Phylogenetic, Ecological, and Physiological Factors as Modulators of the Intestinal Microbiota in Stranded Marine Mammals in Uruguay

ABSTRACT Gut microbiota plays a key role in host physiology and may reflect ecological and health‐related processes, yet it remains poorly studied in marine mammals. We characterized and compared the gut bacterial communities of seven marine mammal species stranded along the Uruguayan coast between 2022 and 2024, including pinnipeds and cetaceans with different trophic habits. Tissue samples from 21 individuals were analyzed using 16S rRNA gene metabarcoding targeting the V3–V4 regions, with amplicon sequence variants (ASVs) inferred using DADA2 and taxonomic assignment based on SILVA 138.1. Microbiota was mainly dominated by Firmicutes, Proteobacteria, and Fusobacteriota, with bacterial genera commonly detected across host species, including Clostridium sensu stricto 1, Paeniclostridium , Photobacterium , and Cetobacterium . Alpha diversity varied among species, with Otaria byronia showing the highest and Pontoporia blainvillei and Phocoena spinipinnis the lowest values. Microbial composition differed among species, between cetaceans and pinnipeds, and between coastal and pelagic species. These results suggest that marine mammal gut microbiota is influenced by ecological, phylogenetic, and individual‐level factors, providing a baseline for future research on marine mammal microbiota in the Southwestern Atlantic.