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-nfd...>’ 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/intr...> 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/1FAIpQLSeLZjdsoEGEXycWZbsKNRR92lGcpFGcB...>
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-...>
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-a...> 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...>
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
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-a...<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.eve...>
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
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