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Carotenoids from different sources have different structures and functions, and their dietary components benefit the health of various organisms. The effects of halophilic Archaea-derived C50 carotenoids on poultry egg quality and gut microbiota remain largely unexplored. In this study, we isolated a carotenoid-secreting strain of Halalkalicoccus paucihalophilus, TRM89021, from the Pamir Plateau. We characterized the carotenoid pigments produced by this strain; the major components were bacterioruberin and its derivatives. The effects of these carotenoids on the egg quality and cecal microbiota composition of hens were investigated. Compared to the basal diet group (BDG), supplementation with carotenoids in the carotenoids-supplemented diet group (CDG) resulted in significantly lower a* and b* scores at week 5 and lower b* scores and Haugh units at week 2, while egg strength and weight were higher. CDG also showed increased yolk antioxidant capacity, higher glutathione peroxidase levels, and significantly lower catalase levels (p < 0.05). Plasma analysis revealed elevated total bilirubin and aspartate aminotransferase levels, along with reduced inorganic phosphorus levels in the CDG (p < 0.05). No significant differences in cecal microbiota diversity were observed between the groups at any taxonomic level. This result suggests that halophilic archaea-derived carotenoids have the potential to be used as natural feed supplements to improve egg quality. Our study provides a theoretical basis for applying archaea-derived carotenoids in poultry diets. Full article