-im-deutschsprachigen-raum/love-data-week/> 2023-02-16, 15:00-17:00, in person (University of Bremen) with zoom option During this international action week, we participate in the panel discussion 'Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences'<https://nfdi4microbiota.de/news/2023-01-13-lovedataweek2023> with NFDI4Biodiversity, NFDI4Health and DataPlant at University of Bremen. · NFDI4Microbiota world café on Electronic Lab Notebooks (ELNs) 2023-02-24, 10:00 - 12:00, online To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we are organizing a world café on 2023-02-24 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Workflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here<https://us02web.zoom.us/meeting/register/tZAqceyppjwpHdRHg7uF7AqPb6Yxq4Phq3…>. · Workshop: Mapping the crosstalk of heterologous ECF sigma factors to the host genome 2023-02-20 - 24 08:00 - 16:00, in person and online 2023-03-06 - 10 08:00 - 16:00, in person and online Five places available for attendance + online participation, more details<https://nfdi4microbiota.de/training/training>. Our third newsletter will be shared with you in the end of January with news from our consortium. Kind regards Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 4 months

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NFDI4Microbiota - Merry Christmas + Outlook 2023

by Goetz, Barbara

Dear NFDI4Microbiota community, We thank you for your helpful contributions in 2022! We are looking back on a very successful year and are pleased to announce that there will be a special focus on 'community engagement' in 2023. In the beginning of 2023 we will announce a few events and planned activities for 2023, as well as our next newsletter. In addition, you will have plenty possibilities to meet us in person at conferences in 2023 and actively participate in events together with other NFDI consortia. We wish you and your families a Merry Christmas, happy holidays and a Happy New Year and look forward to work with you in 2023. [cid:image003.jpg@01D9160E.61469870] On behalf of the Board of Directors and Administration Unit Kind regards Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 5 months

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NFDI4Microbiota Newsletter October

by Paulmann, Carmen

Welcome Dear Reader, With our second NFDI4Microbiota newsletter, we would like to share news about our community activities such as the ambassador program or conferences we have participated in. In this issue, you can also read about Use Cases which will be implemented this year and about our recently published articles. Moreover, we continue presenting upcoming training courses, report on the release of our new web portal and much more. Let us know if you are interested in additional topics that we should cover. We are happy to hear from you<https://nfdi4microbiota.de/contact-form/>! Enjoy reading the newsletter! [cid:f9c998d6-06f8-4b0f-a5d8-168571dbe4bb] —————————————————————————————————————————— Community and Training Ambassador program: Monthly Coffee Talks series has started! Our mission is to be the central hub in Germany for supporting the microbiology community with access to data, analysis services, data/meta data standards and training. Therefore, the connection and interaction with the German microbiology community is key for our success and the goal of the NFDI4Microbiota ambassador program. The ambassadors will help to efficiently assess and communicate the needs of their community and provide them with suitable solutions generated by the consortium. A bilateral exchange with the ambassadors as well as presentations on different topics take place during the monthly Coffee Talk series. More information and the registration link for the ambassador program can be found here<https://nfdi4microbiota.de/ambassador/>. [cid:a4f0adb6-a9df-4862-8ecd-0a06eb519ce5] [cid:8ad45b62-6fd6-4273-9257-380fce5f27e9] Conferences NFDI4Microbiota has presented our activities at various conferences, including ISMB<https://www.iscb.org/ismb2022>, ISME<https://isme18.isme-microbes.org/>, GCB<https://gcb2022.de/>, ECCB<https://eccb2022.org/>, Targeting Microbiota<https://www.microbiota-site.com/> and DGHM<https://www.dghm-kongress.de/>. Moreover, together with representatives of other NFDI consortia, namely NFDI4Health, NFDI4Biodiversity, and KonsortSWD, we participated in the panel discussion ‘Everything FAIR and Open? Restrictions on data publications’ at JCDL 2022<https://2022.jcdl.org/nfdi-satellite-event/>. [cid:0fa23154-ecf4-4dde-8854-76eab66f3742] [cid:0c9091c0-01a6-42ff-8245-ff21cc6b585c] [cid:edc9b149-561e-4244-a57e-c2c41a91983a] [cid:da257049-02f6-40fd-9acb-3c750663b544] Upcoming training and events Within NFDI4Microbiota the support of the community by education and training is an important goal. Therefore, the consortium offers training<https://nfdi4microbiota.de/training/training> on several topics and for different disciplines. Moreover, we are regularly organizing or attending events<https://nfdi4microbiota.de/latest/events.html> such as the first BioHackathon Germany<https://www.denbi.de/de-nbi-events/1454-biohackathon-germany>. The workshop ‘Extending the NFDI4Microbiota Knowledge Base<https://www.denbi.de/de-nbi-events/2-uncategorised/1480-extending-the-nfdi4…>’ will be held during that event from 12th to 16th December 2022 in Wittenberg. NFDI4Microbiota has initiated a dedicated Knowledge Base that will contain information on Research Data Management and Reproducible Data Analysis in the broad field of microbiology. The Knowledge Base is developed in an open, collaborative process on GitHub<https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/RDM/introd…> and offered under a permissive license (CC-BY 4.0). Several NFDI4Microbiota members will participate in the BioHackathon and use that time as a content spring. The BioHackathon will offer a great opportunity to engage in discussions with other participants on various topics such as best practices, bioinformatical tools, Electronic Lab Notebooks and privacy issues. [cid:28221e70-0133-4062-8af4-7c841d8355dc] Registration is open for the following workshops and courses: Title Location Date Link Lecture on Research Data Management Online 2022-11-03, 9.00 to 11.00 a.m. Information and registration<https://www.zbmed.de/en/about/press/latest-news/article/einfuehrung-fdm0/> Single Cell Workshop Online 2022-11-21 to 2022-11-22 Information and registration<https://docs.google.com/forms/d/e/1FAIpQLSeLZjdsoEGEXycWZbsKNRR92lGcpFGcBV-…> Training Course on Metagenome Analysis Bielefeld University 2022-11-23 to 2022-11-25 Information and registration<https://www.denbi.de/training/1494-joint-de-nbi-nfdi4microbiota-training-co…> 1st BioHackathon Germany - Extending the NFDI4Microbiota Knowledge Base Lutherstadt Wittenberg - Leucorea 2022-12-12 to 2022-12-16 Information and registration<https://www.denbi.de/de-nbi-events/1454-biohackathon-germany> ____________________________________________________________________________ Networking and Collaborations Use Cases We are pleased to announce that NFDI4Microbiota currently has six active Use Cases: MULTI: Integration of multi-omics data of microbial species AmpliBench: Replacement or Extension: Systematic Assessment of Differences in Taxonomic Profiling Between Amplicon Sequencing Variants and Operational Taxonomic Units MetaProt: Functional profiling and routine diagnosis of humane microbiomes by metaproteomics Strain-ID: Collecting and matching microbial strain identifiers GUT: Crowd-sourcing high-quality descriptions of novel taxa MetaENVO (preliminary name): Metagenomic databases Learn more about the individual Use Cases and how you can contribute on our web portal<https://nfdi4microbiota.de/latest/usecase> or look forward to the Use Case showcase<https://www.eventbrite.co.uk/e/nfdi4microbiota-use-case-showcase-online-att…> during the NFDI4Microbiota Conference on 9th of November. Here, the project background and core aims of each Use Case will be shortly presented thereby providing the opportunity to give feedback, brainstorm further cooperation and discuss integration possibilities within NFDI4Microbiota. ____________________________________________________________________________ Publications Next steps after 15 stimulating years of human gut microbiome research – Published in microbial biotechnology Gut microbiome research has bloomed over the past 15 years. We have learned a lot about the complex microbial communities that colonize our intestine. Promising avenues of research and microbiome-based applications are being implemented, with the goal of sustaining host health and applying personalized disease management strategies. Despite this exciting outlook, many fundamental questions about enteric microbial ecosystems remain to be answered. Organizational measures will also need to be taken to optimize the outcome of discoveries happening at an extremely rapid pace. This article highlights our own view of the field and perspectives for the next 15 years. READ MORE<https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.13970> <https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.13970> Publication of the feedback from NFDI4Health, GHGA and NFDI4Microbiota on the positions and recommendations of the German Council of Science and Humanities NFDI4Health, GHGA and NFDI4Microbiota particularly welcome the positions and recommendations of the German Council of Science and Humanities on digitization and data use for health research and care and have formulated a joint response to this. Here, the consortia appreciate the strategic goal of establishing a decentralized, research-compatible, networked and interoperable health data infrastructure with a central health research data portal. The plea of the German Council of Science and Humanities for a data protection compliant facilitation of data access with the possibilities of the opt-out procedure is explicitly supported by the participating NFDI consortia. Additionally, improved possibilities for the linkage of different data sources (record linkage) on a national level are pleaded for. READ MORE<https://repository.publisso.de/resource/frl:6434341> (German) [Inline image OWAPstImg645685] NFDI4Microbiota - Enabling data-heavy research on microorganisms and their communities – Published in de.NBI brochure (pages 38-41) Our consortium is engaged in the support of microbiome research and for this builds on the high-performance cloud infrastructure provided by de.NBI. The de.NBI computational infrastructure supplies the network with computational resources on the one hand and massive storage capacities on the other. Furthermore, de.NBI and other partners work together to develop best practices and standards for metadata, training programs and community building. In conclusion, the de.NBI network represents a key component in the provision of NFDI4Microbiota’s solution. READ MORE<https://www.denbi.de/images/Downloads/deNBI_Cloud_Brochure_web.pdf> ______________________________________________________________________ Services and Infrastructure New Release of the NFDI4Microbiota web portal A new version of the NFDI4Microbiota portal<https://nfdi4microbiota.de/> has been released in August 2022. The NFDI4Microbiota services and useful information about the consortium appear in a new design and with an improved structure. New exiting features are an overview of the current Use Cases<https://nfdi4microbiota.de/latest/usecase> and our help desk<https://nfdi4microbiota.de/contact-form/>. Currently, our developer team works on a Content Hub that will function as a Knowledge Base in the future. Here, important resources on research data management and for reproducible data analysis will be available. [cid:43bd7426-43ce-4500-9324-ac6d22c69f8c] Survey on the use of Electronic Lab Notebooks Electronic Lab Notebooks (ELNs) play an important role in documenting research data: they provide clear documentation of experiment planning and implementation and of data generation and processing. One of our aims is is to ensure research data are captured as early in the process as possible in order to feed them directly into the analysis pipeline. In order to understand why or why not researchers use an ELN, and what are/were their hurdles in implementing or using an ELN, we conducted a survey on the use of ELNs which was intended for NFDI4Microbiota partners and participants. Only around 26% of respondents are currently using a ELN indicating a clear need to build awareness. Moreover, the ELNs being used varies greatly and are in need of improvements. To further support the use of ELNs and identify the needs of our community, we will soon organise a workshop. Ultimately, we would like to recommend a single ELN and guide researchers in the selection and implementation of the appropriate ELN for their research. The FAIR annotation of bacterial genomes The annotation of microbial genomes is a key task in bioinformatics and a requirement for many genome-based downstream analyses. Available contemporary command line annotation software tools, however, only provide mere functional descriptions for coding genes instead of linking known sequences to their related public database records. In particular, for proteins of unknown functions, i.e. hypothetical proteins, public databases can provide useful additional information. To address these challenges and to foster FAIR principles in general, the new software tool Bakta systematically assigns database accession numbers from e.g. UniRef and RefSeq to known protein sequences and related UniRef protein clusters as well as functional categories like COG, KEGG Orthology and GO. Recently, even Torsten Seemann, the developer of the famous Prokka tool, endorsed Bakta. It has been published in Microbial Genomics and is available via Docker and Conda as well as online here<https://bakta.computational.bio>. ____________________________________________________________________________________________________________________________________________ Social links and Contact Follow us on Twitter<https://twitter.com/nfdi4microbiota?lang=en> and GitHub<https://github.com/NFDI4Microbiota>! Questions or suggestions<https://nfdi4microbiota.de/contact-form/>? Learn more<https://nfdi4microbiota.de/> about NFDI4Microbiota! Subscription / Unsubscription<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Dirk Heinz - komm. Administrative Geschäftsführerin: Elisabeth Gerndt Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

3 years, 7 months

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NFDI4Microbiota - Showcase of active Use Cases

by Magel, Maja

Dear all, this year, 6 Use Cases<https://nfdi4microbiota.de/latest/usecase> have been selected by NFDI4Microbiota. During the Use Case showcase on the 9th of November 08:30-10:00 AM, you will be able to learn what each Use Case entails. To attend, please use the following link to register for the online part of this hybrid event: https://www.eventbrite.co.uk/e/nfdi4microbiota-use-case-showcase-online-att…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.event…> The showcase will include pitches on the topics * "Integration of multi-omics data of microbial species" (MULTI) * "Crowd-sourcing high-quality descriptions of novel taxa" (GUT) * "Replacement or Extension: Systematic Assessment of Differences in Taxonomic Profiling Between Amplicon Sequencing Variants and Operational Taxonomic Units" (AmpliBench) * "Functional profiling and routine diagnosis of humane microbiomes by metaproteomics" (MetaProt) * "Collecting and matching microbial strain identifiers" (Strain-ID) * "Provenance and usage of metagenome data" (MetaProv) As well as a general introduction to Use Cases in NFDI4Microbiota. Use Cases are generally real scientific projects in the broad field of microbiome research that were selected to aid NFDI4Microbiota facilitate and stimulate data sharing according to FAIR principles concerning microbial data and their associated metadata. The focus of the event is to give you a short overview and to enable future community engagement. NFDI4Microbiota is looking forward to seeing you online. Kind regards, Maja Magel Projektkoordination NFDI4Microbiota Institut für Medizinische Mikrobiologie Research Group Functional Microbiome [cid:image001.png@01D8E93B.E6CA27A0] ________________________________________ 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@01D8E93B.E6CA27A0] ________________________________________ Tel.: +49 (0) 241 80-38117 E-Mail: mmagel(a)ukaachen.de<mailto:mmagel@ukaachen.de> Aufzug D4, Etage 5, Raum 34 Universitätsklinikum Aachen Pauwelsstraße 30 52074 Aachen

3 years, 7 months

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TODAY: BacDive & MediaDive Workshop

by Isabel Schober

Hello everyone, this is a reminder that this year's *Bac/Dive/ <https://bacdive.dsmz.de/> Workshop and Q&A* will take place *today, * *6th October 2022*, *2 - 4 PM CEST online*! Topics: * *Introduction to **Bac**/Dive/**Advanced Search* <https://bacdive.dsmz.de/advsearch> Learn how to build complex queries using the Bac/Dive/ advanced search options and retrieve a custom data set for your research. * *Introduction to the**Bac <https://api.bacdive.dsmz.de/>**/Dive/**API* <https://api.bacdive.dsmz.de/> Learn how to programmatically access Bac/Dive/ data for large scale analysis. * *Introduction to**Media <https://mediadive.dsmz.de/>**/Dive/* <https://mediadive.dsmz.de/> Learn how to find new media recipes for your cultivation in Bac/Dive/'s new sister database and how to use its API to programmatically access media data for large scale analysis. * *Q&A with the developers* Any questions left? You can ask the Bac/Dive/ and Media/Dive/ developers directly! *No registration is needed! *Just join us on Zoom.* * Login details: https://dsmz-de.zoom.us/j/3818375651?pwd=OUVMMEtSZnh3SGxmcEJRUS9oTkcrdz09 /Meeting ID: 381 837 5651// //Passcode: m8j819/ We are looking forward to seeing you there! The Bac/Dive/ Team -- Dr. Isabel Schober 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 Directors: Prof. Dr. Joerg Overmann; Bettina Fischer Local court: Braunschweig HRB 2570 Chairman of the management board: MR Dr. David Schnieders DSMZ - A member of the Leibniz Association www.leibniz-gemeinschaft.de

3 years, 8 months

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2026

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2022