Emily Davenport

Assistant Professor of Biology

Emily Davenport

Research Summary

Understanding the complex relationship humans have with our microbiomes, using high-throughput sequencing technologies and novel computational and statistical techniques.

Huck Graduate Students

Huck Affiliations

Links

Most Recent Publications

MyD88-mediated signaling in intestinal fibroblasts regulates macrophage antimicrobial defense and prevents dysbiosis in the gut

Marina Chulkina, Hanh Tran, Gabriela Uribe, Steven Bruce McAninch, Christina McAninch, Ashley Seideneck, Bing He, Matthew Lanza, Kamil Khanipov, Georgiy Golovko, Don W. Powell, Emily R. Davenport, Irina V. Pinchuk, 2025, Cell Reports

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice

Lev Litichevskiy, Maya Considine, Jasleen Gill, Vasuprada Shandar, Timothy O. Cox, Hélène C. Descamps, Kevin M. Wright, Kevin R. Amses, Lenka Dohnalová, Megan J. Liou, Monika Tetlak, Mario R. Galindo-Fiallos, Andrea C. Wong, Patrick Lundgren, Junwon Kim, Giulia T. Uhr, Ryan J. Rahman, Sydney Mason, Carter Merenstein, Frederic D. Bushman, Anil Raj, Fiona Harding, Zhenghao Chen, G. V. Prateek, Martin Mullis, Andrew G. Deighan, Laura Robinson, Ceylan Tanes, Kyle Bittinger, Meenakshi Chakraborty, Ami S. Bhatt, Hongzhe Li, Ian Barnett, Emily R. Davenport, Karl W. Broman, Maayan Levy, Robert L. Cohen, David Botstein, Adam Freund, Andrea Di Francesco, Gary A. Churchill, Mingyao Li, Christoph A. Thaiss, 2025, Nature Microbiology on p. 1240-1257

Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene

Robert G. Nichols, Emily R. Davenport, 2025, mSystems

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized

Erica P. Ryu, Yoshina Gautam, Diana M. Proctor, Dinesh Bhandari, Sarmila Tandukar, Meera Gupta, Guru Prasad Gautam, David A. Relman, Ahmed A. Shibl, Jeevan Bahadur Sherchand, Aashish R. Jha, Emily R. Davenport, 2024, Microbiome

Correction to: Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized (Microbiome, (2024), 12, 1, (228), 10.1186/s40168-024-01941-7)

Erica P. Ryu, Yoshina Gautam, Diana M. Proctor, Dinesh Bhandari, Sarmila Tandukar, Meera Gupta, Guru Prasad Gautam, David A. Relman, Ahmed A. Shibl, Jeevan Bahadur Sherchand, Aashish R. Jha, Emily R. Davenport, 2024, Microbiome

Chlorpyrifos modulates the mouse gut microbiota and metabolic activity

Robert G. Nichols, Bipin Rimal, Fuhua Hao, Jeffrey Maurice Peters, Emily R. Davenport, Andrew D. Patterson, 2024, Environmental International on p. 109022

Gut-microbiome profiles among Soil-transmitted helminths (STHs) infected Ethiopian children enrolled in the school-based mass deworming program

Bineyam Taye, Zeleke Mekonnen, Kenneth D. Belanger, Emily R. Davenport, 2024, PLoS Neglected Tropical Diseases

What tool or method do you wish existed?

Yvonne Y. Chen, Charles L. Evavold, Matthias Mann, Emily R. Davenport, Margaret McFall-Ngai, Magda Bienko, Hiroki R. Ueda, Lin Tian, Nikki Tjahjono, Polina Anikeeva, Jun Jie Gogo Liu, Tara L. Deans, Xiaohua Shen, 2024, Cell on p. 4433-4438

Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene

Robert Nichols, E Davenport, 2024, mSystems on p. e01480--24

Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain

Abigail Gancz, Andrew Farrer, M Nixon, Sterling Wright, Luis Arriola, Luis Arriola, Christina Alder, Emily Davenport, Christina Adler, Emily R. Davenport, Neville Gully, Neville Gully, Alan Cooper, Alan Cooper, Kate Britton, Kate Britton, Keith Dobney, Keith Dobney, Justin Silverman, Laura Weyrich, Laura S. Weyrich, 2023, Nature Microbiology on p. 2315-2325

Most-Cited Papers

Genetic Determinants of the Gut Microbiome in UK Twins

Julia K. Goodrich, Emily R. Davenport, Michelle Beaumont, Matthew A. Jackson, Rob Knight, Carole Ober, Tim D. Spector, Jordana T. Bell, Andrew G. Clark, Ruth E. Ley, 2016, Cell Host and Microbe on p. 731-743

The human microbiome in evolution

Emily R. Davenport, Jon G. Sanders, Se Jin Song, Katherine R. Amato, Andrew G. Clark, Rob Knight, 2017, BMC Biology

The Relationship between the Human Genome and Microbiome Comes into View

Julia K. Goodrich, Emily R. Davenport, Andrew G. Clark, Ruth E. Ley, 2017, Annual Review of Genetics on p. 413-433

Cross-species comparisons of host genetic associations with the microbiome

Julia K. Goodrich, Emily R. Davenport, Jillian L. Waters, Andrew G. Clark, Ruth E. Ley, 2016, Science on p. 532-535

Genome-wide association studies of the human gut microbiota

Emily R. Davenport, Darren A. Cusanovich, Katelyn Michelini, Luis B. Barreiro, Carole Ober, Yoav Gilad, 2015, PLoS One on p. e0140301

Heritable components of the human fecal microbiome are associated with visceral fat

Michelle Beaumont, Julia K. Goodrich, Matthew A. Jackson, Idil Yet, Emily R. Davenport, Sara Vieira-Silva, Justine Debelius, Tess Pallister, Massimo Mangino, Jeroen Raes, Rob Knight, Andrew G. Clark, Ruth E. Ley, Tim D. Spector, Jordana T. Bell, 2016, Genome Biology on p. 189

Gut microbiome transition across a lifestyle gradient in Himalaya

Aashish R. Jha, Emily R. Davenport, Yoshina Gautam, Dinesh Bhandari, Sarmila Tandukar, Katharine M. Ng, Gabriela K. Fragiadakis, Susan Holmes, Guru Prasad Gautam, Jeff Leach, Jeevan Bahadur Sherchand, Carlos D. Bustamante, Justin L. Sonnenburg, 2018, PLoS Biology on p. e2005396

A Quick Introduction to Version Control with Git and GitHub

John D. Blischak, Emily R. Davenport, Greg Wilson, 2016, PLoS Computational Biology on p. e1004668

The human gut microbiome and health inequities

Katherine R. Amato, Marie Claire Arrieta, Meghan B. Azad, Michael T. Bailey, Josiane L. Broussard, Carlijn E. Bruggeling, Erika C. Claud, Elizabeth K. Costello, Emily R. Davenport, Bas E. Dutilh, Holly A. Swain Ewald, Paul Ewald, Erin C. Hanlon, Wrenetha Julion, Ali Keshavarzian, Corinne F. Maurice, Gregory E. Miller, Geoffrey A. Preidis, Laure Segurel, Burton Singer, Sathish Subramanian, Liping Zhao, Christopher W. Kuzawa, 2021, Proceedings of the National Academy of Sciences of the United States of America

The relationship between the gut microbiome and host gene expression: a review

Robert G. Nichols, Emily R. Davenport, 2020, Human Genetics

News Articles Featuring Emily Davenport

Jun 09, 2025

Two Penn State doctoral students selected for industry internship in Germany

The One Health Microbiome Center (OHMC) in the Huck Institutes of the Life Sciences at Penn State is sending two doctoral students to Hilden, Germany, for a seven-week industry internship at the headquarters of QIAGEN, a global leader in biotechnology for life sciences diagnostics, equipment and research.

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Apr 10, 2025

Graduating senior reflects on undergraduate research experiences at Penn State

Maria Lovallo is a Penn State undergrad from Spring Mills, PA, majoring in Microbiology with a minor in Plant Pathology & Environmental Microbiology. She is also a teaching assistant in Biochemistry and Molecular Biology, and a member of the Huck Institutes’ One Health Microbiome Center.

Full Article

Nov 05, 2024

Microbes in mouth reflect lifestyle choices

New study in Nepal reveals that oral microbiomes differ among traditional foragers, agriculturalists and industrialists, and with behaviors like smoking and diet

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Jul 18, 2024

Microbiome Kickstart Workshop will assist newcomers to the field

The One Health Microbiome Center at Penn State has opened registration for its fifth annual Microbiome Kickstart Workshop. This free, comprehensive, workshop is a cornerstone training event for emerging researchers to launch their microbiome studies and network at Penn State.

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Nov 29, 2023

Study of ancient British oral microbiomes reveals shift following Black Death

The Second Plague Pandemic may have led to oral microbiomes that contribute to modern-day chronic disease, according to new research

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Feb 15, 2023

Free film and panel discussion reveals 'invisible' crisis of the microbial world

At 6 p.m. Thursday, March 2, Penn State’s Microbiome Center will present "The Invisible Extinction" — a movie that spotlights the trailblazing work and charismatic personalities of renowned scientists who aim to save the vanishing microbes that are essential for our survival.

Full Article