Simone Zuffa

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🗓️ Jul 28–Aug 10 2025

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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...

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...

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Milk phospholipid-coated lipid droplets modulate the infant gut microbiota and metabolome influencing weight gain - Microbiome Background The supramolecular structure and composition of milk fat globules in breast milk is complex. Lipid droplets in formula milk are typically smaller compared to human milk and differ in their ...

The last of my PhD projects is finally out! This was a great collaboration with Danone, looking at supplementing infant formula with a novel milk fat globule. #infant #microbiome #nutrition microbiomejournal.biomedcentral.com/articles/10....

As the manuscript is currently under review, I welcome any feedback or question 😁

This project was a massive collaborative effort between @dukepress.bsky.social, @caltech.edu, and @ucsandiego.bsky.social. A big thank you goes to the PIs who made this possible - Rima Kaddurah-Daouk, Sarkis Mazmanian, Rob Knight, and @pieterdorrestein.bsky.social - and all the collaborators! 13/n

We believe this resource and its associated tools will aid future research in the pathophysiology of AD and in the broader context of #biomedicalresearch. Additionally, this dataset contains hundreds of yet-to-be-characterized metabolites that researchers can explore. 12/n

We then reprocessed 1.5k blood samples collected by the Alzheimer Gut Microbiome Project (AGMP) and found phenylacetyl-carnitine to be correlated with #aging, #cognitive impairment, #physical exercise and AD #biomarkers in the cerebral spinal fluid (CSF). 11/n

Looking for these previously #uncharacterized carnitines, we observed phenylacetyl-carnitine to be enriched in inflammatory diseases. This workflow can be applied to any kind of (un)annotated MS/MS spectrum researchers are interested in. 10/n

We then developed #tissueMASST to translate animal findings to human datasets. This MS/MS search tool comprises ~50k LC-MS/MS samples captured from animal models and humans with associated metadata, such as tissue type, disease status, sex, and age. 9/n

Given their possible biological relevance, we did some magic 🪄 and annotated them as benzoyl-carnitine, phenylacetyl-carnitine, and phenylpropionyl-carnitine. We #synthesized the standards and their MS/MS spectra are now part of the GNPS libraries. 8/n

These molecules were classified as modulated by the microbiome and, in an external dataset, were observed responding both to #antibiotics and #prebiotics. Additionally, they positively correlated with #inflammation markers of the mesenteric lymph nodes of the mice. 7/n

Specifically focusing on #carnitines, which were dysregulated across multiple tissues, we generated a cross-tissue molecular network to capture a holistic view. We observed 3 putative carnitines that were not annotated via GNPS MS/MS libraries. 6/n

Having both SPF and GF animals also allowed us to putatively identify if molecular alterations were driven by the #genotype, the #microbiome, or both. Information available for all the molecular features differentiating AD animals from WT. 5/n

Thousands of metabolic features were driving these separations across tissues. Alterations were observed in the #bileacids pool (obviously😉) but also in N-acyl lipids, B vitamins, neurotransmitters, polyamines, and several other classes of molecules. 4/n

Murine models of #Alzheimers Disease (AD) present distinct metabolic profiles across five tissue types captured by this atlas - brain, serum, liver, cecum, and feces. 3/n

We have generated an untargeted #metabolomics atlas from more than 2,000 samples collected from tissues of 300 mice with different genetic backgrounds (3xTg, 5xFAD, C57BL/6J), colonization conditions (SPF, GF), sex, and age. Data and metadata are publicly available. 😁 2/n

A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer’s Disease The etiology of Alzheimer’s Disease (AD) remains largely unclear but is likely driven by gene-environment interactions. Here, we present a multi-organ untargeted metabolomics dataset (2,271 samples) g...

I am excited to share the latest project I have been working on "A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer’s Disease". 1/n www.biorxiv.org/content/10.1...

Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have impli...

Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis www.tandfonline.com/doi/full/10....

Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol Untargeted metabolomics is frequently performed on human fecal samples in conjunction with sequencing to unravel the gut microbiome functionality. As sample collection efforts are rapidly expanding, with individuals often collecting specimens at home, metabolomics experiments should adapt to accommodate the safety and needs of bulk off-site collections and improve high throughput. Here, we show that a 95% ethanol, safe to be shipped and handled, extraction part of the Matrix Method pipeline recovers comparable amounts of metabolites as a validated 50% methanol extraction, preserving metabolic profile differences between investigated subjects. Additionally, we show that the fecal metabolome remains relatively stable when stored in 95% ethanol for up to 1 week at room temperature. Finally, we suggest a metabolomics data analysis workflow based on robust centered log ratio transformation, which removes the variance introduced by possible different sample weights and concentrations, allowing for reliable and integration-ready untargeted metabolomics experiments in gut microbiome research.

Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol | Analytical Chemistry pubs.acs.org/doi/10.1021/...

A study using an n=1 experiment with single standards at 0V CID reported that 70% of detected ions were in-source fragments (ISFs). www.nature.com/articles/s42... This finding was extrapolated to suggest that ISFs affect all metabolomics experiments to this degree. A counterpoint. rdcu.be/ebFwc 1/n

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

Excited to share our correspondence in @naturemetabolism.bsky.social, where we address claims that the “dark metabolome” is merely an in‐source fragmentation artifact. www.nature.com/articles/s42... #Metabolomics #TeamMassSpec

It was a true privilege to have worked on this project! Thanks to @pieterdorrestein.bsky.social, Rob, Rodolfo, @helenamrusso.bsky.social, @simonezuffa.bsky.social, and other co-authors for all the fun we had along the way!

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 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...

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns: Cell www.cell.com/cell/fulltex...

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