Coral reef degradation is associated with gut microbiome shifts in the tomato anemonefish Amphiprion frenatus

Anemonefish in association with anemones are iconic images of tropical coral reefs and essential to maintaining the structure and function of coral reefs. Coral reef degradation may influence host-associated microbiomes, yet its effects on anemonefish gut microbial communities remain poorly understood. This study compared the gut microbiomes of the tomato anemonefish, Amphiprion frenatus, in symbiosis with the bubble anemone host Entacmaea quadricolor , inhabiting two contrasting reef ecosystems: a degraded reef system (Nha Trang Bay - NTB) and a relatively pristine reef system (Van Phong Bay - VPB), Vietnam. Gut microbiomes from 30 fish (n = 15 per bay) were analyzed using 16S rRNA amplicon sequencing. Although Shannon diversity and Evenness did not differ significantly between bays (Shannon: 7.22 ± 0.71 in VPB vs. 6.86 ± 0.70 in NTB; Evenness: 0.84 ± 0.04 vs. 0.85 ± 0.05), fish from VPB harbored significantly richer gut microbiomes, with higher observed ASV richness (407.9 ± 144.7 vs. 282.6 ± 95.3) and Chao1 diversity estimates (626.5 ± 300.9 vs. 367.5 ± 142.8). Beta-diversity analyses showed statistically significant differences in microbial composition and density between sample groups in NTB and VPB (PERMANOVA, R 2 =0.094 p = 0.006). Proteobacteria and Firmicutes were dominant phyla in both communities with Firmicutes accounted for 41.59% of sequences in VPB compared with 38.04% in NTB, whereas Proteobacteria represented 35.88% and 42.59%, respectively. In contrast, NTB fish showed a greater relative abundance of Proteobacteria and Planctomycetota. PICRUSt2-based functional predictions suggested enrichment of fermentation and energy acquisition pathways in VPB fish, whereas microbiomes from NTB were associated with predicted functions related to a variety of biosynthetic and metabolic processes. These findings suggest that habitat conditions may be associated with the carbon and nitrogen cycles mediated by the microbial communities within the anemonefish-anemone symbiotic relationship.