Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation

Abstract

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.

Long‐term apparent survival of a cold‐stunned subpopulation of juvenile green turtles

“…In particular, some turtles were known to experience cold stuns in two consecutive winters (i.e., occasion 2 recaptures). The rehabilitation process itself (i.e., transport and excessive handling) can lead to residual stress and altered behavior (McNally et al, 2021), which also may have led to some degree of unknown delayed mortality or high emigration. Speculation on mechanisms is difficult without knowing the fate of more cold‐stunned individuals or characteristics of the broader St. Joseph Bay green turtle population.…”

What lives on and in the sea turtle? A literature review of sea turtle bacterial microbiota

“…The other three predominant families identified at intake were Arcobacteraceae, Shewanellaceae, and Rhodobacteraceae with mean abundances of 11.8%, 7.7%, and 6.7% respectively. All four of the predominant families fell within the phylum Proteobacteria [37]. In contrast, in clinically healthy Kemp's ridley sea turtles, there was an increase in the family Flavobacteriacea (MA 17%), making it the most abundant bacterial family.…”

“…The first being whether the samples were obtained from live animals, or if the samples were taken following death, either natural or via euthanasia. While sampling post-mortem allows direct samples to be taken from different portions of the gastrointestinal tract, there are likely multiple factors that may have altered the microbiota prior to sampling such as illness, injury, anorexia, or dehydration [37]. Sampling from live sea turtles can also have biases depending on if the animal is wild caught, stranded, debilitated or in a rehabilitation center [31,38].…”

“…Sampling from live sea turtles can also have biases depending on if the animal is wild caught, stranded, debilitated or in a rehabilitation center [31,38]. Additionally, samples used as a proxy (i.e., cloacal, and fecal samples) to estimate the gastrointestinal microbiota in living turtles can influence the results as well [37]. Across the literature cloacal swabs and fecal samples are often used to infer the microbiota population of the gastrointestinal tract, although there are several papers that sample the colon via deep swabs through the cloaca [Additional file 1: Table S1].…”

“…The most abundant families identified, and their corresponding percent mean abundances were Cardiobacteriaceae 16.5%, Flavobacteriaceae 15.5%, and Neisseriaceae 10.4%, all of which fall within the phyla Proteobacteria or Bacteroidetes. Also in 2021, McNally et al investigated the cloacal microbiota of cold stunned Kemp's ridley sea turtles [37]. Cloacal samples were collected at intake to the New England Aquarium and again when the animal was declared clinically healthy.…”