Investigating green sea turtle diet and digestive microbiome using DNA metabarcoding

Lucia Diaz

Green sea turtles are endangered conservation icons living in association with myriad microorganisms that play crucial roles on their feeding ecology. By using DNA metabarcoding targeting the 18S rRNA region from esophageal and cloacal swabs from a juvenile foraging aggregation of green turtles in Guinea-Bissau, we identified their main food item, a red alga belonging to the Rhodymeniophycidae subclass (representing 35.1±27.2% of “amplicon sequence variants”, ASVs). Moreover, targeting the 16S rRNA region allowed to characterize the microbiota associated with the gastrointestinal tract of the same individuals and from their diet items, leading to the finding that the most abundant bacterial phyla across the gastrointestinal sections were Proteobacteria (68.1±13.9% ASVs), Bacteroidetes (15.1±10.1% ASVs) and Firmicutes (14.7±21.7% ASVs). Additionally, we found presence of red algae bacterial indicator ASVs in cloacal compartments, along with ubiquitous bacterial ASVs present in both cloacal and red algae samples, corroborating that green turtles fed on these food items, and proving the contribution of microbes associated with red algae to the turtles digestive microbiome. We conclude that metabarcoding of esophageal swabs is useful for understanding the feeding behaviour of green sea turtles, while cloacal swabs describe better their gastrointestinal microbiota and its relationship with the turtles diet. 


16S rRNA; 18S rRNA; Chelonia mydas; cloaca; eDNA; esophagus; Guinea-Bissau; hatchlings; macrophytes; microbiota