Fig 1.
Oral and cloacal samples collected through rehabilitation.
Swabs collected for each individual turtle (y axis) during rehabilitation. Each color denotes the timepoint in rehab. Convalescence (TP4a) is when the turtle is considered clinically healthy. Prerelease (TP4b) was only collected on turtles that remained in the hospital >30 days after TP4a was collected. Whether antibiotics were received or not is indicated on the y axis. * indicates that the turtle died after that sample was collected.
Fig 2.
Turtle microbial communities at intake.
Hierarchical clustering of intake samples is shown as the dendrogram on the left, with the tips each representing a sample. On the right are the corresponding stacked bar plots representing relative abundance of community composition at the family level (top 30 families). Colored bars at the center specify body site (left bar) and survival (right bar) corresponding to each sample.
Fig 3.
Random forest model predictions for survival.
The 10 most significant ASVs at intake that differ between turtles that survived and those that died for oral samples (A) and cloacal samples (B). Taxonomy information for these ASVs is provided in Table 1.
Table 1.
Taxonomy of the top 10 ASVs predicting survival.
Survival was predicted by random forest modelling for both oral and cloacal samples at intake.
Fig 4.
Shannon diversity index of turtles through rehabilitation.
Oral samples (left) and cloacal samples (right) at each timepoint during rehabilitation. Different letters above boxplots indicate significant differences in means of Shannon diversity (p < 0.05; S2 Table).
Fig 5.
Microbial communities across all timepoints.
Principal coordinate analysis (PCoA) plots of oral samples (A) and cloacal samples (B) based on Bray-Curtis distance. Color indicates timepoint in rehabilitation from intake to convalescence (TP4a)/pre-release (TP4b).
Fig 6.
Microbial communities during rehabilitation to convalescence.
Principal coordinate analysis (PCoA) plots of oral samples (A) and cloacal samples (B) based on Bray-Curtis distance. Color indicates number of days in rehabilitation. Shape indicates whether a turtle was not on antibiotics (circle, N) or on antibiotics (triangle, Y) during rehabilitation.
Fig 7.
Microbial communities during rehabilitation and antibiotics.
Principal coordinate analysis (PCoA) plots of oral (A) and cloacal (B) samples based on Bray-Curtis distance during rehabilitation (TP2). Colors specify the type of antibiotic the turtle was on during hospitalization.
Fig 8.
ASVs of cloacal samples at timepoint 2.
Relative abundance of ASVs (colored by family) that significantly contribute to the differences between antibiotic type of cloacal samples while in rehab.
Fig 9.
Turtle microbial communities at convalescence.
Hierarchical clustering of convalescent samples (timepoint 4a) is shown as the dendrogram on the left, with the tips each representing a sample. On the right are the corresponding stacked bar plots representing relative abundance of community composition at the family level (top 30 families). Colored bars at the center specify body site (left bar) and antibiotic type (right bar) corresponding to each sample.