Publications | Blekhman Lab

2026

Genomics of host–microbiome interactions in humans

P. Ferretti, K. Johnson, S. Priya, and R. Blekhman

Nature Reviews Genetics, 2026

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Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer

K. Della Libera, E. M. Adamowicz, A. Muehlbauer, S. Priya, A. Alazizi, F. Luca, and R. Blekhman

bioRxiv preprint, 2026

Distinct trajectories of urbanization shape the human gut microbiome across South Asia

S. L. Ramachandran, N. Pasupuleti, R. J. Abdill, et al., R. Blekhman, N. Rai, and M. Raghavan

bioRxiv preprint, 2026

Host genotypes interact with microbial communities to modulate gene expression in the human intestine

S. Nirmalan, S. Arif, J. Wei, S. Priya, R. Blekhman, R. Pique-Regi, and F. Luca

medRxiv preprint, 2026

Bacterial fecal microbiome composition associated with HIV stage among rural and peri-urban adults living with HIV in Uganda

B. M. Morawski, E. R. Morton, M. Yunus, C. Muñoz-Zanzi, R. Mejia, R. Blekhman, D. R. Boulware, and S. M. Lofgren

BMC Infectious Diseases, 2026

2025

Integration of 168,000 samples reveals global patterns of the human gut microbiome

R. J. Abdill, S. P. Graham, M. Ahmadian, P. Hicks, A. Chetty, D. McDonald, P. Ferretti, E. Gibbons, M. Rossi, A. Krishnan, V. Rubinetti, F. W. Albert, C. S. Greene, S. Davis, and R. Blekhman

Cell, 2025

Gut microbiome data underscores gaps in global representation — University of Chicago News

Microbiomap.org — the Human Microbiome Compendium portal

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk

P. Ferretti, M. Allert, K. E. Johnson, M. Rossi, T. Heisel, S. Gonia, D. Knights, et al., and R. Blekhman

Nature Communications, 2025

Host transcriptional responses to gut microbiome variation arising from urbanism

S. Arif, S. Nirmalan, A. Alazizi, H Mair-Meijers, et al., M. Poyet, M. Groussin, F. Luca, and R. Blekhman

BioRxiv preprint, 2025

Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism

S. Davison, A. Mascellani Bergo, Z. Ward, et al., R. Blekhman, and A. Gomez

npj Biofilms and Microbiomes, 2025

Compendium Manager: a tool for coordination of workflow management instances for bulk data processing in Python

R. J. Abdill and R. Blekhman

arXiv, 2025

Compendium Manager GitHub

Analyzing human gut microbiome data from global populations: challenges and resources

S. J. Arif, S. P. Graham, R. J. Abdill, and R. Blekhman

Trends in Microbiology, 2025

Science under threat in the United States: how scientists and institutions should respond

R. Blekhman

eLife, 2025

Analysis of metagenomic data

S. Liu, J. Rodriguez, et al., R. Blekhman, K. Della Libera, et al., and S. Mangul

Nature Reviews Methods Primers, 2025

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Maternal Physical Activity and Its Relationship to the Human Milk Metabolome and Infant Body Composition

C. Lu, J. M. Dreyfuss, T. Hua, et al., K. E. Johnson, R. Blekhman, et al.

Journal of Clinical Endocrinology & Metabolism, 2025

2024

Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome

K. E. Johnson, T. Heisel, M. Allert, A. Fürst, N. Yerabandi, D. Knights, K. M. Jacobs, E. F. Lock, L. Bode, D. A. Fields, M. C. Rudolph, C. A. Gale, F. W. Albert, E. W. Demerath, and R. Blekhman

Cell Genomics, 2024

Human Cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth

K. E. Johnson, N. Hernandez-Alvarado, M. Blackstad. Heisel, M. Allert, D. A. Fields, et al., F. W. Albert, E. W. Demerath, and R. Blekhman

Nature Communications, 2024

Multi-omic approaches for host-microbiome data integration

A. Chetty and R. Blekhman

Gut Microbes, 2024

Social and environmental predictors of gut microbiome age in wild baboons

M. Dasari, K. Roche, D. Jansen, J. Anderson, S. C. Alberts, J. Tung, J. A. Gilbert, R. Blekhman, S. Mukherjee, and E. A. Archie

eLife, 2024

Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type

L. Grieneisen, A. Hays, E. Cook, R. Blekhman, and S. Tecot

American Journal of Primatology, 2024

2023

Universal gut microbial relationships in the gut microbiome of wild baboons

K. Roche, J. R. Björk, M. Dasari, L. Grieneisen, D. Jansen, T. J. Gould, L. R. Gesquiere, L. B. Barreiro, S. C. Alberts, R. Blekhman, J. A. Gilbert, J. Tung, S. Mukherjee, and E. A. Archie

eLife, 2023

How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome

L. Grieneisen, R. Blekhman, and E. A. Archie

Gut Microbes, 2023

Microbes with higher metabolic independence are enriched in human gut microbiomes under stress

I. Veseli, Y. T. Chen, M. Schechter, et al., B. Jabri, R. Blekhman, A. D. Willis, et al., and A. Murat Eren

eLife, 2023

2022

Public human microbiome data are dominated by highly developed countries

R. J. Abdill, E. M. Adamowicz, and R. Blekhman

PLOS Biology, 2022

Studies of human microbiome have ignored the developing world — Science

Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration

S. Priya, M. B. Burns, T. Ward, R. Mars, E. Adamowicz, E. F. Lock, P. C. Kashyap, D. Knights, and R. Blekhman

Nature Microbiology, 2022

BiomeHorizon: visualizing microbiome time series data in R

I. Fink, R. J. Abdill, R. Blekhman, and L. Grieneisen

mSystems, 2022

Synchrony and idiosyncrasy in the gut microbiome of wild baboons

J. R. Björk, M. Dasari, L. Grieneisen, T. J. Gould, J.-C. Grenier, V. Yotova, N. Gottel, et al., S. C. Alberts, J. A. Gilbert, J. Tung, R. Blekhman, and E. A. Archie

Nature Ecology & Evolution, 2022

Codiversification of gut microbiota with humans

T. A. Suzuki, L. Fitzstevens, V. T. Schmidt, et al., A. L. Muehlbauer, N. Marchi, et al., Ran Blekhman, L. Segurel, G. Ko, N. D. Youngblut, P. Kremsner, and R. E. Ley

Science, 2022

2021

Gut microbiome heritability is nearly universal but environmentally contingent

L. Grieneisen, M. Dasari, T. J. Gould, J. R. Björk, J.-C. Grenier, V. Yotova, D. Jansen, N. Gottel, et al., S. C. Alberts, J. Tung, E. A. Archie, and R. Blekhman

Science, 2021

Host genetics influence the gut microbiome — Science

Gut microbiome affected by genetics more than once thought — GEN

The gut microbiome in konzo

M. S. Bramble, N. Vashist, A. Ko, S. Priya, et al., R. Blekhman, D. Tshala-Katumbay, and E. Vilain

Nature Communications, 2021

A global metagenomic map of urban microbiomes and antimicrobial resistance

D. Danko and The International MetaSUB Consortium

Cell, 2021

Subway swabbers find a microbe jungle and thousands of new species — New York Times

Interspecies variation in hominid gut microbiota controls host gene regulation

A. L. Muehlbauer, A. L. Richards, A. Alazizi, M. Burns, A. Gomez, J. B. Clayton, K. Petrzelkova, C. Cascardo, J. Resztak, X. Wen, R. Pique-Regi, F. Luca, and R. Blekhman

Cell Reports, 2021

Multi-omics analyses show disease, diet, and transcriptome interactions with the virome

K. Mihindukulasuriya, R. A. T. Mars, A. J. Johnson, T. Ward, S. Priya, et al., R. Blekhman, M. D'Amato, G. Farrugia, D. Knights, S. A. Handley, and P. C. Kashyap

Gastroenterology, 2021

2020

Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome

R. A. T. Mars, Y. Yang, T. Ward, S. Priya, et al., R. Blekhman, G. Farrugia, J. Swann, D. Knights, and P. C. Kashyap

Cell, 2020

Interactions between the gut microbiome and host gene regulation in cystic fibrosis

G. Dayama, S. Priya, D. E. Niccum, A. Khoruts, and R. Blekhman

Genome Medicine, 2020

International authorship and collaboration across bioRxiv preprints

R. J. Abdill, E. M. Adamowicz, and R. Blekhman

eLife, 2020

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

K. R. Chng and The International MetaSUB Consortium

Nature Medicine, 2020

Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

L. Grieneisen, A. L. Muehlbauer, and R. Blekhman

Philosophical Transactions of the Royal Society B, 2020

Traditional human populations and nonhuman primates show parallel gut microbiome adaptations to analogous ecological conditions

A. K. Sharma, K. J. Petrželková, B. Pafčo, et al., R. Blekhman, B. White, K. E. Nelson, S. R. Leigh, and A. Gomez

mSystems, 2020

2019

Tracking the popularity and outcomes of all bioRxiv preprints

R. Abdill and R. Blekhman

eLife, 2019

What bioRxiv's first 30,000 preprints reveal about biologists — Nature

Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

L. E. Grieneisen, M. J. E. Charpentier, S. C. Alberts, R. Blekhman, G. Bradburd, J. Tung, and E. A. Archie

Proceedings of the Royal Society B, 2019

Megaphages infect Prevotella and variants are widespread in gut microbiomes

A. E. Devoto, J. M. Santini, M. R. Olm, et al., R. Blekhman, F. M. Aarestrup, B. C. Thomas, and J. F. Banfield

Nature Microbiology, 2019

Improving the usability and archival stability of bioinformatics software

S. Mangul, L. Martin, E. Eskin, and R. Blekhman

Genome Biology, 2019

Rxivist.org: Sorting biology preprints using social media and readership metrics

R. Abdill and R. Blekhman

PLOS Biology, 2019

Challenges and recommendations to improve the installability and archival stability of omics computational tools

S. Mangul, T. Mosqueiro, R. J. Abdill, et al., G. Dayama, L. Grieneisen, L. Martin, J. Flint, E. Eskin, and R. Blekhman

PLOS Biology, 2019

Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

A. K. Sharma, B. Pafčo, K. Vlčková, et al., M. B. Burns, R. Blekhman, K. J. Petrželková, and A. Gomez

BMC Genomics, 2019

Gut microbiota has a widespread and modifiable effect on host gene regulation

A. L. Richards, A. L. Muehlbauer, A. Alazizi, M. B. Burns, A. Findley, et al., T. J. Gould, C. Cascardo, R. Pique-Regi, R. Blekhman, and F. Luca

mSystems, 2019

Plasticity in the human gut microbiome defies evolutionary constraints

A. Gomez, A. Sharma, E. Mallott, et al., M. Burns, R. Blekhman, M. Remis, R. Stumpf, B. Wilson, H. Gaskins, P. Garber, B. White, and S. Leigh

mSphere, 2019

2018

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment

M. B. Burns, J. Montassier, I. Abrahante, J. Priya, S. Priya, et al., R. Blekhman

PLOS Genetics, 2018

Interaction between host microRNAs and the gut microbiota in colorectal cancer

C. Yuan, M. B. Burns, S. Subramanian, and R. Blekhman

mSystems, 2018

Gut microbiota diversity across ethnicities in the United States

A. W. Brooks, S. Priya, R. Blekhman, and S. R. Bordenstein

PLOS Biology, 2018

Transposon mutagenesis screen in mice identifies TM9SF2 as a novel colorectal cancer oncogene

C. Clark, M. Maile, P. Blaney, et al., S Priya, M. B. Burns, S. Subramanian, R. Blekhman, J. Abrahante, and T. Starr

Scientific Reports, 2018

2017

Functional genomics of host–microbiome interactions in humans

F. Luca, S. S. Kupfer, D. Knights, A. Khoruts, and R. Blekhman

Trends in Genetics, 2017

HOMINID: A framework for identifying associations between host genetic variation and microbiome composition

J. Lynch, K. Tang, S. Priya, J. Sands, M. Sands, E. Tang, S. Mukherjee, D. Knights, and R. Blekhman

GigaScience, 2017

Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation

D. Xu, P. Pavlidis, R. O. Taskent, N. Alachiotis, C. Flanagan, M. DeGiorgio, R. Blekhman, S. Ruhl, and O. Gokcumen

Molecular Biology and Evolution, 2017

The secret about human evolution found in spit — The Guardian

2015–2016

Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns

A. Gomez, K. Petrzelkova, M. B. Burns, et al., E. Morton, J. D. Umana, F. Carbonero, et al., and R. Blekhman

Cell Reports, 2016

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

Y. Nédélec, J. Sanz, G. Baharian, et al., R. Blekhman, F. Luca, R. Pique-Regi, A. Alapati, and L. B. Barreiro

Cell, 2016

Host genetic variation impacts microbiome composition across human body sites

R. Blekhman, J. K. Goodrich, K. Huang, Q. Sun, R. Bukowski, J. T. Bell, T. D. Spector, A. Keinan, R. E. Ley, D. Gevers, and A. G. Clark

Genome Biology, 2015

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment

M. B. Burns, J. Montassier, J. Abrahante, et al., and R. Blekhman

Genome Medicine, 2015

Social networks predict gut microbiome composition in wild baboons

J. Tung, L. B. Barreiro, M. B. Burns, J.-C. Grenier, J. Lynch, L. E. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, and E. A. Archie

eLife, 2015

2014

Human genetics shape the gut microbiome

J. K. Goodrich, J. L. Waters, A. C. Poole, J. L. Sutter, O. Koren, R. Blekhman, M. Beaumont, W. Van Treuren, R. Knight, J. T. Bell, T. D. Spector, A. G. Clark, and R. E. Ley

Cell, 2014

Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic phenotypes

R. Blekhman, Q. Tang, A. Archie, et al.

Scientific Reports, 2014

Lab Publications