Explore the tools and computational frameworks developed by Dr. Shanlin Ke's lab for microbiome research.
The microbiota can directly protect their host against infection by pathogens, a phenomenon known as colonization resistance. However, identifying the microbes involved in microbiota-mediated colonization resistance against a specific pathogen has been an outstanding challenge. GMPT introduces a computational framework designed to identify candidate causal microbes that directly influence microbiota-mediated colonization resistance.
GMPT effectively reveals the microbiome’s role in colonization resistance, which can be validated using a classical Generalized Lotka-Volterra model. The framework has been successfully applied to synthetic microflora and two different mouse studies.
GMPT has shown significant promise in microbiome research, helping to identify key microbial species involved in pathogen resistance and improving our understanding of microbiome-mediated protection mechanisms.