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Respiratory disease is a common cause of morbidity and mortality in sea turtles, including the Kemp’s ridley sea turtle (Lepidochelys kempii). Although culture-dependent methods are typically used to characterize microbes associated with pneumonia and to determine treatment, culture-independent methods can provide a deeper understanding of the respiratory microbial communities and lead to a more accurate diagnosis. In this study, we characterized the tracheal lavage microbiome from cold-stunned Kemp’s ridley sea turtles at three time points during rehabilitation (intake, rehabilitation, and convalescence) by analyzing the 16S rRNA gene collected from tracheal lavage samples. We retrospectively developed a radiographic scoring system to grade the severity of lung abnormalities in these turtles and found no differences in diversity or composition of microbial communities based on radiographic score. We also found that the culture isolates from tracheal lavage samples, as well as other previously reported sea turtle pathogens, were present in variable abundance across sequenced samples. In addition to the tracheal microbial community of live turtles, we characterized microbial communities from other segments of the respiratory tract (glottis, trachea, anterior lung, posterior lung) from deceased turtles. We found a high degree of variability within turtles and a high degree of dissimilarity between different segments of the respiratory tract and the tracheal lavage collected from the same turtle. In summary, we found that the pulmonary microbial community associated with pneumonia in sea turtles is complex and does not correlate well with the microbial community as identified by tracheal lavage. These results underscore the limitations of using tracheal lavage for identification of the causative agents of pneumonia in sea turtles.

Microbial communities of animals play a role in health and disease, including immunocompromised conditions. In the northeastern United States, cold-stunning events often cause endangered Kemp's ridley turtles (Lepidochelys kempii) to become stranded on beaches in autumn. These sea turtles are admitted to rehabilitation facilities when rescued alive and are presumed immunocompromised secondary to hypothermia. To better understand the role that microbes play in the health of cold-stunned sea turtles, we characterized the oral and cloacal microbiome from Kemp's ridley turtles at multiple timepoints during rehabilitation, from admission to pre-release, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites and among turtles that survived and those that died. We found that clinical parameters such as presence of pneumonia or values for various blood analytes did not correlate with oral or cloacal microbial community composition. We also investigated the effect of antibiotics on the microbiome during rehabilitation and prior to release and found that the type of antibiotic altered the microbial community composition, yet overall taxonomic diversity remained the same. The microbiome of cold-stunned Kemp's ridley turtles gradually changed through the course of rehabilitation with environment, antibiotics, and disease status all playing a role in those changes and ultimately the release status of the turtles.

Blood was collected from wild captured green and Kemp's ridley turtles off the west coast of Florida, USA. Blood gases and biochemical values were analyzed using a point of care (POC) device in the field. Analytes include pH, partial pressure of carbon dioxide (pCO2), partial pressure of oxygen (pO2), total carbon dioxide (TCO2), bicarbonate (HCO3), base excess (BE), oxygen saturation (sO2), lactate, sodium (Na), potassium (K), chloride (Cl), total carbon dioxide (TCO2), anion gap, ionized calcium, glucose, blood urea nitrogen (BUN), creatinine (Crea), hematocrit (Hct), and hemoglobin (Hb). These are novel data for wild healthy Kemp's ridley turtles, and results for green turtles were generally consistent with past studies of green turtles with exceptions primarily in blood gas values. Ninety percent of the green turtles had fibropapillomatosis (FP), but none of the blood analytes were correlated with disease severity. Only BUN was correlated with weight of green turtles, and there was no correlation between blood parameters and weight of Kemp's ridley turtles. This study provides data that are useful in understanding the physiologic status of sea turtles specific to this region, allowing for comparisons to other populations, life stages, and disease states.