Functional Metabolomics Lab

I am super excited that our paper on inter-laboratory comparability of non-targeted LC–MS/MS analysis of dissolved organic matter was just published in ES&T.

pubs.acs.org/doi/10.1021/...

Community composition and strain identity drive metabolic competition and Staphylococcus aureus colonization resistance in Synthetic Nasal Communities The human nasal microbiome is a low-diversity ecosystem whose assembly principles and mechanisms of colonization resistance remain poorly understood. In particular, Staphylococcus aureus colonization ...

Preprint from our lab and @func-metabo-lab.bsky.social: In synthetic nasal communities a single Corynebacterium propinquum strain can exclude Staphylococcus aureus through nutrient competition. www.biorxiv.org/content/10.6...

A huge thank you to Nike and the Forchhammer Lab and to Khaled Selim and all co-authors, especially our Natural-Product-Partner-in-Crime Chambers Hughes for solving the structure of 2’-deoxyxanthopterin B2, and Karoline Steuer-Lodd and the Ansel Hsiao lab for generating the mutants.

Our data show that CutA binds copper more strongly in the presence of pteridines, suggesting that these metabolites act as co-factors that modulate copper binding and redox homeostasis.

New paper from our team:
Led by @nike-wagner.bsky.social, we just published our findings on how the metabolite class of pteridines binds to the previously cryptic CutA protein. We used our native metabolomics approach to identify pteridines as ligands of CutA.
www.pnas.org/doi/10.1073/...

Combining the new tool with the bioluminescent bioreporter strains from Heike Brötz-Oesterhelt and her students Julian Schubert and Leonard Boldt was a key element to achieve the high sensitivity of the bioactivity assays needed for microfractions.

Most importantly, the paper wouldn't have been possible without Christian Geibel, who led the project, optimized the method, and pushed the paper over the finish line.

Thanks a lot Christian and everybody else at the University of Tuebingen and UC Riverside who were involved in the project 🧡🧡🧡

Another key component was the analysis software, which Simon Knoblauch, back then a master’s student in our group, built and which, thanks to the help of @mingxunwang.bsky.social, is now available through @gnps2.bsky.social.

Its great to see the project in completion after almost four years ago, when Albert Hernandez, a mechanical engineer from UCSD, joined us in Tübingen, and started building the microspotter.

This was a large interdisciplinary effort together with the groups of Heike Brötz-Oesterhelt within the @cmfi.bsky.social Tübingen, and @mingxunwang.bsky.social at @ucriverside.bsky.social.

YouTube video by Functional Metabolomics Lab Microspotter1.0

Making use of high-speed, low-volume fractionation, we can achieve similar sampling rates for bioactivity measurements as for the mass spec DDA cycles, which enables correlation of LC-MS and LC-bioactivity data and pinpoints individual active metabolites.
www.youtube.com/watch?v=PTC9...

We are super excited that our new paper on microfluidic-based LC-MS/MS fractionation in combination with bioluminescence bioreporters readouts, for compound-resolved bioactivity metabolomics, was just published: pubs.acs.org/doi/10.1021/...

Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling - Nature Communications To improve annotation in non-targeted metabolomics studies, authors develop a Multiplexed Chemical Metabolomics (MCheM) platform, combining post-column derivatization with integrated data processing. ...

New paper from the group. Together with Chambers Hughes, Giovanni Vitale and our amazing collaborators, we developed a multiplexed chemical metabolomics workflow to assign functional groups in non-targeted LC-MS/MS data:

www.nature.com/articles/s41...

Behind the paper story:
go.nature.com/45ljV4d

We are super excited to start a new project with support from the Simons Foundation.
We will leverage our metabolomics tools and SynCom models to study how microbes shape the production, transformation, and fate of marine DOM.
Thanks so much @simonsfoundation.org‬ for making this possible!

Turf algae redefine the chemical landscape of temperate reefs, limiting kelp forest recovery In temperate regions experiencing rapid ocean warming, kelp forests are being replaced by chemically rich turf algae. However, the extent to which these turf algae alter the surrounding chemical envir...

If you want to read more about how the changing reef exo-metabolome, driven by invasive red algae, affects kelp survival, you can find the paper here: www.science.org/doi/10.1126/...

We are pretty stoked that our paper on chemical shifts in kelp forests in the Gulf of Maine made it onto the front cover of ‪@science.org
Big congratulations to Shane Farrell and everybody involved! ✌️✌️✌️

Exciting invited talk by Daniel Petras @daniel-petras.bsky.social Functional #Metabolomics Approaches for Understanding Microbial Community Dynamics at the Molecular Level. #ICTC13 @func-metabo-lab.bsky.social

Thanks for the shout-out! Most credits are due to @nike-wagner.bsky.social

Another success story of native MS. Pteridines, found also in #cyanobacteria, bind to cutA, possibly bridging copper homeostasis and cellular redox regulation.
doi.org/10.1101/2025...
More about functional metabolomics at #ICTC13 from @daniel-petras.bsky.social (Invited speaker).

This was a big collaborative effort with multiple groups from
@cmfi.bsky.social (Forchhammer, Selim, Link, Hughes) and @maxplanck.de Tuebingen (Hartmann), from microbiology phenotyping to metabolomics, natural product structure elucidation, and biophysical interaction studies. 🧡

We screened cell extracts from the cyanobacterium Synechococcus, for interaction with the homotrimer CutA, which can be found across the tree of life. Our results identified pteridines, to be ligands which enhances CutA copper binding and redox balance.

New reprint from the team: Lead by @nike-wagner.bsky.social, we used our native metabolomics setup to shed new light onto the function of the CutA protein.
www.biorxiv.org/content/10.1...

There will be also a remote participation option and all sessions will be recorded.
The recordings from our past summer schools are on youtube and linked on our web page:
www.functional-metabolomics.com/resources

Good news: We will have another summer school on non-targeted metabolomics this year! Organized by Martin Hansen and Scott Jarmusch, this year's summer school will be hosted at DTU in Copenhagen from August 18-22, inc. a summer camp style accommodation option at DTU.
Sign up:
tinyurl.com/NTMS2025

New preprint from our collaboration with @aliciaperezlorente.bsky.social from Diego Romero's group, who spend some time with us at @cmfi.bsky.social. It's great to see all the puzzle pieces coming together, providing a detailed snapshot of the molecular interplay between Bacillus and and Botrytis.

YouTube video by Functional Metabolomics Lab La Pavoni - Espresso Tutorial

We are very proud that after a long repair/upgrade and moves across continents, our most critical piece of equipment is fully functional again. 💪💪💪
Big thanks to Jorge and Karo for fixing it and for generating the tutorial.
❤️
www.youtube.com/watch?v=Bf43...

YouTube video by Functional Metabolomics Lab VMOL Seminar #29 - mzmine series: 2. Multimodal Data Processing (Ansgar Korf)

In case you missed part 2 of our our #mzmine seminar series on @ansgarkorf.bsky.social on:
- LC-MS²
- GC/EI-MS
- MALDI imaging
the recording is online here:
www.youtube.com/watch?v=cGA5...

Coming up next:
Dec 3rd, 5 PM CET / 8 AM PST
@steffenheu.bsky.social on analyzing LC-MS and LC-IMS-MS data

Contact Information VMOL Seminar Please sign up here if you want to participate regularly in the VMOL Seminar (Tuesdays 17:00 PM CET / 8:00 AM PST on Zoom). Regístrese aquí si desea participar regularmente en el Seminario VMOL (marte...

If you wana stop by, you can sign up to the VMOL seminar email list here:
docs.google.com/forms/d/e/1F...

(we will send out the zoom link the day before the seminar)

Next Tuesday, Nov 19, 5 pm CET / 8 am PST we will have the next #VMOL seminar #mzmine series on multimodal data processing using mzwizard.

And in case you wana watch the last mzmine seminar on non-targeted LC-MS/MS data processing, you can find the recording here: youtu.be/UnqVtZngzl0

Eco-Metabolomics Workshop 2024 Recording of the Eco-metabolomics workshop 2024: The Comprehensive Metabolomics Study of Ecological Interactions with hands-on sessions Organized by Dr. Carl...

In case you wana check out the different lectures, we uploaded the recordings to our youtube channel:
www.youtube.com/playlist?lis...