Advancing microbial pangenomics through human pangenomics

Although the term pangenome originated in the study of microbial species, recent advances in eukaryotic pangenomics have been driven largely by the need to manage the substantial computational challenges posed by population-scale eukaryotic datasets. This review evaluates the extent to which existing eukaryotic pangenome tools and methods can be extended to microbial species. We first survey current eukaryotic and microbial pangenomic approaches and then examine opportunities and challenges in adapting eukaryotic methods to microbial genomes, with particular emphasis on scalability, data quality, evolutionary complexity, and benchmarking. Finally, we highlight areas where existing approaches generalize well and where substantive redesign and redevelopment are needed.