The Gram-negative bacterial type VI Secretion System (T6SS) delivers toxins to kill orinhibit the growth of susceptible bacteria, while others target eukaryotic cells. Deletionof atsR, a negative regulator of virulence factors in B. cenocepacia K56-2, increasesT6SS activity. Macrophages infected with a K56-2 ΔatsR mutant display dramaticalterations in their actin cytoskeleton architecture that rely on the T6SS, which isresponsible for the inactivation of multiple Rho-family GTPases by an unknownmechanism. We employed a strategy to standardize the bacterial infection ofmacrophages and densitometrically quantify the T6SS-associated cellular phenotype,which allowed us to characterize the phenotype of systematic deletions of each genewithin the T6SS cluster and ten vgrG encoding genes in K56-2 ΔatsR. None of thegenes from the T6SS core cluster and the individual vgrGs were directly responsiblefor the cytoskeletal changes in infected cells. However, a mutant strain with all vgrGgenes deleted was unable to cause macrophage alterations. Despite not being able toidentify a specific effector protein responsible for the cytoskeletal defects inmacrophages, our strategy resulted in the identification of the critical core componentsand accessory proteins of the T6SS assembly machinery and provides a screeningmethod to detect T6SS effectors targeting the actin cytoskeleton in macrophages byrandom mutagenesis.