Black-spot linked gut microbiota shifts in Oujiang color carp: insights from TYR knockout and metabolomic integration.

Abstract

Background: Growing insights into gut microbiota reveal their surprising role in shaping external traits in fish, including the regulation of skin pigmentation. This study explores whether black-spot pigmentation influences the abundance of gut microbiota. We investigate how black-spot pigmentation in Oujiang color common carp shapes gut microbiome composition, gene expression, and metabolite, revealing a coordinated gut-skin color axis. To validate these findings, we used a TYR knockout group, which included both mutant black-spotted (TYR ^+/-) and non black-spotted (TYR ^-/-) fish, enabling functional comparison across pigmentation phenotypes.

Results: We demonstrate that black-spotted (RB and WB) fish groups contained less total microbiome composition among them. We observed significant differences in microbiota composition, with genera such as Acinetobacter, Bacillus, and Staphylococcus being more less abundant in wild black-spotted (RB and WB) groups. Gene expression profiling revealed significant differential regulation, with 27 genes markedly upregulated in the black-spotted group. Interestingly, we identified RAB9B, JUN, EGR1, PURB, HS2ST1, and ARL8 as key genes functionally correlated with the gut microbiome and metabolite profiles. Notably, Xanthine metabolites were significantly upregulated in RB and WB groups, highlighting a strong connection to purine metabolism. These genes are primarily involved in tyrosine signaling transduction, the immune system, and metabolic pathways. In parallel, blood metabolomic analysis identified 3 significantly elevated metabolites associated with nucleotide, amino acid, and lipid metabolism. Furthermore, 9 lipid-derived nutrients from muscle tissue were significantly upregulated in the black-spotted group, underscoring a strong link between pigmentation phenotype and systemic metabolic alterations. To support this, knocking out TYR converted black-spotted fish to a white phenotype and showed total microbiome profiles, 5 selective bacterial taxa, and 4 consistently expressed genes that mirrored those of wild-type black-spotted fish. Moreover, human gut microbiome data showed Bacillus and Pseudomonas were less abundant in black skin populations, reflecting patterns seen in fish.

Conclusions: Our results draw a root map to uncover a potential gut-skin-color axis, where black-spot pigmentation not only marks external phenotypic variation but also aligns with distinct microbial signatures.