L Li

Functional redundancy matters: the more overlapping microbial functions you have, the more resilient your #microbiome. We showed a strong negative correlation between redundancy loss and increase in #antimicrobial resistance protein upon #drug treatment of microbiomes.
@quadraminstitute.bsky.social

From #drug cabinet → gut #microbiome: screening 312 therapeutic compounds, we mapped 4.6 million microbial protein-level responses to reveal how our drugs don’t just target us, they hit our gut microbes too.

rdcu.be/eMmcT

The microbiologist's guide to metaproteomics Metaproteomics within the multi-omics framework provides a comprehensive view of microbial systems by identifying proteins, quantifying their levels, detecting posttranslational modifications (PTMs),...

The microbiologist's guide to metaproteomics
onlinelibrary.wiley.com/doi/full/10.... #Bioinformatics #microbiome #metaproteomics #proteomics #MS

The microbiologist's guide to metaproteomics Metaproteomics within the multi-omics framework provides a comprehensive view of microbial systems by identifying proteins, quantifying their levels, detecting posttranslational modifications (PTMs),...

Are you new to #metaproteomics but don't know where to start? Then this guide, written by experts of the Metaproteomics Initiative, is for you! onlinelibrary.wiley.com/doi/full/10....

Group Leader in Functional Microbiome Research - Quadram Institute Applications are invited for a Group Leader in Functional Microbiome Research to join the laboratory of Professor Daniel Figeys at Quadram Institute Bioscience (QIB), based in Norwich, UK. Background:...

🚀 Interested in the interactions of xenobiotics with the gut microbiome? Join us @quadraminstitute.bsky.social to apply precision microbiome assays to xenobiotics. Apply by 28 May 2025. 👉 quadram.ac.uk/vacancies/gr...
#microbiome #PrecisionNutrition #metaproteomics #metabolics #metagenomics

Compared to conventional methods, OSaMPle increased bacterial peptide identifications by 3.2x and protein identifications by 1.7x. Using OSaMPle, we analyzed mouth rinse samples from IBD patients and found significant shifts in bacterial protein expression. 3/3 #Metaproteomics

We developed OSaMPle (Optimized Salivary MetaProteomic sample analysis workflow) to enrich bacterial cells from saliva and mouth rinse, reducing host contamination and enabling deeper oral metaproteomics. 2/3

The oral microbiome is linked to various inflammatory conditions, including IBD. However, analyzing functional changes at the protein level has been challenging due to host protein interference. 🧵 1/3

OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients

I couldn’t be prouder—this is the work of the very first master's student that I've supervised. Salivary metaproteomics is tricky due to host/debris interference. Yuan et al. developed a microbial cell enrichment step and achieved cleaner data with better insights. www.nature.com/articles/s41...

Metaproteomics deserves a dedicated β-diversity metric Introducing PhyloFunc: A Phylogeny-Informed Functional Beta-Diversity Metric for Metaproteomics Metaproteomics deserves a dedicated β-diversity metric In microbiome research, comparing functional p…

Metaproteomics deserves a dedicated β-diversity metric:
microbiolly.wordpress.com/2025/03/19/p...

Systematic Metaproteomics Mapping Reveals Functional and Ecological Landscapes of Human Gut Microbiota Responses to Therapeutic Drugs Therapeutic compounds significantly alter the composition of the gut microbiota, yet their functional and ecological impacts, particularly at the protein level, remain largely unexplored. In this stud...

🚨 We mapped 4.6M #microbial protein responses to 312 compounds, uncovering 3 distinct functional gut #microbiome states and revealing how neuropharma triggers deep shifts (lower functional redundancy, higher #AMR proteins).

www.biorxiv.org/content/10.1...

microbiomejournal.biomedcentral.com/articles/10....

PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis - Microbiome Background Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-...

🦠 In #metaproteomics, proteins are often treated as independent features, ignoring their ecological relationships.
🌱 We developed PhyloFunc, a beta diversity metric that integrates phylogeny into functional distance calculations, offering a more ecologically meaningful way to compare microbiomes.

The Microbiologist’s Guide to Metaproteomics Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic...

🎉 Excited to share this amazing Metaproteomics Initiative community effort aims to make metaproteomics accessible and easy to use for microbiome researchers. Grateful for this unforgettable journey of collaboration! 🌍🔬 #Metaproteomics #Collaboration #Science chemrxiv.org/engage/chemr...

Thank you for sharing Manuel!

The Microbiologist’s Guide to Metaproteomics Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic...

If you want to get started with #metaproteomics , this guide is a good starting point. This was an amazing metaproteomics community effort to get all the key information together led by Tim Van Den Bossche and Leyuan Li
chemrxiv.org/engage/chemr...