One of the most endangered vertebrates in Europe, the black olm subspecies (Proteus anguinus parkelj Sket & Arntzen 1994), is endemic to only a few square kilometers large area of the karst region of Bela krajina in Southeast Slovenia. Kostanjšek et al. (2019) discovered that the normal bacterial cutaneous microbiota of the black olm specimen was almost entirely replaced by enterobacteria and aeromonads, which could indicate fecal microbiota pollution of its natural habitat. The thesis aimed to analyze the composition of the skin microbiota on a larger sample of the black olm subspecies. We analyzed the amplicon sequencing data of cutaneous bacteria, fungi, archaea, and eukaryotes in four specimens of the black olm subspecies and nine white olm specimens from the phylogenetic lineage of Ljubljanica river and Dolenjska lineage. Since the Aeromonas genus was present in only one black olm specimen and in very low relative abundance (< 1%), we conclude that the prevalence of fecal bacteria in the skin microbiota of the black specimen of preliminary research was an isolated case of dysbiosis. While beta diversity statistical tests (PERMANOVA, ANOSIM) showed that the host's phylogenetic lineage could explain a part of bacterial skin community variance, the same was not true for other investigated taxonomic groups. Our analysis is the first black olm skin microbiota study to examine the diversity of fungi, archaea, and eukaryotes. Further added value of our work is a pipeline for sequencing data analysis using Qiime2, written in Python in the form of Jupyter Notebooks.
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