Penn Virome Characterization Center

The Oro-Respiratory-Gut Virome Axis Over Space and Time

Our Mission

The Penn Virome Characterization Center (Penn-VCC) aims to define the composition and dynamics of the human virome in a healthy population. We focus on priority body sites — the Oral/Dental, Gut (stool), Respiratory Tract (upper and lower), and Blood from infants into adulthood — to quantify and analyze virome populations, including viruses of humans, bacteria (phage), and eukaryotic commensals.

Research Interests

Our interdisciplinary teams combine clinical research, biospecimen analysis, metagenomics, and computational biology to better understand virus-host interactions and their impact on human health.

Human Virome Diversity

Characterizing viral communities across multiple body sites to understand virome composition in healthy populations.

Metagenomic Sequencing

Developing advanced sequencing and viral enrichment workflows for accurate identification of bacteriophages and eukaryotic viruses.

Respiratory and Gut Microbiomes

Investigating interactions between microbial ecosystems in healthy individuals.

Pediatric Virome Research

Studying virome development in healthy children.

Computational Biology & Bioinformatics

Applying statistical modeling, sequence assembly, and large-scale data analysis to complex virome datasets.

Ethics and Data Sharing

Addressing ethical, legal, and social implications of human virome research, participant privacy, and public data deposition.

Featured Publications

mSystems Optimizing methods for virome analysis based on studies of a synthetic viral community
Jiayi Duan, Andrew D. Marques, Matthew Hogenauer, et al.

A foundational study establishing standardized protocols for Viral Particle Enrichment (VPE) and benchmarking.
Mol Biol Evol Uncovering viral protein acquisition events and human-specific folds with pairwise comparisons of predicted protein structures
Julia C. Malnak, Saira Montermoso, Frederic Bushman, and Noam Auslander

Classify highly divergent viruses, trace lateral gene transfer, and uncover features associated with viral host range by represnting viruses with structural protein clusters.
Microbiome Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction
Carter Merenstein, Lev Litichevskiy, Christoph Thaiss, Ronald G Collman, Frederic D Bushman

Quiescent prophages dominate mouse gut viromes, with significant shifts in dynamics driven by aging and dietary restriction.
Cell Rep The naked mole-rat microbiome is associated with healthy aging and social structure
Ceylan Tanes, Naomi G Wilson, Megan Smith, et al.

Demonstrates that naked mole-rat gut microbiomes resist the significant age-related changes observed in mice.