DOI: 10.5061/dryad.qv9s4mwj5
title: Effects of exogenous elevation of corticosterone on immunity and the skin microbiome of Eastern Newts (Notophthalmus viridescens): Data & R scripts

description: The amphibian chytrid fungus, Batrachochytrium salamandrivorans (Bsal)
 threatens salamander biodiversity. The factors underlying Bsal
 susceptibility may include glucocorticoid hormones (GCs). The effects of
 GCs on immunity and disease susceptibility are well studied in mammals,
 but less is known in other groups, including salamanders. We used
 Notophthalmus viridescens (Eastern Newts) to test the hypothesis that GCs
 modulate salamander immunity. We first determined the dose required to
 elevate corticosterone (CORT; primary GC in amphibians) to physiologically
 relevant levels. We then measured immunity (neutrophil-lymphocyte ratios,
 plasma bacterial killing ability [BKA], skin microbiome, splenocytes,
 melanomacrophage centers [MMCs])  and overall health in newts
 following treatment with CORT or an oil vehicle control. Treatments were
 repeated for a short (2 treatments over 5 days) or long (18 treatments
 over 26 days) time period. Contrary to our predictions, most immune and
 health parameters were similar for CORT and oil-treated newts.
 Surprisingly, differences in BKA, skin microbiome, and MMCs were observed
 between newts subjected to short and long-term treatments, regardless of
 treatment type (CORT, oil vehicle). Taken together, CORT does not appear
 to be a major factor contributing to immunity in Eastern Newts, although
 more studies examining additional immune factors are necessary.
description: The data and files pertain to Experiments 1 through 3 of the
 manuscript and are organized into 3 file lists: 1.
 Physiological & Immunological Data (Experiments 1 through
 3) The datasets were generated from the quantification
 of corticosterone in plasma samples (Experiments 1 through 3), and various
 immunological measures from blood and tissue samples (Experiment 3).  Bd
 data (initial and the change in Bd load) were generated from extracted DNA
 from skin swabs collected from captive salamanders in Experiment 3. qPCR
 analysis was used to quantify Bd infection loads (genomic equivalents, GE)
 initial and the change in Bd load. To complement these data, an additional
 data file was generated from the quantification of corticosterone and
 cortisol in plasma samples collected from salamanders not used in
 Experiments 1, 2, or 3. 2. Skin Microbiome (Experiment
 3) The dataset was generated from extracted DNA from
 skin swabs collected from captive salamanders in Experiment 3.
 Specifically, sequenced DNA was processed in QIIME2 v2021.8, then used for
 analysis of alpha and beta diversity metrics in R (version 4.0.2) and IBM
 SPSS Statistics software version 27.  3. Final Bd load
 (Experiment 3) The dataset was generated from extracted
 DNA from skin swabs collected from captive salamanders in Experiment 3.
 qPCR analysis was used to quantify Bd infection loads (genomic
 equivalents, GE) at the end of the experimental period. Many salamanders
 cleared Bd infections (final infection load = 0 GE) resulting in
 zero-inflated data. To address this, these data were analyzed in R
 (version 4.2.2) using zero-inflated gamma regression models.
description: Qiime2 v2021.8, R version 4.0.2 and 4.2.2 (https://www.R-project.org) and IBM SPSS Statistics software version 27 (IBM, Corp, Armonk, New York, USA).