At the Interface of Human Genomics and Microbiome Research

Based at The University of Chicago, we are part of the Section of Genetic Medicine in the Biological Sciences Division

Our Research

We study how human genes can control and interact with the microbiome. We utilize high-throughput genomics technologies and employ computational, statistical, machine learning, and population genetic analytical approaches, with the goal of understanding how we interact with our microbial communities, how host-microbe interactions affect human disease, and how the symbiosis between us and our microbiome evolved.

  Key Recent Publications

Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome
Johnson et al., Cell Genomics, 2024
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Abdill, Graham, et al., bioRxiv, 2023
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration
Priya et al., Nature Microbiology, 2022
Public human microbiome data are dominated by highly developed countries
Abdill et al., PLOS Biology, 2022
Gut microbiome heritability is nearly universal but environmentally contingent
Grieneisen et al., Science, 2021
Interspecies variation in hominid gut microbiota controls host gene regulation
Muehlbauer et al., Cell Reports, 2021
Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome
Mars et al., Cell, 2020
Tracking the popularity and outcomes of all bioRxiv preprints
Abdill & Blekhman, eLife, 2019
Gut microbiota diversity across ethnicities in the United States
Brooks et al., PLOS Biology, 2018
Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
Burns et al., PLOS Genetics, 2018
Functional genomics of host–microbiome interactions in humans
Luca et al., Trends in Genetics, 2017
Genetic ancestry and natural selection drive population differences in immune responses to pathogens
Nédélec et al. Cell, 2016
Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns
Gomez et al., Cell Reports, 2016
Host genetic variation impacts microbiome composition across human body sites
Blekhman et al., Genome Biology, 2015

  Lab News

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 (bioRxiv)
Full dataset for download (Zenodo)
MicroBioMap R package (github)
Website (microbiomap.org)

An R package for visualizing microbiome time series data

R package, code, and user guide (GitHub)
Publication (mSystems, 2022)

A website to sort through bioRxiv preprints and find relevant, trending papers

Rxivist.org website
Data & code (GitHub)
Our paper on preprint trends (eLife 2019)
Our paper describing Rxivist.org (PLOS Biology 2019)

A framework for identifying host genetic variants associated with microbiome composition

Software, code, and instructions (GitHub)
Online network visualization tool
Paper (GigaScience)

  Our Work in the Media

  • Consequences of the globalized gut
    University of Chicago, 2023
  • Studies of human microbiome have ignored the developing world, potentially compromising treatments
    Science, 2022
  • Is Staying Home Harming Your Child’s Immune System?
    New York Times, 2020
  • The Extinction Happening Inside You
    MinuteEarth on YouTube, 2020
  • Coronavirus Research Is Moving at Top Speed — With a Catch
    Wired, 2020
  • What bioRxiv’s first 30,000 preprints reveal about biologists
    Nature, 2019
  • The Emerging Field of Microbiome Science
    HBO VICE, 2017
  • The Secret About Human Evolution Found in Spit
    The Guardian, 2017
  • Microbes Meet Cancer
    The Scientist, 2016
  • Everything You Need to Know About Poop

    New York Magazine, 2016

  • Is Gut Science Biased?
    FiveThirtyEight, 2016
  • Giving Up Hunting & Gathering Changed Our Microbiome
    Newsweek, 2016