Data and code accompanying the preprint Filek et al. 2023 "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 "Bacterial and fungal assemblages of the gut and carapace of loggerhead sea turtles (Caretta caretta)" by Filek K, Vuković BB, Žižek M, Kanjer L, Trotta A, Di Bello A, Corrente M, Bosak S (2023 preprint)

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.

Manuscript abstract

Background

The research on microbial communities of marine megafauna species represents a valuable source of knowledge that could be used for species conservation programs. Loggerhead sea turtles are marine flagship species with a currently thriving population in the Mediterranean Sea due to strong conservation efforts. In our study we aimed to further understand their biology in relation to their associated microorganisms. We investigated bacterial and fungal community structure of cloacal, oral swabs and carapace biofilm samples obtained from 18 juvenile, subadult and adult turtles as well as 8 respective enclosures, during a period of 3 years, by amplicon sequencing of 16S rRNA gene and ITS2 region of nuclear ribosomal gene.

Results

Our results reveal a trend of decreasing diversity of distal gut bacterial communities with the age of turtles. Notably, Tenacibaculum genus shows higher relative abundance in juveniles than in adults. Differential abundance of genera like Tenacibaculum, Moraxellaceae, Cardiobacteriaceae, and Campylobacter was observed in both cloacal and oral samples in addition to having distinct microbial compositions such as Halioglobus genera in oral samples. Fungal communities in loggerheads' cloaca were diverse and varied significantly among individuals, differing from those of tank water. However, we could not identify discernible patterns related to age, sex, or clinical status due to study limitations.

Conclusion

This study provides a comprehensive view of the loggerhead sea turtle bacterial microbiota and marks the first report of distal gut fungal communities studied via amplicon sequencing. Our findings expand the known microbial diversity repertoire of loggerheads, highlighting interesting taxa specific to individual body sites. This contributes to establishing a baseline understanding of the loggerhead bacterial and fungal microbiome.