Santosh lamichhane
@santoshlamichhane.bsky.social
PI, Academy Research fellow, Docent (Adj. Prof.) UTU, Finland 🇫🇮 Born in 🇳🇵
Curious about what gut microbes are doing inside us 🤔
Metabolomics- Lipidomics- Microbial metabolism-type 1 diabetes-autoimmunity
Curious about what gut microbes are doing inside us 🤔
Metabolomics- Lipidomics- Microbial metabolism-type 1 diabetes-autoimmunity
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.
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
June 13, 2025 at 6:12 AM
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.
Reposted by Santosh lamichhane
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
May 30, 2025 at 2:16 PM
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
Reposted by Santosh lamichhane
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.
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
May 24, 2025 at 8:21 AM
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.
Reposted by Santosh lamichhane
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
March 11, 2025 at 5:29 AM
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
Reposted by Santosh lamichhane
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
The HuMet Repository - Watching human metabolism at work
www.sciencedirect.com/science/arti...
All data provided in an interactive repository:
humet.org
March 5, 2025 at 12:58 PM
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
The HuMet Repository - Watching human metabolism at work
www.sciencedirect.com/science/arti...
All data provided in an interactive repository:
humet.org
Reposted by Santosh lamichhane
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.
March 3, 2025 at 8:25 PM
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
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
March 1, 2025 at 5:28 AM
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
Reposted by Santosh lamichhane
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
February 28, 2025 at 10:10 AM
I'm happy to share a correspondence in @naturemetabolism.bsky.social in which I was involved. #metabolomics #lipidomics www.nature.com/articles/s42...
Reposted by Santosh lamichhane
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.
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
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
February 27, 2025 at 6:52 PM
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.
Reposted by Santosh lamichhane
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!
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
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
February 26, 2025 at 2:27 AM
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!
Reposted by Santosh lamichhane
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
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
February 26, 2025 at 2:24 AM
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
www.medrxiv.org/content/10.1...
#T1D #bileacids #autoimmunity #metabolomics
Reposted by Santosh lamichhane
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.
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
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
February 26, 2025 at 2:27 AM
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.
www.medrxiv.org
February 25, 2025 at 7:09 PM
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.
Reposted by Santosh lamichhane
February 24, 2025 at 6:28 PM
Reposted by Santosh lamichhane
🚨 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
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
February 17, 2025 at 10:33 AM
🚨 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
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
Reposted by Santosh lamichhane
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...
February 17, 2025 at 4:21 PM
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...
Reposted by Santosh lamichhane
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
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
February 14, 2025 at 9:05 PM
Reposted by Santosh lamichhane
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
February 14, 2025 at 6:50 PM
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.
Reposted by Santosh lamichhane
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
Another impactful study of this metabolite: pubs.acs.org/doi/full/10.1021/jf0718906
February 7, 2025 at 6:42 PM
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
Another impactful study of this metabolite: pubs.acs.org/doi/full/10.1021/jf0718906
Reposted by Santosh lamichhane
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
February 7, 2025 at 4:45 AM
Metabolites driving chemotaxis in prokaryotes www.nature.com/articles/s41...
Reposted by Santosh lamichhane
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
Download: github.com/mzmine/mzmin...
youtu.be/AFv55sUn9Lg
New features in mzmine 4.5
YouTube video by mzio GmbH
youtu.be
January 28, 2025 at 1:11 PM
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
Download: github.com/mzmine/mzmin...
youtu.be/AFv55sUn9Lg
Reposted by Santosh lamichhane
Our latest article "Data sharing restrictions are hampering precision health in the EU"
Here is the open acces link:
rdcu.be/d6Bgd
#precisionmedicine 🧬💊🧪
Here is the open acces link:
rdcu.be/d6Bgd
#precisionmedicine 🧬💊🧪
January 17, 2025 at 12:59 PM
Our latest article "Data sharing restrictions are hampering precision health in the EU"
Here is the open acces link:
rdcu.be/d6Bgd
#precisionmedicine 🧬💊🧪
Here is the open acces link:
rdcu.be/d6Bgd
#precisionmedicine 🧬💊🧪
Reposted by Santosh lamichhane
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...
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...
www.nature.com
January 17, 2025 at 6:33 PM
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...
Reposted by Santosh lamichhane
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...
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...
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.
www.nature.com
January 14, 2025 at 9:36 AM
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...
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...
Reposted by Santosh lamichhane
Happy new year to all! We are back again with TWO featured metabolites. Check it out at cmmc.gnps2.org/molecule_month/
January 7, 2025 at 8:06 PM
Happy new year to all! We are back again with TWO featured metabolites. Check it out at cmmc.gnps2.org/molecule_month/