High salinity selects for halotolerant gut microbiota in the mummichog Fundulus heteroclitus

Mummichogs ( Fundulus heteroclitus ) are euryhaline fish that maintain osmoregulation across a range of salinities, but how their gut microbiomes respond remains poorly understood. Using Illumina 16S amplicon and Oxford Nanopore full-length 16S sequencing, we show that salinity is associated with reproducible gut microbiome restructuring. While alpha diversity did not differ significantly between low-salinity (5 ppt) and high-salinity (50 ppt) groups, beta diversity revealed distinct shifts in microbial communities. Specifically, high-salinity microbiomes were dominated by halotolerant Vibrio and Ahrensia species while low-salinity microbiomes retained more taxonomically diverse communities. These findings suggest host-associated microbes may contribute to osmotic homeostasis under salinity stress.