Research Topics

Biogeography of edaphic Listeria

image-right While stochasticity can not be ignored, bacteria are smart enough to decide where to live and know how to live better. They interact; they evolve; they adapt; they disperse; and they survive. To better understand what ecological and evolutionary strategies bacteria employ to occupy space in nature, I carried out soil sampling at a nation-wide scale in search of Listeria, a diverse Gram-positive bacterial genus containing 2 pathogenic (L. monocytogenes and L. ivanovii) and 18 non-pathogenic species (note: a number of new species coming up!!). By quantifying the importance of deterministic factors (e.g., soil property, climate, landuse) and stochastic factors and by using population genomics, I explore the impact of various ecological and evolutionary processes on the biogeographic pattern of Listeria.

Check out this fun video showing how we obtained and processed soil samples collected across the contiguous US! Shout out to our amazing sampling team!

Microevolution of antimicrobial-resistant Samonella enterica

image-right Genetic variation in a pathogen can occur as a result of dissimilarities of ecological niches, which may represent distinct hosts or geographic areas. S. enterica, an important human and animal pathogen, contains >2,500 recognized serotypes, which display a broad range of epidemiological and ecological characteristics. The emergence of antimicrobial-resistant strains of S. enterica poses a growing threat to public health. By using comparative genomics, I examine how antimicrobial-resisatant S. enterica representing distinct serotypes differ in genomic content and microevolutionary pattern, and the influence of host range, host type and geographic origin on the arising of genetic variations. I also investigate the role of positive selection in the evolution of antimicrobial resistance, adaptation to host and serotype diversification in S. enterica.

Ecological forces of edaphic Escherichia coli

image-right While providing essential ecosystem services, high quality habitat (e.g., forest) for wildlife in watershed adjacent to produce fields may increase risk for contamination of agricultural products by enteric bacteria, including E. coli. In order to understand how landscape of watershed influences the biogeographic pattern of edaphic E. coli, I compare the distribution of E. coli collected from watersheds with different landscape patterns, and assess the effect of environmental selection and dispersal including dispersal limitation and wildlife-driven dispersal on the distribution of E. coli.

Community assembly mechanism of bacteria

image-right The mechanisms underpinning the community assembly of bacteria have been under debate for a long time on two schools of thoughts, deterministic theory and neutral theory. My previous efforts in understanding the community assembly of bacteria in freshwater lake and oil-contaminated soil suggest that deterministic and neutral processes are jointly responsible for bacterial community assembly, and the importance of those processes vary with different bacterial groups by traits (e.g., relative abundance, habitat specialization). Bacterial communities in nature are diverse and complex. I’m highly motivated to fully understand the community assembly mechanism of bacteria by taking eco-evolutionary factors, temporal factor, spatial scales, and bacterial traits into account.