Toward integrating a molecular understanding of the herbivore–carnivore trophic adaptations in cichlid fishes

Abstract Cichlid fishes have repeatedly evolved equivalent herbivorous and carnivorous trophic adaptations in various waterbodies, creating natural experiments for uncovering how diet reshapes molecular systems. This review synthesizes cichlid-specific genomics, transcriptomics, and physiology to explain how the entire system, from prey detection to digestion, is re-wired to allow cichlids to feed on plant- versus animals. Diet shifts modulate digestive enzyme and transporter expression, redirect hepatic carbohydrate, lipid, and amino-acid metabolism, and remodel intestinal epithelium, barrier function, and mucosal immunity. Gut microbiomes track trophic mode and contribute complementary metabolic capacities that feed back onto host pathways. Developmental programs for oral and pharyngeal jaws and dentition impose mechanical filters on prey size and material properties, while chemosensory repertoires and brain appetite circuits bias intake and integrate endocrine and microbial cues. Together, these findings indicate that trophic transitions in cichlids are best understood as coordinated, system-wide changes linking sensory detection, feeding morphology, digestion, metabolism, and host–microbiome interactions. This integrative perspective strengthens the utility of cichlid fishes as a tractable model for studying rapid dietary adaptation under shifting resource regimes.