Litopenaeus vannamei also known as the Pacific white shrimp, is the most common shrimp species cultured in-land around the world. L. vannamei is native to the Pacific coastlines ranging from the state of Sonora, Mexico, to the northern parts of Peru, where water temperatures are >20°C year-round. These shrimps can reach a maximum length of 23 cm and weight up to 45 g in the wild. Because this species of shrimp can reach very large sizes in a short period of time, it has a high production value for fisheries and aquaculture farms. L. vannamei production in 2014 was between 180,000 and 200,000 tons, and it is expected to increase by 10% in 2030. The main production challenge for L vannamei inland-aquaculture is the risk for disease outbreak. In recent years, there has been a considerable increase in disease outbreaks and early mortality syndrome in Asia, U.S.A., Mexico, and Central and South America. The feed used in most aquaculture operations is mainly fishmeal. The high protein present in the feed can easily make water parameters such as levels of ammonium, nitrite, and nitrate uncontrollable. Animal maintained under such conditions are stressed and could negatively affect their growth, immunity, and tissue integrity. A cost and growth effective feed replacement can be plant-based such as cottonseed meal, which in previous experiments has demonstrated to result in similar growth capacity for shrimp as commercially available feed, while having high survival rate and better water parameter management when compared to the fishmeal-based feed. An aspect of shrimp growth that is not regularly taken into consideration is the L. vannamei’s gut microbiota, which constitutes of the microorganisms found in the stomach, hepatopancreas and intestines. Throughout the life of L. vannamei crustaceans, the gut microbiota provides metabolic benefits, supports hormonal functions, stimulates the immune system, and has been associated with higher product weight and survivability. In the present study, feeds with different animal-to-plant ratios were utilized in a growth experiment using L. vannamei. After 30 days of the assigned feed consumption, the guts of shrimp under four different diets were extracted to analyze microbial diversity using Illumina 16S-amplicon sequencing technology and bioinformatics. Results demonstrated differences in gut microbiota composition between shrimp fed a 100% plant-based diet and the other three diets containing animal ingredients. In all the diets that had animal products the dominant phyla in decreasing order of abundance were Actinobacteria, Proteobacteria and Bacteroidetes, whereas the dominant phyla in the plant-based feed were Proteobacteria, Actinobacteria and Bacteroidetes. These results demonstrate how the abundance of dominant bacteria phyla can fluctuate in response to changes in diet, and that the feed containing animal ingredients greatly influences the presence of specific bacterial consortium. In conclusion, this study enhances the understanding we currently have on the shrimp’s gut microbiota and their relationship to feed sources in an effort to benefit the aquaculture industry. Further studies are needed to understand how this change in gut microbiota affects the survivability and overall health of the shrimp.