Fecal Microbiota Characterization of Seychelles Giant Tortoises (Aldabrachelys gigantea) Living in Both Wild and Controlled Environments

A microbiome is defined as a complex collection of microorganisms and their genetic material. Studies regarding gut microbiomes of different animals have provided ecological and evolutionary information showing a strong link between health and disease. Very few studies have compared the gut microbiota of animals housed under controlled conditions and those in wild habitats. Little research has been performed on the reptile gut microbiota, and what studies do exist are mainly focused on carnivorous reptiles. The aim of this study was first to describe the overall microbiota structure of Aldabra giant tortoises (Aldabrachelys gigantea) and, second, to compare the microbiota of tortoises living under natural conditions and tortoises living in controlled environments, such as zoological and botanical parks, in Italy and in the Seychelles. Seventeen fecal samples were collected from giant tortoises located on Curieuse Island (CI, n = 8), at the Botanical Garden (BG, n = 3) in Mahé (Seychelles Islands) and at Parco Natura Viva–Garda Zoological Park (PNV, n = 6) in Verona (Italy). The V3-V4 region of the 16S rRNA gene was amplified in order to characterize the gut microbiota profile. Overall, the major phyla identified were Bacteroidetes 42%, Firmicutes 32%, and Spirochaetes 9%. A higher microbial diversity (alpha indices) was observed for the BG samples as compared to the PNV samples (Shannon: 5.39 vs. 4.43; InvSimpson: 80.7 vs. 25; Chao1: 584 vs. 377 p < 0.05). The results in the present study showed a significant difference in beta diversity between the samples from CI, BG, and PNV (p = 0.001), suggesting a different bacterial fecal profile of giant tortoises at the different habitats. This study provided novel insights into the effects of different environmental conditions on the gut microbial communities of giant tortoises. In particular, differences were reported regarding the bacterial gut community structure between tortoises in natural and in controlled environments. These results could help to improve the management of giant tortoises under human care, thus enhancing ex-situ conservation efforts far from the species geographic range.