Analysis of the fecal microbiome in Kemp’s ridley sea turtles Lepidochelys kempii undergoing rehabilitation

Abstract

The impact of the intestinal and fecal microbiome on animal health has received considerable attention in recent years and has direct implications for the veterinary and wildlife rehabilitation fields. To examine the effects of rehabilitation on the microbiome in Kemp’s ridley sea turtles Lepidochelys kempii, fecal samples from 30 incidentally captured juveniles were collected during rehabilitation. Samples were analyzed to determine alpha- (α) and beta- (β) diversity as well as the taxonomic abundance of the fecal microbiota during rehabilitation and in response to treatment with antibiotics. The fecal microbial communities of animals housed in rehabilitation for a ‘short-term’ stay (samples collected 0-9 d post-capture) were compared with ‘long-term’ (samples collected 10+ d post-capture) and ‘treated’ groups (samples collected from turtles that had received antibiotic medication). Results of this study indicate that the most dominant phylum in fecal samples was Bacteroidetes (relative abundance, 45.44 ± 5.92% [SD]), followed by Firmicutes (26.62 ± 1.58%), Fusobacteria (19.49 ± 9.07%), and Proteobacteria (7.39 ± 1.84%). Similarly, at the family level, Fusobacteriaceae (28.36 ± 17.75%), Tannerellaceae (15.41 ± 10.50%), Bacteroidaceae (14.58 ± 8.48%), and Ruminococcaceae (11.49 ± 3.47%) were the most abundant. Our results indicated that both antibiotic-treated and long-term rehabilitated turtles demonstrated a significant decrease in β-diversity when compared to short-term rehabilitated turtles. Our results likewise showed that the length of time turtles spent in rehabilitation was negatively correlated with α- and β-diversity. This study demonstrates the importance of a judicious use of antibiotics during the rehabilitation process and emphasizes the importance of limiting the length of hospital stays for sick and injured sea turtles as much as possible.