11:04 a.m.
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!
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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/>.
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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/>;.
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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-nfdi4microbiota-knowledge-base>’
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/introduction>
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.
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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/1FAIpQLSeLZjdsoEGEXycWZ...
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-course-on-metagenome-analysis>
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>
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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-attendance-for-hybrid-event-tickets-444534794537>
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.
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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/10.1111/1751-791...
<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>
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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.
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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>.
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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!
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Unsubscription<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.de/>
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