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

Abstract

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 were 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 was 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 toward the end of the rehabilitation period, prior to the release of the pups in the wild. IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups ( Monachus monachus ), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal’s conservation practices through its microbiome.