Aims: A simple in vitro model system was applied in this study assessing the dynamics of the microbial community associated with the shrimp gut system to understand the changes that influence dietary variables. Methodology and results: The diversity and abundance of microbiome were monitored within two different treatment slurries inoculated with shrimp faecal samples as to mimic the effect of diet manipulation, and 16S rRNA gene of MiSeq Illumina-based sequencing was applied. The different diets tested were a commercial standard diet and a prodigiosin added diet. There was very clear separation between the commercial standard diet and prodigiosin added diet as revealed by the total viable counts (TVC) and sequencing data. It suggested that the microbial community of the shrimp gut system exhibited a dynamic response with the treatments and allochthonous bacterial present. The prodigiosin added diet was clearly separated from the commercial standard diet serving as a potential shrimp feed additive. The sequencing data analysis showed that members of the genera Vibrio, Shigella and Photobacterium became predominant on the commercial standard diet treatment. The prodigiosin-added diet treatments indicated an abundance of members of the genera Micrococcus, Arthrobacter, and Shigella. Conclusion, significance and impact of study In vitro model system-based testing of diets could be a useful method to determine the potential effect of diet manipulation on shrimp gut system microbiome members.