Integrons are genetic elements that enable bacterial adaptation by collecting new genes encoded in integron cassettes (ICs) to create a reservoir of adaptive functions. These cassettes typically lack their own promoters and rely on the integron platform for their expression. Integrons, well-known for spreading antibiotic resistance genes in clinically relevant Gram-negative species, include Mobile Integrons (MIs), that transport over 170 resistance genes. In contrast, Sedentary Chromosomal Integrons (SCIs), ubiquitous in Vibrio species, are primarily found within bacterial chromosomes. However, their functions are not related to antimicrobial resistance and are largely unexplored. SCIs, typified by the Superintegron (SI) in Vibrio cholerae, represent ancient and highly variable regions in bacterial genomes. The SI is extensive, housing 179 integron cassettes, mostly with unknown functions. Although 19 cassettes encode toxin-antitoxin (TA) systems, which stabilize the array, the intricacies of the SI are challenging to study due to its size and unique integrase. To investigate the SI's impact on V. cholerae, we developed the SeqDelTA approach, enabling the gradual deletion of the SI. This deletion facilitates the use of standard genetic tools without SI interference. Our in-depth analysis of the resulting ?SI strain, covering various aspects, demonstrated no significant alterations in V. cholerae's physiology. Despite their extended coevolution, SCIs appear to be genetically isolated from the host genome. Overall design: Gene expression analysis of RNA-seq data at exponential (OD600 0.8) and stationary (OD600 2.8) growth phase at 37°C in LB medium of Vibrio cholerae N16961 (A001) and a V. cholerae ?SI, where the superintegron has been deleted (B522) Three biological replicates per condition and strain are included.