Dissertations and Theses
Date of Degree
6-3-2023
Document Type
Dissertation
Degree Name
Doctor of Philosophy (Ph.D.)
Department
Epidemiology and Biostatistics
Advisor(s)
Levi Waldron
Committee Members
Heidi Jones
C. Mary Schooling
Zachary Shahn
Curtis Huttenhower
Subject Categories
Bioinformatics | Epidemiology | Microbiology | Public Health
Keywords
microbiome, epidemiology, metagenomics, reporting, antibiotics, causal inference, predictive modeling
Abstract
I consider two key areas in the growing field of human microbiome research: improving the quality of study reporting and the impact of antibiotics on participants in human gut microbiome research studies. In the first chapter, a team of evaluators used the Strengthening the Organization and Reporting of Microbiome Studies (STORMS) checklist to assess recently published microbiome literature. I found moderate agreement and reliability between evaluators, identified several items in STORMS that could be improved, and confirmed that the STORMS checklist can serve as a tool for assessing the reporting quality of published microbiome study. The next chapter considers pre-exposure gut microbiome composition as a potential effect modifier of the relationship between antibiotics and post-exposure microbiome. In a cohort study of infants, I find that it does modify this relationship for several important bacterial taxa linked to infant development. The fourth chapter looks at four datasets comparing stool microbiome measurements recently following antibiotics exposure to unexposed controls and fits predictive models for recent antibiotics exposure in each dataset. The results are mixed with smaller, more controlled studies having excellent model results while models becoming worse in less controlled conditions. The implications of this dissertation for improving the rigor of human microbiome research are discussed.
Recommended Citation
Mirzayi, Chloe A., "Improving Microbiome Research Through Enhanced Reporting and Modeling the Effects of Antibiotic Usage" (2023). CUNY Academic Works.
https://academicworks.cuny.edu/sph_etds/97