Background <p>The gut microbiome plays a crucial role in the metabolic health and pathogen resistance of various host animals. It is also well established that external environmental factors can influence the gut microbiome, leading to differences in its composition. However, the functional implications of these differences remain poorly understood. This study examined the gut microbiome of medaka (<i>Oryzias latipes</i> species complex) by comparing domesticated and wild populations, with the aim of gaining insights into the functional significance of their specific characteristics, particularly those of the wild-type microbiome.</p> Results <p>For the comparative analysis of the gut microbiome, 48 domesticated and 122 wild medaka were collected from multiple laboratories, pet stores and streams across Japan. The results showed that wild medaka exhibited significantly higher gut microbiome diversity, with a broader range of bacterial members. In contrast, the gut microbiome of domesticated medaka harbored lower microbial diversity and was consistently dominated by <i>Aeromonas</i>, a typical opportunistic pathogen in fish. Additionally, 88.6% of <i>Aeromonas</i> isolates from domesticated medaka exhibited haemolytic activity. Moreover, a domesticated rearing experiment with wild populations showed no proliferation or dominance of <i>Aeromonas</i> in their gut, as observed in domesticated medaka. A further rearing experiment revealed that pre-exposing antibiotic-treated medaka to sediments from their natural habitats prevented <i>Aeromonas</i> colonisation, even when reared under domesticated conditions.</p> Conclusions <p>These findings suggest that the habitat-derived wild gut microbiome can inhibit <i>Aeromonas</i> proliferation in domesticated fish, highlighting its potential to mitigate opportunistic diseases in aquaculture.</p> Graphical abstract <p></p>