NFDI4Microbiota Annual Conference 2025 - “From Lab to Publication: Bridging the Gap with Best Practices”In-Person Event

30 Sept 2025, 12:00 → 2 Oct 2025, 14:00 Europe/Berlin

ZB MED – Information Centre for Life Sciences (Cologne)

Alice McHardy, Konrad Förstner

We welcome you to the

4^th NFDI4Microbiota Annual Conference 2025

 

The motto of this year's conference is “From Lab to Publication – Bridging the Gap with Best Practices”! The conference will take place from 30 September to 2 October 2025 at the ZB MED – Information Centre for Life Sciences in Cologne.

You will have the chance to learn how to use our services and to make your data FAIR through dedicated hands-on workshops and with the opportunity to test your newly gained skills with a small training dataset.

This year's conference will once again feature inspiring keynotes and interactive poster sessions.

We look forward to your participation!

 

Registration deadline: 11 September 2025

Floor_Plan_and_Timetable.pdf

Tuesday 30 September

12:00 → 13:30 Lunch and Registration

13:30 → 13:45 Opening and Closing

13:30 Welcome and Introduction

Speaker: Konrad Förstner (NFDI4Microbiota Speaker, ZB MED)

13:45 → 14:45 Keynotes

13:45 Once Upon a Lab: A FAIRy Tale of ELNs (online presentation)

With the ever increasing realisation that a majority of scientific research data that is published is not “FAIR” (Findable, Accessible, Interoperable, Reusable) there has been a strong push in recent years to implement digital tools within the labs (namely Electronic Lab Notebooks) to combat this. However, implementing an Electronic Lab Notebook (ELN) is no mean feat, it is a highly complex sociotechnical endeavour. Furthermore, we need to understand that implementing an ELN is not the end of the journey; digital tools and digitally produced data are arguably no more FAIR than the original paper based lab book if they are not utilised to their full extent. This talk will explore the barriers and considerations that need to be taken into account for a successful implementation, drawn from over a decade of experience of working in this sphere.

Speaker: Dr Samantha Pearman-Kanza (University of Southampton)

14:45 → 15:15 A user journey. Basic Services in action

This user journey demonstrates eight Base4NFDI services in action. Meet our small imaginary research team and find out how they use Base4NFDI services for their research and research data management. Find out how this helps them get things done and stick to the FAIR principles throughout their project's entire research data lifecycle.

Speaker: Alois Wieshuber (Base4NFDI / DESY)

15:15 → 15:45 Coffee Break

15:45 → 17:45 From Bench to Browser: Microbiome Analysis Without Coding Skills

Workshops for the following target audience:

• Wet lab scientists with knowledge of microbiology and no experience in programming
• All those who are interested in the workshop topics

15:45 Workshop 1: Managing your 16S Amplicon Data: An Introduction to Qiita

Taking the step from running experiments in the wet lab, and generating samples, to analyzing your own 16S Amplicon sequencing data can be quite daunting. Thus, in this workshop, we aim to introduce you to Qiita, a microbial study management platform used to manage and compute studies with 16S microbiome data. This framework establishes an easily accessible way for non-computational scientists to analyse their own data with the option of using pre-defined workflows or building their own. We will give you a compact overview on what you need to get started, possible pitfalls when it comes to data preparation, and show you how to use Qiita for your needs.

Speakers: Anna Rehm (Justus-Liebig-University Giessen), Stefan Janssen (Justus-Liebig-University Giessen)

15:45 → 17:45 From Lab Bench to Data Bench: Practical Research Data Management for Scientists

Workshops for the following target audience:

• Wet lab scientists, data stewards, principal investigators
• All those who are interested in the workshop topics

15:45 Workshop 3: GSC standards, where to find them and how to use them

Standardised and well annotated metadata are a cornerstone of the FAIR data principles. In this workshop, we will begin with the metadata standards developed and maintained by the Genomic Standards Consortium (GSC), which provides checklists and extensions for a variety of environments and biomes. We will then zoom in on the minimal metadata standards for environmental and biological context proposed by the NFDI4Microbiota consortium, built on the GSC framework. Next, you’ll learn how to choose biome-specific ontologies and use the Ontology Lookup Service (OLS) to annotate your metadata, including how to record the value NULL. Finally, we will move to the NMDC Sandbox submission portal (ORCID required), to validate your tables with DataHarmonizer and export compliant, annotated metadata. By the end of the workshop, participants will be able to create reusable metadata annotations that enhance the reach and impact of their data.

Speaker: Martin Bole (Helmholtz Centre for Environmental Research)

15:45 → 17:45 From Pipelines to Portals: Next-Generation Tools for Microbiome Analysis

Workshops for the following target audience:

• Bioinformaticians, software developers, computational biologists
• All those who are interested in the workshop topics

15:45 Workshop 7: Identifying Identifiers: Harnessing StrainInfo’s tools to find and resolve strain designations in literature and metadata

Extracting meaningful biological entities (e.g. sequence accession numbers and species names) from unstructured text is an essential yet complex task. In microbiology, the identification is further complicated by the use of different designations (e.g. DSM 20543 and LMG 28910) for the same strain. Learn how to identify strain designations in literature and sequence metadata by leveraging StrainInfo's API and libraries. A workshop ideal for bioinformaticians, data scientists and researchers with a beginner-level understanding of Python, where participants will be guided through hands-on exercises. By the end of the workshop, attendees will have written a script capable of extracting strain identifiers from both literature and sequence metadata. This script will utilize the StrainInfo API to identify these strains and collect key information such as alternative designations, type strain status, taxonomy and more.

Speaker: Artur Lissin (DSMZ)

18:00 → 20:00 Diner

Wednesday 1 October

08:30 → 09:00 Morning Coffee and Registration

09:00 → 10:30 Keynotes

09:00 The enduring challenge of setting up a FAIR lab

A consensus has been reached that research data must be FAIR. Most researchers understand it as making their data findable, accessible, interoperable, and reusable during or after the publication process. However, by this stage, it often turns out that some key information about experiments is missing or the experimental design is irreparably incomplete or flawed, questioning the validity of the corresponding datasets. One solution is producing FAIR data from the very inception of the study—rather than trying to make them FAIR post hoc. This requires a FAIR lab, a kind of lab organisation where all ins and outs of the research process can be traced back to their origins, starting with unambiguous identification of samples and reagents, faithful registration of protocols and metadata, and ending by the quality control of final data, their sharing and linking to publications. Acceding to this higher level of responsibility for own research data takes a significant change in lab culture.

Speaker: Dr Alexandre Smirnov (University of Strasbourg - CNRS)

10:30 → 11:00 Coffee Break

11:00 → 12:30 Panel Discussion

11:00 Panel discussion: Wet-Lab Meets AI – How and Where?

Speakers: Alexandre Smirnov (University of Strasbourg - CNRS), Alice McHardy (Helmholtz Centre for Infection Research), Ines Krohn (University of Hamburg), Lorenz Reimer (DSMZ), Ulisses Nunes da Rocha (Helmholtz Centre for Environmental Research)

12:30 → 13:30 Lunch

13:30 → 15:00 From Lab Bench to Data Bench: Practical Research Data Management for Scientists

Workshops for the following target audience:

• Wet lab scientists, data stewards, principal investigators
• All those who are interested in the workshop topics

13:30 Workshop 4: Notebook 2.0: How to switch to ELNs in your lab

Discover how Electronic Lab Notebooks (ELNs) enhance reproducibility, collaboration, and FAIR compliance in microbiota workflows. We will demonstrate best practices in eLabFTW - a free and open source favorite in the field - by covering its interface, metadata features, and integrations, then guide you through a hands-on exercise to create and manage a sample project. By the end, you’ll be ready to implement ELNs in both wet-lab and bioinformatics settings.

Speaker: Clemens Thölken (Philipps-Universität Marburg)

13:30 → 15:00 From Pipelines to Portals: Next-Generation Tools for Microbiome Analysis

Workshops for the following target audience:

• Bioinformaticians, software developers, computational biologists
• All those who are interested in the workshop topics

13:30 Workshop 8: Federated and FAIR: Scalable Data Management with Aruna v3 (Part I)

Modern microbiome research, as addressed by NFDI4Microbiota, depends on scalable and interoperable infrastructures. Aruna v3 introduces a federation-first approach to research data management, eliminating central coordination while preserving institutional autonomy. Built on peer-to-peer technologies, Aruna ensures secure and efficient metadata replication, data locality-aware compute integration, and governance across distributed domains.

The attendees of this workshop will be introduced to the Aruna Version 3 architecture and its new features. Furthermore, the presentation will comprise a demonstration of practical applications within the field, in addition to the provision of a set of guidelines on the establishment of FAIR-compliant data pipelines for the management of research data that is both scalable and secure.

Speakers: Jannis Hochmuth (Justus-Liebig-University Giessen), Lukas Brehm (Justus-Liebig-University Giessen)

15:00 → 15:30 Coffee Break

15:30 → 16:30 From Lab Bench to Data Bench: Practical Research Data Management for Scientists

Workshops for the following target audience:

• Wet lab scientists, data stewards, principal investigators
• All those who are interested in the workshop topics

15:30 Workshop 5: RDM Basics: Writing DMPs and Applying Metadata Standards

This workshop covers fundamental research data management (RDM) practices, including drafting a Data Management Plan (DMP) and working with common metadata standards. Through brief interactive examples, participants will learn how to structure a DMP and tag datasets using existing schemas.

Speaker: Clemens Thölken (Philipps-Universität Marburg)

15:30 → 16:30 From Pipelines to Portals: Next-Generation Tools for Microbiome Analysis

Workshops for the following target audience:

• Bioinformaticians, software developers, computational biologists
• All those who are interested in the workshop topics

15:30 Workshop 8: Federated and FAIR: Scalable Data Management with Aruna v3 (Part II)

Modern microbiome research, as addressed by NFDI4Microbiota, depends on scalable and interoperable infrastructures. Aruna v3 introduces a federation-first approach to research data management, eliminating central coordination while preserving institutional autonomy. Built on peer-to-peer technologies, Aruna ensures secure and efficient metadata replication, data locality-aware compute integration, and governance across distributed domains.

The attendees of this workshop will be introduced to the Aruna Version 3 architecture and its new features. Furthermore, the presentation will comprise a demonstration of practical applications within the field, in addition to the provision of a set of guidelines on the establishment of FAIR-compliant data pipelines for the management of research data that is both scalable and secure.

Speakers: Jannis Hochmuth (Justus-Liebig-University Giessen), Lukas Brehm (Justus-Liebig-University Giessen)

16:30 → 20:00 Poster Session

16:30 Poster presentation

17:30 → 20:00 Finger Food during Poster Session

Thursday 2 October

08:30 → 08:45 Morning Coffee and Registration

08:45 → 10:15 Keynotes

08:45 Small but effective! Small proteins impacting large membrane complexes in Methanosarcina mazei

Small open reading frame (sORF)-encoded proteins, with less than 100 amino acids in length, have attracted increasing attention over the past decade after being largely overlooked due to limitations in classical bioinformatics and biochemical methodologies. In the methanoarchaeal model organism Methanosarcina mazei, differential RNA sequencing has predicted 1,340 putative sORFs, 407 of which have been validated at the translational level through ribosome profiling (Tufail et al. 2024; Weidenbach et al. 2021). By enriching the low molecular weight proteome and combining top-down and bottom-up proteomic analysis, a total of 234 small proteins were validated on protein level (Herdering et al. unpublished). Despite this progress, the majority of these novel sORFs remain functionally unannotated, as they often lack recognizable domains or homologs with known functions

Using a combination of biochemical and genetic approaches, we characterized a subset of these newly identified small proteins that specifically interact with large membrane-associated proteins in M. mazei (e.g., Habenicht et al. 2023). Our work reveals that these small proteins, highly conserved within methanogenic archaea, play regulatory roles in key carbon and nitrogen metabolic pathways. During the talk two further examples will be introduced. (i) The trimethylamine transporter MttP belongs to the drug/metabolite exporter (DME) family, a group of efflux proteins found across all domains of life and implicated in the transport of a wide range of metabolites and compounds. However, unlike most of the ubiquitously distributed DME family members, we demonstrated that Methanosarcina-derived MttP forms a stable complex with two previously uncharacterized small proteins. (ii) Another newly identified small protein, sORF16, which is only 49 amino acids in length, is shown to tightly associate with the large tetrahydromethanopterin S-methyltransferase (Mtr) complex, a membrane associated key enzyme in hydrogenotrophic and methylotrophic methanogenesis. Notably, sORF16 plays a potential role in regulating methanogenesis pathways in response to environmental changes. These findings emphasize the functional significance of sORF-encoded small proteins and highlight their underexplored regulatory potential in microbial systems.

Tufail, Muhammad Aammar, Britta Jordan, Lydia Hadjeras, Rick Gelhausen, Liam Cassidy, Tim Habenicht, Miriam Gutt, et al. 2024. “Uncovering the Small Proteome of Methanosarcina Mazei Using Ribo-Seq and Peptidomics under Different Nitrogen Conditions.” Nature Comm. https://doi.org/10.1038/s41467-024-53008-8.

Weidenbach, Katrin, Miriam Gutt, Liam Cassidy, Cynthia Chibani, and Ruth A. Schmitz. 2021. “Small Proteins in Archaea, a Mainly Unexplored World.” Journal of Bacteriology, September. https://doi.org/10.1128/JB.00313-21.

Habenicht T, Weidenbach K, Velazquez-Campoy A, Buey RM, Balsera M, Schmitz RA.2023. „Small protein mediates inhibition of ammonium transport in Methanosarcina mazei—an ancient mechanism?” Microbiol Spectr11:e02811-23. doi.org/10.1128/spectrum.02811-23

Speaker: Prof. Ruth Schmitz-Streit (Kiel University (CAU))

10:15 → 10:45 Coffee Break

10:45 → 12:15 From Bench to Browser: Microbiome Analysis Without Coding Skills

Workshops for the following target audience:

• Wet lab scientists with knowledge of microbiology and no experience in programming
• All those who are interested in the workshop topics

10:45 Workshop 2: Running microbiome analyses on CloWM

High-throughput sequencing has made metagenomics routine, but turning raw reads into biologically meaningful insights still requires considerable computational expertise, and resources. NFDI4Microbiota’s Cloud-based Workflow Manager (CloWM) aims to lower this barrier by providing end-to-end metagenomic analyses in the cloud, empowering researchers to focus on biology rather than infrastructure - no installation required, free for academic use.

What we will cover:
-Navigating CloWM’s interface
-Managing data within CloWM’s data buckets
- Exploring & executing best-practice metagenomic workflows (SPIRE workflow, nHUMAnN, SameStr)
- Accessing & downloading outputs
- Interpreting results & planning next steps

Speaker: Daniel Podlesny (EMBL)

10:45 → 12:15 From Lab Bench to Data Bench: Practical Research Data Management for Scientists

Workshops for the following target audience:

• Wet lab scientists, data stewards, principal investigators
• All those who are interested in the workshop topics

10:45 Workshop 6: Using the virus database VirJenDB to access metadata and sequences for bioinformatics analyses

Virus research depends on accurate sequence and metadata, but is often hampered by errors in user-submitted data and a lack of standardized metadata practices. Viral genomes are small and highly variable and current challenges in their organization are compounded by inconsistencies in related metadata (e.g., taxonomy, segment nomenclature, lifecycle definitions). VirJenDB (VJDB; virjendb.org) aims to provide a platform to address these challenges with a metadata-driven, integrative virus sequence database. Virus metadata and sequences from primary and secondary sources such as NCBI Virus, ENA, BVBRC, and community standards like MIGS-VI and ENA Sample Checklists have been merged and harmonized into an integrated dataset. The integrated dataset is used to enable development of metadata schema extensions and through different applications supports virus researchers throughout the data lifecycle. The VJDB dataset is accessible through the web portal, and provides input to bioinformatics webtools (future feature). In this demo, we will start with an overview of virus resources and demonstrate how to use currently available features of the VJDB portal: searching and refining results, downloading data, and exploring metadata schemas. Note that the demo content is subject to change depending on user demands.

Speaker: Kilian Ossetek (Friedrich Schiller University Jena)

10:45 → 12:15 From Pipelines to Portals: Next-Generation Tools for Microbiome Analysis

Workshops for the following target audience:

• Bioinformaticians, software developers, computational biologists
• All those who are interested in the workshop topics

10:45 Workshop 9: CAMI benchmarking portal: towards standards and best practices in computational metagenome analyses

We invite you to a hands-on workshop on the CAMI Benchmarking Portal (https://cami-challenge.org, Meyer et al., NAR 2025), an online platform that automates comprehensive evaluation and ranking of software for metagenomic analyses. The portal builds upon the metrics, datasets, and best practices established by the community-driven initiative for Critical Assessment of Metagenome Interpretation (CAMI).

This workshop will cover:
- An overview of the CAMI resources available to the community, including benchmark datasets, standards, and integrated evaluation software
- Exploring and interpreting results from CAMI benchmarking challenges and other users, and how to use the performance rankings to derive software recommendations, such as for integration in workflows
- Submitting your own metagenome assembly, genome and taxonomic binning, and taxonomic profiling results on CAMI datasets for benchmarking

The workshop is intended for researchers, developers, or anyone interested in microbiome analysis, metagenomics, and bioinformatics tool development, as well as good benchmarking principles.

Speaker: Fernando Meyer (Helmholtz Centre for Infection Research)

12:15 → 12:30 Opening and Closing

12:15 Closing Plenary and Take-home Recommendations

12:30 → 13:30 Lunch and Farewell