Macrobes

We are!

The Macrobe + microbe interaction lab in the Department of Biology at the Pennsylvania State University. We use a combination of wet lab and computational approaches to understand what determines microbiome composition within a host, and how the relationship between the host and the microbiome affects host health and evolution.

Emily Davenport
Assistant Professor
Department of Biology
Huck Institutes of the Life Sciences
Office: 305 Wartik Laboratory, Penn State University

Research Professors

Robert Nichols
Assistant Research Professor [June 2023 - ]
USDA NIFA Postdoctoral Fellow [January 2020 - June 2023]
Department of Biology

Office: 306 Wartik Laboratory, Penn State University

Davenport Lab publications:

• The relationship between the gut microbiome and host gene expression: a review. Human Genetics
• Chlorpyrifos modulates the mouse gut microbiota and metabolic activity. Environment International
• Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene. mSystems
• Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine. bioRxiv

Graduate Students

Naomi Huntley
PhD Student [September 2022 - ]
Department of Biology

Office: 306 Wartik Laboratory, Penn State University
Awarded the Microbiome Center Data Analysis Leadership Fund (2022)
OHMC-Qiagen Internship selectee (2025)
Awarded Honorable Mention for the Fox Degree Completion Award from the J. Jeffrey and Anne Marie Fox Graduate School (2026)
Awarded Best Poster in the Human Health Category at the One Health Microbiome Center Symposium (2026)

Davenport Lab publications:

• Analysis of metagenomic data. Nature Reviews Methods Primers
  

Hanh Tran
PhD Student [January 2024 - ]
Technician [June 2022 - August 2023]
Molecular, Cellular, and Integrative Biosciences (MCIBS) Graduate Program

Office: 306 Wartik Laboratory, Penn State University
NSF GRFP Honorable Mention (2025)
NIH T32 EGR Training Grant Appointee (2024 - 2026)

Davenport Lab publications:

• MyD88-mediated signaling in intestinal fibroblasts regulates macrophage antimicrobial defense and prevents dysbiosis in the gut. Cell Reports
• Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine. bioRxiv
• SCiMS: Sex Calling in Metagenomic Sequences. Microbiome
  
  

Staff

Bethany Swencki-Underwood
Research Technnologist (joint with Jordan Bisanz) [July 2024 - ]
Departments of Biology and Biochemistry and Molecular Biology

Lab: 302 Wartik Laboratory, Penn State University

Undergraduates

Luscinia Quance
Undergraduate Researcher [January 2024 - ]
Shreyer Honors College
Major: Biology
Office: 306 Wartik Laboratory, Penn State University

Davenport Lab external posters:

• Optimizing Caco2 coculture models for the study of host-microbiome interactions, poster presentation, ASM Microbe 2026
  
  

Eliana Garza
Undergraduate Researcher [January 2025 - ]
Major: Biochemistry and Molecular Biology; Minor: Spanish
Office: 306 Wartik Laboratory, Penn State University

Katerina Novic
Undergraduate Researcher [August 2025 - ]
Major: Biology; Minor: Biochemistry and Molecular Biology

Eberly Undergraduate Research Support Awardee
Office: 306 Wartik Laboratory, Penn State University

Anwi Tadzong
Undergraduate Researcher [August 2025 - ]
Major: Biomedical Engineering; Pre-Dental
Office: 306 Wartik Laboratory, Penn State University

Josh Miller
Undergraduate Researcher [August 2025 - ]
Major: Biochemistry and Molecular Biology
Office: 306 Wartik Laboratory, Penn State University

Ellie Marshall
Undergraduate Researcher [September 2026 - ]
Major: Biology
Office: 306 Wartik Laboratory, Penn State University

Alumni

Postdocs

Nur Shahir
Postdoctoral Fellow [June 2020 - July 2022]
Department of Biology
Currently a Lead Scientist at Booz Allen Hamilton

Staff

Sean O’Rourke
Undergraduate Researcher [January 2021 - May 2021]
Technician [June 2021 - July 2022]
Major: Biology - Neuroscience option
Currently a Staff Associate at Columbia University Irving Medical Center

Xavier Mack
Technician [July 2023 - June 2024 ]
Currently a Technician at Pennsylvania State University

Graduate Students

Nicholas Locatelli
PhD Student (co-advised with Iliana Baums) [September 2022 - July 2024]
Currently: Postdoc at Cornell University
NIH T32 CBIOS Training Grant Appointee
Awarded the Dr. John Randall Shuman Troxell Memorial Scholarship in Biology (2023)

Erica Ryu
Postdoc [January 2026 - March 2026]
Currently: Computational Biologist at Foundation Medicine
Awarded the Dr. John Randall Shuman Troxell Memorial Scholarship in Biology (2022)
Awarded the J. Ben and Helen D. Memorial Fund Award (2022)
NSF GRFP Honorable Mention (2021)
NIH T32 CBIOS Training Grant Appointee (2021- 2022)

Davenport Lab publications:

• Host genetic determinants of the microbiome across animals: From Caenorhabditis elegans to cattle. Annual Review of Animal Biosciences
• Microbiome: Taming the beasts inside. eLife
• Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized. Microbiome
• Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine. bioRxiv

Polina Tikhonova
PhD Student [March 2022 - August 2026]
Currently: Postdoc at University of North Carolina at Chapel Hill
NIH TL1 Translational Research Training Program Appointee (2024- 2025)

Davenport Lab publications:

• Microbiome responses to anthelmintic treatment depend on pre-treatment helminth infection status in young Ethiopian children. Communications Medicine
  
  

Undergrads

Yiyan Zhang
Undergraduate Researcher [January 2021 - July 2021]
Majors: Statistics - Biostatistics, Mathematics - System Analysis
Currently in the Computational Biology PhD program at UNC

Kyrah Williams Undergraduate Researcher [May 2021 - August 2021]
Major: Biology - Genetics

Jovial Joseph
Undergraduate Researcher [January 2021 - May 2022]
Major: Accelerated PreMedical-Medical Program
Currently: MD Candidate at Sidney Kimmel Medical College
Eberly Undergraduate Research Support Awardee

Mansi Chandra Undergraduate Researcher [June 2022 - August 2022]
Juniata College, Major: Bioinformatics
Currently: PhD student at the University of Arkansas for Medical Sciences

Shanisa McGuire Undergraduate Researcher [June 2022 - October 2022]
Major: Biochemistry and Molecular Biology, Molecular and Cellular Biology

Aureo Zanon Undergraduate Researcher [July 2021 - May 2023]
Major: Biology and Statistics; Minor: Math
Erickson Discovery Grant Awardee 2022
Currently in the Bioinformatics PhD program at University of Illinois Chicago

Shivani Kumar
Undergraduate Researcher [January 2023 - August 2023]
Major: Biology, Minor: Computer Science
Currently: PhD student at St. Jude Children’s Research Hospital

Meera Gupta Undergraduate Researcher [October 2021 - December 2023]
Major: Accelerated Premedical-Medical Program
Currently: MD student at Jefferson Medical School
Eberly Undergraduate Research Support Awardee 2022

Davenport Lab publications:

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

Evan Lloyd
Undergraduate Researcher [January 2023 - December 2023]
Major: Biology

Steven Kadavil
Undergraduate Researcher [January 2023 - May 2023]
Major: Computer Science

Maria Lovallo
Undergraduate Researcher [August 2022 - August 2025]
Major: Microbiology, Minor: Plant Pathology
Currently in the Molecular and Cell Biology PhD program at the University of Connecticut
NASA Pennsylvania Space Grant Consortium Awardee (2022)
Profiled by the Huck Institute of the Life Sciences in 2025

Chris Kuetche
Undergraduate Researcher [September 2025 - ]
Major: Biology, Minor: Psychology
Currently: Masters student at Northeastern University

Patricia Brocious
Undergraduate Researcher [August 2023 - May 2026]
Schreyer Honors College
Honors thesis title: “Using co-culture systems to disentangle direct vs. indirect effects of the microbiome on host gene expression regulation”
Major: Biology
Currently: PhD Student at Mount Sinai
Eberly Undergraduate Research Support Awardee (2025, 2026)
Eberly Undergraduate Research Conference Presentation Travel Support award (2025)
Awarded a Schreyer Honors College Travel Award (2025)

Davenport Lab publications/external posters:

• Direct vs. indirect effects of the host microbiome on gene expression and regulation, poster presentation, ASM Microbe 2025
• Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine. bioRxiv
  

Jack Stevenson
Undergraduate Researcher [December 2023 - ]
Major: Biology

Kinsley Wilson
Summer Research Opportunties Program (SROP) Student [June 2026 - July 2026]
Spellman College
Major: Health Science

Davenport Lab external presentations:

• Isoform-centered Multi-Omics Analysis Investigating Host-Gut Microbiome Interconnection, selected oral presentation, ABRCMS 2026
  

Damien Perry
Summer Research Opportunties Program (SROP) Student [June 2026 - July 2026]
University of Houston
Major: Biological Sciences - Microbiology

Davenport Lab external poster:

• The Microbiome: Effects on Flight Performance in Drosophila melanogaster, poster presentation, ABRCMS 2026

Visitors

Bineyam Taye
Sabbatical visitor [January 2023 - December 2023]
Associate Professor of Biology and Global Public & Environmental Health
Colgate University