Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish

Variation in the composition of skin-associated microbiomes has been attributed to host species, geographic location, and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch, and growth, but not temperature gain while basking, sex, personality, or colour morph. We suggest that the overall increase in the alpha and beta diversity estimates..., Estimation of alpha and beta diversity
All statistical analyses were performed in Rstudio v1.3.1093 (53) with R v3.6.0. We included three alpha diversity estimates. Observed number of ASVs (100% identical ‘amplicon sequence variants’) was used to illustrate the partitioning of ASVs according to sample type and environment. Statistical analysis of richness was based on estimates generated with default settings in the breakaway function (package breakaway v4.6.11). To incorporate an alpha diversity measurement that takes abundance and evenness into account we used Shannon-Weaver diversity index estimated from data subsampled to the smallest sample size (3775 reads per sample) using the diversity function in the vegan package (v2.5-6).
Apart from the subsampling prior to the Shannon index, raw data was used throughout the analyses. However, to explore the contribution of rare ASVs, we conducted a filtering step for comparison with the results based on raw data. To this end, we followed the..., , This README file was generated on 2023-11-13 by Hanna Berggren.

GENERAL INFORMATION

1. Title of Dataset: \"Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish\"

2. Author Information
A. Principal Investigator Contact Information
Name: Anders Forsman
Institution: Linnaeus University
Address: Kalmar, Sweden
Email:

B. Associate or Co-investigator Contact Information
Name: Hanna Berggren
Institution: Linnaeus University
Address: Kalmar, Sweden
Email:

We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (*Cyprinus carpio*) before and after translocation from laboratory conditions to a semi-natural environment. We collected microbiome samples from dorsal and ventral body sites for each individual (*n* = 27) and environment (laboratory versus po...