Data and code accompanying the paper Filek et al. 2024 "Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities" Microbial Ecology
Also relevant for preprint: Filek et al. 2024 "Bacterial and fungal assemblages of the gut and carapace of loggerhead sea turtles (Caretta caretta)"
Supplementary materials, data, and code for data analyses and visualizations for Turtle BIOME project manuscript "Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities" by Filek K, Vuković BB, Žižek M, Kanjer L, Trotta A, Di Bello A, Corrente M, Bosak S (2024) published in Microbial Ecology
doi: https://doi.org/10.1007/s00248-024-02388-x
Sequencing data with non-biological sequences removed is available at EMBL ENA at accessions PRJEB62752 and PRJEB68298 for 16S rRNA gene and PRJEB62762 for ITS2 region sequences. Epizoic samples’ sequencing data obtained from Kanjer et al. (2022) and used in this study can be found at ENA under accession PRJEB51458. In the manuscript there is a wrong accession number listed: PRJEB68216 instead of the correct one PRJEB68298.
The repo contains supplementary materials for the manuscript as well as data and code/scripts used for analyses and visualizations (in Qiime 2 and R). The code and all of the files (including classifiers and denoising files that were too large for GitHub) can be found on ZENODO as well under doi:10.5281/zenodo.8054926.
Research on microbial communities associated with wild animals provides a valuable reservoir of knowledge that could be used for enhancing their rehabilitation and conservation. The loggerhead sea turtle (Caretta caretta) is a globally distributed species with its Mediterranean population categorized as least concern according to the IUCN Red List of Threatened Species as a result of robust conservation efforts. In our study, we aimed to further understand their biology in relation to their associated microorganisms. We investigated epi- and endozoic bacterial and endozoic fungal communities of cloaca, oral mucosa, carapace biofilm. Samples obtained from 18 juvenile, subadult, and adult turtles as well as 8 respective enclosures, over a 3-year period, were analysed by amplicon sequencing of 16S rRNA gene and ITS2 region of nuclear ribosomal gene. Our results reveal a trend of decreasing diversity of distal gut bacterial communities with the age of turtles. Notably, Tenacibaculum species show higher relative abundance in juveniles than in adults. Differential abundances of taxa identified as Tenacibaculum, Moraxellaceae*, *Cardiobacteriaceae, and Campylobacter were observed in both cloacal and oral samples in addition to having distinct microbial compositions with Halioglobus taxa present only in oral samples. Fungal communities in loggerheads’ cloaca were diverse and varied significantly among individuals, differing from those of tank water. Our findings expand the known microbial diversity repertoire of loggerhead turtles, highlighting interesting taxa specific to individual body sites. This study provides a comprehensive view of the loggerhead sea turtle bacterial microbiota and marks the first report of distal gut fungal communities that contributes to establishing a baseline understanding of loggerhead sea turtle holobiont.