Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation

ABSTRACT The role of animal host-associated microbiomes is becoming more apparent and defined for wild animals, especially for the species under conservation strategies. This study investigated the succession of fecal and skin bacterial microbiota of two rescued female Mediterranean monk seal ( Monachus monachus ) pups for most of their rehabilitation period. Bacterial species richness and diversity was assessed by high-throughput sequencing of nine freshly collected fecal samples and four skin swabs per individual. Both the fecal and skin microbiota highly overlapped in their containing operational taxonomic units (OTUs) and abundance patterns. The fecal microbiota was separated in two distinct periods, and was dominated by OTUs related to the Shigella , Streptococcus , Enterococcus , Lactobacillus and Escherichia genera in the first period, while in the second period the dominating genera were the Clostridium, Blautia, Fusobacterium, Edwardsiella and Bacteroides. The skin microbiota was highly similar between the two individuals in each sampling and were dominated by Psychrobacter-, Elizabethkingia- and Bergeyella -related OTUs. The provided antibiotic treatment along with the provided probiotics and nutritional supplements, resulted in a major turnover of the bacterial microbiota with the potentially detrimental OTUs being eliminated towards the end of the rehabilitation period, prior to the release of the pups in the wild.