We have developed a fully automated sampling platform that enables dense, high-frequency longitudinal microbiome profiling within individual hosts. This approach overcomes the limitations of sparse sampling and allows direct observation of ecological transitions and circadian dynamics in the gut microbiome.
By capturing fine-scale temporal fluctuations, we aim to characterize coordinated microbial dynamics and reveal how collective microbial behavior aligns with host physiological states.

Leveraging recent advances in long-read sequencing technologies, we are advancing genome-resolved metagenomic analysis to reconstruct complete strain-level genomes across diverse microbiomes.
Beyond bacterial chromosomes, we systematically investigate mobile genetic elements (MGEs), including bacteriophages and plasmids, as well as horizontal gene transfer (HGT) dynamics. This integrated framework enables a comprehensive understanding of the genetic architecture that shapes microbiome ecosystems.
Through these efforts, we aim to establish a refined structural basis for reassessing microbiome–host interactions in health and disease.

By analyzing diverse human and animal cohorts, we investigate the structural determinants of inter-individual microbiome variation. We identify microbiome features associated with disease states, host phenotypes, and environmental factors.
Our goal is to translate these findings into the discovery of therapeutic microbial targets and microbiome-derived biomarkers, ultimately contributing to future diagnostic and intervention strategies.