Ai Zhang

Program: Human and Statistical Genetics

Current advisor: Gautam Dantas, PhD

Undergraduate university: Beijing University of Technology, 2016

Enrollment year: 2022

Research summary
I study how the infant gut and skin microbiomes adapt to their environments, focusing on microbial genomic and functional changes that drive resilience, pathogenicity, and host interactions.

The human microbiome dynamically adapts to environmental and physiological pressures, shaping both health and disease. My thesis investigates microbial adaptation across two distinct host environments: the infant gut and the human skin.
In Aim 1, I examine how the gut microbiome adapts functionally during the weaning period, when infants transition from milk to solid foods. Using longitudinal metagenomic and metatranscriptomic sequencing from twin and mother–infant cohorts, I identify strain-level persistence, metabolic pathway shifts, and horizontal gene transfer events that support microbial resilience and metabolic flexibility.
In Aim 2, I characterize genomic determinants of pathogenicity in Cutibacterium acnes across diverse host niches. Through comparative genomics of 467 clinical and commensal isolates, I analyze antimicrobial resistance genes, virulence factors, and plasmid-associated mobile genetic elements that may drive the bacterium’s dual roles as a commensal and opportunistic pathogen. Together, these studies reveal how host environment and microbial genetics jointly shape adaptation, with implications for nutritional and therapeutic strategies promoting microbiome health.

Graduate publications
Shi Y, Liu L, Chen J, Wylie KM, Wylie TN, Stout MJ, Wang C, Zhang H, Shih YT, Xu X, Zhang A, Park SH, Jiang H, Liu L. 2024 Simplified methods for variance estimation in microbiome abundance count data analysis. Front Genetics, 15():1458851. PMCID: PMC11532193