Harsha Gouda

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The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities With the exception of molecules acquired through the lungs, skin absorption, or part of a medication regime, nearly all molecules in our bodies origin…

The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities

#CurrOpinMicrobiol by @harshagouda.bsky.social et al from @pieterdorrestein.bsky.social

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

We show how most dietary molecular features remain unknown, which are then further diversified by the gut microbiome, leading to more unkowns. Some cool experiments from @amcaraballor.bsky.social

The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities With the exception of molecules acquired through the lungs, skin absorption, or part of a medication regime, nearly all molecules in our bodies origin…

The interactions between food, microbiome and host that modulate health can be complex. Here, we offer a perspective on how mass spectrometry can be leveraged to address some of these challenges to understand host and microbial metabolism of food. A step closer to personalized health and nutrition.

Poster is made, printed and ready to go! Looking forward to my first mass-spec conference #ASMS2025 at Baltimore next week!

How much ultra-processed food do you eat? Blood and urine record it Samples could provide an objective measure of diets and help to unravel their contribution to disease.

Molecules in urine and blood can reveal how much of a person’s diet comes from ultra-processed foods

https://go.nature.com/4kybHea

New @science.org
Exposomics. We're not doing nearly enough to understand and mitigate our toxic environmental exposures. A very insightful perspective
www.science.org/doi/10.1126/...

Should I return to my home country after my PhD abroad? A graduate student from southeast Asia, now based in a European country and missing her homeland, agonizes over her next career move.

Should you return home after earning your PhD abroad? This Nature article explores the dilemmas faced by international researchers considering a move back to their home countries. A thought-provoking read for anyone navigating global academic careers. 

www.nature.com/articles/d41...

QC:MXP version 2.0 is now available to download for free from my GitHub page: www.qcmxp.org
Repeat-injection-based Quality Control, Batch Correction, Exploration & Data Cleaning. #Metabolomics #AnalyticalChemistry #Matlab

This is figure 1, which shows season of fertilization predetermines the metabolic fate of brown adipose tissue in human adults.

Individuals who were conceived in colder seasons are more likely to show higher brown adipose tissue activity, increased energy expenditure and a lower BMI, and lower fat accumulation around internal organs, suggests a study in Nature Metabolism. https://go.nature.com/4i3EYM0 🧪

Reviewer notes: That’s a very nice mediation analysis you have there. It would be a shame if something happened to it. Mediation analysis has gotten a lot of flak, including classic titles such as “Yes, but what’s the mechanism? (Don’t expect an easy answer)” (Bullock et al., 2010), “What mediation analysis can (not) ...

New blog post! In which I explain the issue with mediation analysis and sketch out one way to deal with the underlying causal inference problem -- in just a bit over 1,000 words!

If you have never found the time to read up on this, now is your chance.

www.the100.ci/2025/03/20/r...

In the world of LLMs, why am I going to YouTube? To learn the basics!

We moved a conference halfway around the globe to avoid visa discrimination Event organizers often overlook the visa-related difficulties that researchers in low- and middle-income countries face. This must change.

Event organizers often overlook the visa-related difficulties that researchers in low- and middle-income countries face. This must change, says Kara Hanson

https://go.nature.com/3DioEc0

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

Discovery of metabolites prevails amid in-source fragmentation #NatMetab www.nature.com/articles/s42...

To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question Untargeted metabolomics often produce large datasets with missing values. These missing values are derived from biological or technical factors and can undermine statistical analyses and lead to biase...

Another fun paper that was started by a good and important question by Prajit - an undergrad in the lab - about imputation. We then teamed up with the Kelley lab as they are good at such benchmarking in data science. So fun to work woth them. pubs.acs.org/doi/10.1021/...

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 #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

A new resource rating >50,000 foods from 3 grocery stores
(Walmart, Target, and Whole Foods) for degree of processing and breakdown of ingredients
www.nature.com/articles/s43...
Website for consumers www.truefood.tech

Such a wonderful SIMB workshop on @gnps2.bsky.social covering classical mol networking, FBMN, ion identity based mol networking, FBMN-STATS, gnps-dashboard, CMMC-kb, Modifinder, MicrobeMASST, MassQL, and limited ReDU - many were covered at a workshop for the first time. 1/4

So fun at SIMB teaching the gnps ecosystem.

Metabolic changes of the blood metabolome after a date fruit challenge

doi.org/10.1016/j.jf...

7/12

An accurate IDMS‐based method for absolute quantification of phytohemagglutinin, a major antinutritional component in common bean Abstract Phytohemagglutinin (PHA), a natural tetramer comprising PHA-E and PHA-L subunits that preferentially bind to red and white blood cells, respectively, constitutes a significant antinutrition...

An accurate IDMS-based method for absolute quantification of phytohemagglutinin, a major antinutritional component in common bean #JFoodSci ift.onlinelibrary.wiley.com/doi/10.1111/...

Welcome to the wonderful #mzmine @mzmine.bsky.social team in Bluesky @bsky.app .
So nice to have you in #ICTC13 metabolomics workshop !
Check it out at www.ictc13.gr

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies - Genome Biology Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction ...

New tensor factorization paper out today — a fun collaboration with Pixu Shi, Liat Shenhav, Rob Knight, & Anru_Zhang! 🎉 Check it out here: genomebiology.biomedcentral.com/articles/10....

HAHAHA 🤯

I’m starting to fall in love with math again. It was enzyme kinetics in grad school, now it’s testing different models on clinical data.

Hunt more coyote, get more coyote Humans often assume killing will solve the problem. Here's yet another example of why we are wrong.

What if I told you that if you have coyote "problems" (as in, you feel there are too many), killing them...can make it WORSE?

Me on @rolandkays.com 's latest paper, so glad his lab is studying this!

teamtrash.substack.com/p/hunt-more-...

Here's the visual proof of why vaccines do more good than harm See year by year how vaccines beat back nine dangerous infectious diseases

Sadly, it’s a good time to once again share this amazing infographic that we ran at @science.org more than 7 years ago
🧪 #IDsky
www.science.org/content/arti...

Yes :)

I heard back from the AHA post doc fellowship today, not the brightest of the news I received, but has been a good learning lesson.