Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta)

Abstract

Background Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation. 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. 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. 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. Results 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. 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. Additionally, Proteobacteria and Bacteroidetes dominated oral and cloacal microbiota, while Kiritimatiellaeota were abundant in cloacal samples. Unclassified reads were abundant in the aforementioned groups, which indicates high incidence of yet undiscovered bacteria of the marine reptile microbial communities. Conclusions 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. 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.

Surface microbiota of Mediterranean loggerhead sea turtles unraveled by 16S and 18S amplicon sequencing

“…Some of these organisms require the sea turtle substratum to attach and thrive, and thus their survival is inextricably linked to the wellbeing and fitness of their hosts. The existing body of literature on loggerhead and other sea turtle microbiomes includes mainly studies investigating the internal microbiota, such as those living in the gut, cloaca, faces, and oral cavities (Abdelrhman et al, 2016;Arizza et al, 2019;Biagi et al, 2019;Scheelings et al, 2020a,b;Filek et al, 2021). The epimicrobiomes of sea turtles, in turn, have received far less attention.…”

A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What’s New?

“…Stress monitoring is possible both by cortisol measurement [127,128] and by detecting a suppression in secretory Immunoglobulin A, an indicator of chronic stress [129], given that baseline values are established for the species and population under investigation. Both bacterial pathogens excreted orally such as Mycobacterium bovis in Australian brushtail possums and oral microbiomes can be assessed by extracting bacterial DNA and RNA from saliva [130,131]. A wide range of viruses can be isolated from saliva including economically relevant viruses such as foot-and-mouth disease virus [132,133], and classical and African swine fever [134,135] as well as viruses of conservation concern such as the elephant endotheliotropic herpesvirus [136].…”

“…Antibody detection in saliva has, for example, been attempted for M. bovis antibodies in wild boar [140]. The collection of saliva samples can be carried out directly by rolling a cotton swab over the oral mucosa of a restrained animal [127,128,131,136,137], or indirectly by using artificial baited objects or natural objects from the animals' environment that they routinely interact with. An artificial object that can be attractive to a range of inquisitive mammalian species including, for example, suids and primates, are ropes covered in bait [133][134][135]137,140].…”

“…Some objects such as cotton ropes may contain natural PCR inhibitors that need to be considered when samples are processed [135,137]. Generally, in saliva samples, it needs to be considered that the oral microflora can be sensitive to external conditions [131] and that low pathogen excretion can occur, potentially reducing the sensitivity of surveillance efforts using saliva [134].…”

Surface microbiota of Mediterranean loggerhead sea turtles unravelled by 16S and 18S amplicon sequencing

“…Some of these organisms require the sea turtle substratum to attach and thrive, and thus their survival is inextricably linked to the wellbeing and fitness of their hosts. The existing body of literature on loggerhead and other sea turtle microbiomes includes mainly studies investigating the internal microbiota, such as those living in the gut, cloaca, faeces, and oral cavities (Abdelrhman et al, 2016;Arizza et al, 2019;Biagi et al, 2019;Scheelings et al, 2020bScheelings et al, , 2020aFilek et al, 2021). The epimicrobiomes of sea turtles, in turn, have received far less attention.…”