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

Keynotes

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Samantha Pearman-Kanza - Once Upon a Lab: A FAIRy Tale of ELNs (online presentation)

Senior Enterprise Fellow at the University of Southampton

 

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. 

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Alexandre Smirnov - The enduring challenge of setting up a FAIR lab

Group leader of UMR7156 - "Génétique Moléculaire, Génomique, Microbiologie" (GMGM), University of Strasbourg - CNRS

 

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.

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Ruth Schmitz-Streit - Small but effective! Small proteins impacting large membrane complexes in Methanosarcina mazei

 Director of the Institute of General Microbiology, Kiel University (CAU)

 

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