Bacterial GWAS: A Comprehensive Assessment of Challenges, Methods and Alternatives

Abstract

Genome-wide association studies (GWAS) have proven to be a successful method for identifying associations between human genotypes and phenotypes. Due to advances in sequencing technologies and the subsequent growth of bacterial datasets, bacterial GWAS is increasingly becoming a viable research method for identifying bacterial genotype-phenotype associations. However, bacterial GWAS cannot be performed using established methods used in human GWAS due to genomic differences. Specialized software to perform bacterial GWAS has been developed, utilizing regression models, phylogenetic trees, and machine learning to overcome the unique genomic challenges. Here, we will discuss these challenges of bacterial GWAS, the software methods that have been developed and our recommendations on their usage, and discuss alternative methods for identifying genotype-phenotype associations in bacteria.