![]() Most studies of microbial communities have focused on the distal gut of humans or captive mammals but there are recent growing efforts in investigations of free-ranging wild animals. Moreover, we can consider the host and its microbial commensals as a distinct biological entity (holobiont and hologenome) susceptible to the processes of natural selection. biochemical pathways in nutrient acquisition. It is estimated that the host’s collection of bacteria could contain at least 100 times the genes as in the host’s genome, often adding to the metabolic functions’ repertoire, e.g. Microbial communities associated with vertebrates can influence host’s evolution, development, immune system maturation, physiology, nutrient acquisition, health and disease. Finally, our investigation of effects of captivity on the gut-associated microbial community provides a baseline for studying the impact of husbandry conditions on turtles’ health and survival upon their return to the wild. We provide the first insights into the oral microbial communities of wild and rehabilitated loggerhead sea turtles, and establish a framework for quick and non-invasive sampling of oral and cloacal microbial communities, useful for the expansion of the sample collection in wild loggerhead sea turtles. Unclassified reads were abundant in the aforementioned groups, which indicates high incidence of yet undiscovered bacteria of the marine reptile microbial communities. Additionally, Proteobacteria and Bacteroidetes dominated oral and cloacal microbiota, while Kiritimatiellaeota were abundant in cloacal samples. Our results show that the oral microbiota is more sensitive to environmental shifts than the cloacal microbiota, and that it does retain a portion of microbial taxa regardless of the shift from the wild and into rehabilitation. We describe the oral and cloacal microbiota of Mediterranean loggerhead sea turtles by 16S rRNA gene sequencing to compare the microbial communities of wild versus turtles in, or after, rehabilitation at the Adriatic Sea rescue centers and clinics. Describing oral and cloacal microbiota of wild animals could shed light on the previously unknown aspects of sea turtle holobiont biology, ecology, and contribute to best practices for husbandry conditions. Understanding the microbial communities of sea turtles in the wild and how affected they are by captivity, is one of the stepping stones in improving the conservation efforts. ![]() Loggerhead sea turtles ( Caretta caretta) are a keystone species in marine ecosystems and are considered vulnerable in the IUCN Red List, which led to growing efforts in sea turtle conservation by rescue centers around the world. Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation.
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