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Santosh lamichhane @santoshlamichhane.bsky.social · Jun 13

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.

Pieter Dorrestein @pieterdorrestein.bsky.social · Jun 12

If you have ever wondered what might happen to short chain fatty acids made by the microbiome. Here is a large class of metabolites and how they link to biology. www.cell.com/cell/fulltex...

The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids

Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library containing hundreds of N-acyl lipids, including conjugates with short-chain fatty acids. This resource enabled the...

www.cell.com

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Reposted by Santosh lamichhane

Pieter Dorrestein @pieterdorrestein.bsky.social · May 30

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

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Reposted by Santosh lamichhane

Tomáš Pluskal @pluskal-lab.org · May 24

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.

Nature Biotechnology @natbiotech.nature.com · May 23

Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - @pluskal-lab.org @iocbprague.bsky.social go.nature.com/4k1n5iC

Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology

A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.

go.nature.com

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Santosh lamichhane @santoshlamichhane.bsky.social · Mar 15

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

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Santosh lamichhane @santoshlamichhane.bsky.social · Mar 13

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.

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Reposted by Santosh lamichhane

Chris Pook @drchrispook.bsky.social · Mar 11

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

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Reposted by Santosh lamichhane

Karsten Suhre @ksuhre.bsky.social · Mar 5

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

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Reposted by Santosh lamichhane

Pieter Dorrestein @pieterdorrestein.bsky.social · Mar 3

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.

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Santosh lamichhane @santoshlamichhane.bsky.social · Mar 1

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

Pieter Dorrestein @pieterdorrestein.bsky.social · Feb 28

Reverse metabolomics made these two papers a reality. www.nature.com/articles/s41... and www.cell.com/cell/fulltex... but hard for others to do similar analysis as the data science is at a high level. So @vincentlamoureux.bsky.social wanted to enable others with this powerful strategy rdcu.be/ebIF2

A guide to reverse metabolomics—a framework for big data discovery strategy

Nature Protocols - In this reverse metabolomics protocol, a tandem mass spectrometry spectrum is used as a search term to probe public metabolomic data. Analysis of the metadata connected with...

rdcu.be

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Reposted by Santosh lamichhane

Michael Witting @metabomichael.bsky.social · Feb 28

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

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

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

www.nature.com

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Reposted by Santosh lamichhane

Pieter Dorrestein @pieterdorrestein.bsky.social · Feb 27

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.

Cell Press @cellpress.bsky.social · Feb 27

The #InternationalSpaceStation is overly sterile; making it “dirtier” could improve astronaut health, microbiologists say. cell.com/cell/fulltex...

Learn more in @cp-cell.bsky.social
@pieterdorrestein.bsky.social, Rob Knight

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns

With long-term space travel and extraterrestrial habitation becoming feasible, understanding how space environmental exposures, microbial communities, and molecular profiles differ from Earth is cruci...

cell.com

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Santosh lamichhane @santoshlamichhane.bsky.social · Feb 27

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 🙏🏾.

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Reposted by Santosh lamichhane

Petter Brodin @petterbrodin.bsky.social · Feb 26

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!

Matej Oresic @matejoresic.bsky.social · Feb 26

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

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...

www.medrxiv.org

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Reposted by Santosh lamichhane

Matej Oresic @matejoresic.bsky.social · Feb 26

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

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...

www.medrxiv.org

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Reposted by Santosh lamichhane

Pieter Dorrestein @pieterdorrestein.bsky.social · Feb 26

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.

Matej Oresic @matejoresic.bsky.social · Feb 26

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

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...

www.medrxiv.org

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Santosh lamichhane @santoshlamichhane.bsky.social · Feb 25

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.

www.medrxiv.org

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Reposted by Santosh lamichhane

microbialcmmc.bsky.social @microbialcmmc.bsky.social · Feb 24

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

cmmc.gnps2.org

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Reposted by Santosh lamichhane

EMN Metabolomics Society @emn-metsoc.bsky.social · Feb 17

🚨 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

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Reposted by Santosh lamichhane

Tomáš Pluskal @pluskal-lab.org · Feb 17

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...

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Reposted by Santosh lamichhane

microbialcmmc.bsky.social @microbialcmmc.bsky.social · Feb 14

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

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

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Reposted by Santosh lamichhane

David Michaels @drdavidmichaels.bsky.social · Feb 14

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.

Volume 135: Perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS)

monographs.iarc.who.int

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Reposted by Santosh lamichhane

microbialcmmc.bsky.social @microbialcmmc.bsky.social · Feb 7

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

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Reposted by Santosh lamichhane

Marc-Emmanuel Dumas @marcedumas.bsky.social · Feb 7

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

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 ...

www.nature.com

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Reposted by Santosh lamichhane

mzmine @mzmine.bsky.social · Jan 28

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

New features in mzmine 4.5

YouTube video by mzio GmbH

youtu.be

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Santosh lamichhane @santoshlamichhane.bsky.social · Jan 21

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

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