Massachusetts General Hospital · Harvard Medical School · Broad Institute
Li Lab
Computational host-microbiome biology — turning multi-omics data into mechanistic insight at the host-microbe interface.
What We Study
Research Areas
Gut Microbial Metabolism & Cardiometabolic Health
Most microbiome–cardiometabolic studies rest on cross-sectional snapshots. We use six years of paired fecal metagenomes and LC-MS/MS metabolomes from the Framingham Heart Study to ask how microbial metabolism tracks with host cardiometabolic trajectories — work that began with our discovery of Oscillibacter as a cholesterol-metabolizing genus.
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Methods for Microbial Ecology & Metabolomics
Method development runs through everything we do, building on BEEM and BEEM-Static, our algorithms for recovering absolute abundances from compositional data. We are extending it in three directions: spatiotemporal dynamics from fecal metagenomes, annotation of uncharacterized LC-MS and MS/MS features, and linking metabolites to the microbes that produce them.
Read moreLatest News
All newsMetastrand — antisense transcription in the gut microbiome
CISID New Investigator Award to decode sepsis heterogeneity
Appointed Associated Investigator at CISID, Broad Institute
Recent Publications
All pubsAntisense transcription reveals disease-associated adaptations in the human gut microbiome
Nature Microbiology · 2026
Identifying microbial protease allergens through protein language model-guided homology
Cell systems · 2026