Flatfish intestinal microbiota depend on various host traits, and vary with sediment type and bottom trawling effort.

The intestinal microbiota of fishes support digestion, nutrient uptake and play an important role in the immune system, development and reproduction. Flatfish live in close contact with the seafloor, and are particularly exposed to anthropogenic disturbances such as bottom trawling. Bottom trawling impacts the ecosystem in various ways and recent evidence indicates that the microbial composition and diversity in marine sediments varies with fishing intensity. It is presently unknown whether this trawling signal applies to the seafloor alone or also extends to microbiota of marine holobionts inhabiting it, such as flatfishes. Here, three flatfish species (Buglossidium luteum, Limanda limanda and Pleuronectes platessa) were sampled across the southeastern North Sea. We characterized the intestinal microbiota using 16S rDNA metabarcoding of 162 individuals, and disentangled how intestinal microbial composition and diversity are jointly shaped by various host traits (species, sex, age, weight, and condition factor) and environmental factors (sediment type and trawling intensity). Intestinal diversity varied among species and changed with age, weight and sediment type. Community composition was dependent on species, age, condition factor and sediment type. In addition, we found that trawling intensity explained shifts in intestinal microbial community composition, suggesting that the known impacts of bottom trawling on the benthic environment may cascade to intestinal microbiota of flatfish. Our findings provide important insight into host-microbiota interactions in marine ecosystems and highlight the interplay between host traits and environment as drivers of intestinal microbial diversity and community composition in flatfish.