Decoding the Human Microbiome
Our lab pioneers cutting-edge computational approaches to map the intricate networks connecting human biology with our microbial ecosystems. By integrating genomics, deep learning, and systems biology, our research reveals fundamental principles of host-microbiome crosstalk that shape human health, disease susceptibility, and evolutionary adaptation.
- Read more about our research and latest publications
- See our new lab location on the University of Chicago campus
- We're hiring! See how you can join the lab
Key Recent Publications
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Abdill, Graham, et al., Cell, 2025
Abdill, Graham, et al., Cell, 2025
Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome
Johnson et al., Cell Genomics, 2024
Johnson et al., Cell Genomics, 2024
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration
Priya et al., Nature Microbiology, 2022
Priya et al., Nature Microbiology, 2022
Public human microbiome data are dominated by highly developed countries
Abdill et al., PLOS Biology, 2022
Abdill et al., PLOS Biology, 2022
Gut microbiome heritability is nearly universal but environmentally contingent
Grieneisen et al., Science, 2021
Grieneisen et al., Science, 2021
Lab News
- Congrats to Dr. Kelsey Johnson on starting her new faculty position at USC! 09/2025
- Congrats to Dr. Samantha Graham on defending her PhD! 08/2025
- Welcome to new postdoctoral associate Lauren Gonsalves! 06/2025
- Welcome to new MD-PhD student Tess Brunner! 10/2024
- Congrats to Dr. Sambhawa Priya on being named a Chicago DFI Fellow! 09/2024
- Congrats to Dr. Mattea Allert on defending her PhD! 08/2024
- Congrats to Dr. Kelsey Johnson on her NIH K99 award! 07/2024
The Human Microbiome Compendium: An ongoing project to build a dataset of the human microbiome at an unprecedented scale
Integration of 168,000 samples reveals global patterns of the human gut microbiome (Cell, 2025)Full dataset for download, version 1.1 (Zenodo)
MicroBioMap R package (github)
Website (microbiomap.org)
Our Work in the Media
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The Human Microbiome Compendium on the cover of Cell
Cell, 2025
