Speakers: Sonny Lee, PhD

Sonny Lee, PhD

Assistant Professor
Division of Biology
Kansas State University


Sonny Lee is currently an Assistant Professor at the Division of Biology, Kansas State University. From 2016–2019, he performed his postdoctoral research at the University of Chicago Medicine in Drs. Eugene Chang and Meren’s lab, focusing on using high-resolution metagenomics to answer pressing questions regarding fecal microbiota transplantation (FMT). Currently, his lab focusses on elucidating the mechanism between host-microbe interaction, with model systems ranging from plant-soil to coral holobiont, and swine and mouse gut.
Sonny completed his Ph.D. at Auckland University in New Zealand and his undergraduate studies at Florida Institute of Technology. His research interests lie in the area of microbial ecology, ranging from bioinformatics to microbial cultivation and elucidating microbial mechanism during stressful environmental conditions. He has collaborated actively with researchers in several other disciplines of immunology and macroecology.
Sonny has traveled with his partner around the world from USA to New Zealand, and back to Chicago and finally settling in Manhattan, Kansas. And because that clearly isn’t enough chaos, two puppies were brought into their lives some time in 2015. Besides becoming a proud and obsessed dog-dad, Sonny also enjoy diving, running long distances, fiction books, and enjoying good food, beer, and live theatre. Now he usually manages to read one book a month.


The Impact of Microbiota in Early Life on IBD Development: From Metabarcoding to Metagenomes

Epidemiological studies identified associations between antibiotics exposure in early life and increased risk of developing inflammatory bowel diseases (IBD) later in life. We demonstrated a causative relationship between peripartum antibiotic-induced gut dysbiosis and IBD onset in a murine model. We further examined gut microbiota community membership and functional potential over time using metagenomic shotgun. We found that maternal peripartum antibiotic exposure restructures both the bacteriome and mycobiome membership and alters the functions of the whole microbiome community in offspring relative to those observed in unexposed pups. Among offspring from antibiotic-exposed dams, differences in gene profiles related to nitrogen metabolism were observed between pups that eventually developed overt spontaneous colitis versus those that did not. In the course of disease, community-wide differences in nitrogen metabolism appeared at 8 weeks after withdrawal of antibiotic treatment (11 weeks of age), which was prior to the onset of clinical symptoms. We then performed ex-vivo experiments examining the metabolizing capacity associated with the computationally predicted pathway using living microbiota samples to obtain physiological insights into these differences beyond genetic information. Our study demonstrated that the functional changes of the gut microbiota related to nitrogen metabolism precedes the clinical onset of colitis.