Santosh lamichhane

Yet another new function of bile acids -and relevance of the microbiome in regulating the efficacy of medications.
#microbiome #IBD. Discovered using #metabolomics repository scale analysis.
#opendata Thanks to all the collaborators and Vincent for leading it. www.biorxiv.org/content/10.6...

There so much to learn what microbes are doing inside us. Glad to be part of this work, thanks to Pieter and the whole team.

It’s so nice that an important paper led by yasin - is out. www.nature.com/articles/s41.... This paper is a key milestone as it is the foundation for data science across data repositories through indexing and metadata harmonization of 1.6 million files (although much more now due to updates). 1/n

This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.

Wow, that's so cool.. Happy belated holi, which is one of my fav festivals..

San Diego is so much fun. If you have time, I would also suggest walking by La Jolla cove to the La Jolla Tide Pools area.

I'm looking at a paper in a decent journal that claims to have separated glucose, mannose and fructose on a Waters C18 BEH column. There's no detailed methodology and there's no chromatograms. This seems just impossible. What do we do about this sort of thing? #Metabolomics

Free access to 2,656 metabolites from 9 platforms measured at 56 time points and covering 6 challenges "suffered" by 15 healthy volunteers:

The HuMet Repository - Watching human metabolism at work

www.sciencedirect.com/science/arti...

All data provided in an interactive repository:

humet.org

We thank all the co-authors - and many others that are not part of the paper - for the wonderful discussion on this topic. The discussion is an important education to the field and needs to be accurately presented - including existing computational solutions to handle.

Many discoveries will (probably have already) line up due to this crucial data driven strategy. Grateful to @pieterdorrestein.bsky.social and the entire team that i could contribute and be part of this very important data driven reverse #metabolomics workflow led by @vincentlamoureux.bsky.social

Discovery of metabolites prevails amid in-source fragmentation - Nature Metabolism Nature Metabolism - Discovery of metabolites prevails amid in-source fragmentation

I'm happy to share a correspondence in @naturemetabolism.bsky.social in which I was involved. #metabolomics #lipidomics www.nature.com/articles/s42...

It’s not every day one gets to publish an article with NASA astronauts. This journey started in 2019 and withe the goal to understand the microbial and chemical make-up of the space station. We had lots of experience with analysis from swabs on earth.

So, cool. I was lucky enough to witness some of these bile acid treasures in person, during my visit to UCSD (your lab) last year 🙏🏾.

Early in life, secondary bile acids are generated by colonizing microbes, associated with risks of immune-mediated diseases and act as immunomodulatory substances. Great collaborative study now online!

Trajectories of microbiome-derived bile acids in early life - Insights into the progression to islet autoimmunity Recent studies reveal that gut microbes produce diverse bile acid conjugates, termed microbially conjugated bile acids (MCBAs). However, their regulation and health effects remain unclear. Here, we an...

Happy to share this preprint from our team, great collaboration with Mikael Knip, @pieterdorrestein.bsky.social, @lahesmaalab.bsky.social, and @petterbrodin.bsky.social . Special kudos to @santoshlamichhane.bsky.social.
www.medrxiv.org/content/10.1...
#T1D #bileacids #autoimmunity #metabolomics

This is such nice work, glad we could be part of it. Is shows how microbial bile acid amidates that differs in diabetic infants during their development could lead to immune dysbiosis.

Check out our new #preprint, a collaborative effort to explore emerging #bile acids (also referred as MCBAs) during early life. Briefly, here we analyzed MCBAs in early life and found distinct age-related trajectories linked to gut #microbiota, #immune modulation & islet #autoimmunity progression.

got microbial metabolites? Add to the public knowledgebase available through GNPS2!

cmmc.gnps2.org

🚨 Abstract deadline alert! 🚨

Friendly reminder to submit your oral abstract before March 6 – don’t miss the chance to showcase your work at hashtag#MetSoc2025!

Registration is now open: lnkd.in/eFZGi4CK

#Metabolomics #EMN

We will be hosting the first @mzmine.bsky.social Community Meeting at @iocbprague.bsky.social. Please register if you wish to learn about the latest developments in mzmine. More info: docs.google.com/document/d/1...

Baat Gene Knockout Alters Post-Natal Development, the Gut Microbiome, and Reveals Unusual Bile Acids in Mice Bile acids (BAs) are steroid detergents in bile that contribute to fat absorption, cell signaling, and microbiome interactions. The final step in thei…

sciencedirect.com/science/article/pii/S0022227522001304?via%3Dihub

nature.com/articles/s41575-024-00914-3

science.org/doi/10.1126/science.adl4100

nature.com/articles/s41586-020-2047-9

Important #PFAS news - Independent experts convened by the WHO's International Agency for Research on Cancer have classified #PFOA as carcinogenic to humans (Group 1) and #PFOS possibly carcinogenic to humans (Group 2B). In the past, manufacturers' mercenary scientists have questioned that evidence.

How does metabolomics help agriculture? Human health? A brief overview of this fungal metabolite-Fumonisin B2- shows the importance of this overlap. Check out more at cmmc.gnps2.org

Another impactful study of this metabolite: pubs.acs.org/doi/full/10.1021/jf0718906

An atlas of metabolites driving chemotaxis in prokaryotes - Nature Communications In this meta-analysis, the authors compile results from 60 years of chemotaxis research into a database of prokaryotic chemoeffectors that compares and analyses their effects as attractant, repellent ...

Metabolites driving chemotaxis in prokaryotes www.nature.com/articles/s41...

New features in mzmine 4.5 YouTube video by mzio GmbH

New #mzmine release out now! Matching millions of reference spectra against thousands of samples was never faster. Go and test it today.

Download: github.com/mzmine/mzmin...

youtu.be/AFv55sUn9Lg

Meanwhile, this year winter here is mild and Finns keep cycling on the frozen roads 😉

Our latest article "Data sharing restrictions are hampering precision health in the EU"
Here is the open acces link:
rdcu.be/d6Bgd
#precisionmedicine 🧬💊🧪

Two-layer homolog network approach for PFAS nontarget screening and retrospective data mining - Nature Communications PFAS are a wide class of ubiquitous chemically persistent environmental pollutants. Here the authors combine nontarget screening with a two-layer network approach to identify large numbers of PFAS fro...

Here the authors used molecular networking to discover PFASs and reanalyze public data sets to show they are observed in data from seven countries. Such a nice reuse of public data - but also alarming as they are seen in data going back to 2005. www.nature.com/articles/s41...

Free fatty acid receptor 4 modulates dietary sugar preference via the gut microbiota - Nature Microbiology Bacteroides vulgatus, a gut bacterium, promotes GLP-1 secretion through its metabolite, pantothenate, inhibiting sugar preference in mice.

Could gut bacteria be the reason behind your sugar cravings? 🤤

Check out this new paper by Zhang et al. linking a gut microbe, a free fatty acid receptor, and sugar intake.

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

Happy new year to all! We are back again with TWO featured metabolites. Check it out at cmmc.gnps2.org/molecule_month/