Detection of microbiota change caused by inborn errors of immunity (IEIs) through 16S rRNA sequence analysis (DSI-SRP)
This DSI-SRP fellowship funded Qi (Kathy) Liu to work in the laboratory of Dr. Janet Markle in the Department of Pathology, Microbiology and Immunology during the summer of 2022. Qi (Kathy) is a senior with majors in Mathematics and Biological Sciences: Molecular & Cellular.
Inborn errors of immunity (IEIs) are immunodeficiencies caused by rare genetic mutations.
Because many children with IEIs have gastrointestinal (GI) inflammation, the interaction
between gut microbiota and the host immune system, and how different host genetic variants may perturb this interplay is an interesting and clinically relevant topic to investigate. Qi’s (Kathy) research project focused on patients with specific genetic mutations that cause IEIs. Through the 16S rDNA sequence analysis, Qi (Kathy) wanted to determine which bacteria are over- or under-represented in the microbiota of these patients relative to healthy control children. This summer, Qi (Kathy) conducted the computational analysis with R to discover how the abundance and variety of gut microbiota in patients with IEIs differ from those of healthy age-matched children. Different patients’ microbiota composition was compared at multiple phylogenic levels (e.g., order, class, genus). Qi (Kathy) also used various data visualization and statistical tools to present the data and draw conclusions about gene-microbiome relationships. She will continue working on the project by incorporating more patient samples into the data analysis after completing the DSI summer research program.
In addition to receiving support through a DSI-SRP fellowship, this project was supported and facilitated by the DSI Data Science Team through their regular summer workshops and demo sessions.