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Abstract Genetic modification of microbes is central to many biotechnology fields, such as industrial microbiology, bioproduction, and drug discovery. Understanding how specific genetic modifications influence observable bacterial behaviors is crucial for advancing these fields. In this study, we propose a supervised model to classify bacteria harboring single gene modifications to draw connections between phenotype and genotype. In particular, we demonstrate that the spatiotemporal patterns ofVibrio choleraegrowth, recorded in terms of low-resolution bright-field microscopy videos, are highly predictive of the genotype class. Additionally, we introduce a weakly supervised approach to identify key moments in culture growth that significantly contribute to prediction accuracy. By focusing on the temporal expressions of bacterial behavior, our findings offer valuable insights into the underlying mechanisms and developmental stages by which specific genes control observable phenotypes. This research opens new avenues for automating the analysis of phenotypes, with potential applications for drug discovery, disease management, etc. Furthermore, this work highlights the potential of using machine learning techniques to explore the functional roles of specific genes using a low-resolution light microscope.