Bacteria organisms populating the gastrointestinal tract (GIT) play a very important role in supporting host physiology and environmental adaptation. This study investigated the bacterial diversity and composition across GIT regions of Oreochromis niloticus grouped by size (4–20 g, 21–50 g, 51–150 g, >200 g). Total bacterial counts, Enterobacteriaceae, and Vibrionaceae were quantified. Results showed significant disparities by size and GIT region, with posterior intestines harboring the highest bacterial loads. Enterobacteriaceae peaked in larger fish (>200 g), while Vibrionaceae surged in intermediate-sized fish (21–50 g), suggesting size-dependent colonization.
Dominant genera (Bacillus, Lactococcus, Staphylococcus, Lactobacillus, Clostridium) exhibited distinct distribution patterns, with diversity increasing in larger fish, particularly in posterior intestines. Smaller fish showed reduced microbial diversity. These findings highlight the dynamic relationship between fish size, GIT region, and microbial communities, emphasizing their role in aquaculture sustainability and bacterial disease management.