The effect of Vibrio parahaemolyticus IPNGS16 on the bacterial profile of the gut of Penaeus vannamei was assessed by 16S metagenomic analysis. The V3 hypervariable region of the bacterial 16S rDNA was amplified by PCR. Sequencing reads were generated using the 2×150 (300 cycles) for the base-read length chemistry of the Illumina MiniSeq platform. The web-based Shaman and MicrobiomeAnalyst platforms were used to analyze the sequences. The phyla Proteobacteria, Bacteroidetes, and the genera Vibrio, Ruegeria, Nautella, and Pseudoalteromonas were found among the most abundant taxonomic ranks in control, diseased, and healthy shrimp. Alpha and beta indices showed significant differences between shrimp survival in the control condition and dying shrimp (lower diversity). Metabolism (carbohydrate and amino acid metabolism-related genes and, to a lesser extent, energy, lipid, and cofactors and vitamin metabolism-related genes) of dying and surviving shrimp was affected by Vibrio infection. The top metabolic functions (cell cycle, glycine, serine, threonine, cysteine, methionine, purine, pyrimidine, pyruvate, and quorum sensing) in dying and surviving shrimp were affected by Vibrio, especially quorum sensing. The interaction network analysis showed fewer interactions in dying shrimp than control and surviving shrimp. Proteobacteria, Bacteroidetes, Vibrio, and Ruegeria predominated in all samples, and Vibrio changed bacterial diversity and metabolism in the intestine of P. vannamei. Ruegeria and Pseudoalteromonas showed negative interactions with Vibrio, suggesting their use as probiotics. This study sheds light on the Vibrio infection in the gut microbiota of shrimp.