Characterisation of the microbiome and resistome in the loggerhead sea turtle (Caretta caretta) in the Mediterranean basin

Loggerhead sea turtles (Caretta caretta) are considered sentinel species for investigating the anthropogenic impacts on the marine environment within a One Health framework. Longitudinal sampling of rehabilitating individuals at C.Re.Ta.M. (National Reference Center for the welfare of marine turtles) provides an opportunity to assess temporal changes in gut microbial communities.

Fecal samples were collected from 20 Caretta caretta individuals at admission (T0) and after one month of rehabilitation (T1) to investigate gut microbiome during the rehabilitation. Genomic DNA was used to amplify and sequence the V3–V4 region of the 16S rRNA gene. In addition, the resistome was assessed by PCR at admission.

Overall, microbial community structure remained stable over time, with no consistent cohort-wide shift. However, genus-level analyses revealed individual-specific trajectories driven by changes in the relative abundance of dominant taxa. Specifically, age class specific patterns were observe. Juveniles showed an increase in Clostridium_sensu_stricto_1 (0.47 ± 0.98; 6.02 ± 9.41) and a decrease in Fusobacterium (3.37 ± 3.92; 0.80 ± 1.02) from T0 to T1. Conversely, subadults showed a decrease in Bacteroides (8.17 ± 4.78; 4.35 ± 2.89) and Clostridia_vadinBB60_group (8.78 ± 7.07; 2.46 ± 2.61). Microbiome dynamics differed between age classes, and curved carapace length (CCL) was significantly associated with both the direction and extent of compositional changes (p = 0.044), suggesting size-dependent microbial dynamics. Although no linear association between microbiome and resistome emerged across the entire cohort, an exploratory extreme-tercile comparison indicated higher within-host turnover in individuals with higher resistome levels (p = 0.0428). Among the antibiotic classes analyzed, the highest resistance levels were observed against tetracyclines (80%) and β-lactams (75%).

These findings indicate that the gut microbioma of Caretta caretta remains stable during rehabilitation while exhibiting size-dependent compositional changes. Integrating microbiome and resistome analyses may support health assessment and environmental surveillance.