Gut microbiome variation across life stages of Mugil cephalus in a Mediterranean estuary revealed by rRNA gene metabarcoding

Abstract The gut microbiome plays a crucial role in fish health, yet its diversity across life stages remains poorly understood, especially in juveniles. This study provides a comprehensive assessment of the gut microbiome in wild adult and juvenile Mugil cephalus from the Mediterranean estuary, Ashtum El-Gamil, Egypt, by integrating prokaryotic 16S and eukaryotic 18S rRNA gene metabarcoding with functional gene prediction. Gut bacterial, archaeal, and eukaryotic communities were compared with those in the surrounding water and sediment to evaluate environmental influences. 16S rRNA gene analysis revealed distinct gut microbial profiles across life stages, with juveniles exhibiting higher bacterial richness, whereas adults showed greater archaeal richness. Shared gut microbiome members, including Flavobacterium and Nitriliruptoraceae, were also detected in the surrounding environment, suggesting environmental contributions to gut microbiome establishment. Dominant gut bacterial taxa included Proteobacteria, Bacteroidetes, Actinobacteria, and Planctomycetes, while archaea were primarily represented by Euryarchaeota and Thaumarchaeota. The 18S rRNA gene survey identified Macrocyclops albidus (Crustacea), Brachionus plicatilis (Rotifera), and the flatworm Crossobothrium sp., all of which are implicated in various trophic interactions . 16S rRNA gene-based functional inference revealed clear metabolic divergence between life stages, with juveniles enriched in oxidative and detoxifying pathways, while adults exhibited anaerobic and methanogenic activities, reflecting life stage–specific nutritional strategies and adaptive responses. These findings highlighted the role of environment and host ontogeny in shaping gut microbiome diversity in M. cephalus .