7:52 a.m.
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!
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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
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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/tZAqceyppjwpHdRHg7uF7AqPb6Yxq4Phq3fL>.
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.
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The NFDI4Microbiota consortium met in Cologne.
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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.
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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
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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
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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.
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Social links and Contact
Follow us on Twitter and GitHub!
Questions or suggestions?
Learn more about NFDI4Microbiota!
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