Abstract
The human gut microbiome has been extensively studied, revealing its susceptibility to various factors such as genetics, diet, and environment. The gut microbiome influences and is impacted by the host’s health status.1-4 While there is considerable knowledge about the gut microbiomes of livestock,5 the microbiomes of wild animals remain comparatively underexplored due to challenges in sample acquisition.6 Exploring the microbiomes of wild animals undergoing rehabilitation offers a viable alternative to studying those in their natural, free-ranging habitats.
The Sealcentre Pieterburen, in the Netherlands, rehabilitates an average of 250 grey seals (Halichoerus grypus) and harbor seals (Phoca vitulina) per year. Animal rehabilitation centres provide a unique opportunity to study the microbiome of wild animals because subjects will be handled for their treatment and can therefore be sampled longitudinally. However, being held in temporal captivity for rehabilitation might influence the animals’ microbiome because of a less varied and suboptimal diet, possible medical treatment, and exposure to a different environment. The current study aimed to describe the gut microbiome of stranded harbor seals while in rehabilitation.
For this, we investigated the distal gut microbiome of two harbor seal cohorts, 50 pups (0–30 days old at arrival) and 23 weaners (more than 60 days old at arrival), while they were kept in rehabilitation at the Sealcentre Pieterburen. Fecal samples were collected using rectal swabs from all seals at arrival, during rehabilitation (on days 8 and 15), and before release (only seals that did not receive antimicrobial treatment were included in the study). The alpha diversity (richness and Shannon index) and the beta diversity were calculated at admission, and the other sampling points for pups and weaners separately, and the association with several variables like age and sex was determined over time or at admission and release. Moreover, differences in the abundance of bacterial species at admission and release were determined.
Our results showed that the gut microbiome of young harbor seals stranded in the Netherlands comprises Proteobacteria, Firmicutes, Bacteroidota, Fusobacteriota, Campylobacterota, and Actinobacteriota. In addition, we observed that during rehabilitation, there was an increase in the relative abundance of some of the Campylobacterota spp. and Actinobacteriota spp. The alpha diversity of the pups’ microbiome increased significantly during their rehabilitation, while there were no significant changes in alpha diversity over time for weaners. We hypothesize that aging is the main reason for the observed changes in the pups’ microbiome and less due to feeding or time in rehabilitation, as we did not see similar trends in rehabilitated weaner seals. At release, the sex of a seal pup was significantly associated with the microbiome’s alpha and beta diversity. For weaners, variation in the microbiome composition (beta diversity) at release was partly explained by the sex and the age of the seal. We mainly observed variables known to change the gut microbiome composition (e.g., age and sex) and concluded that rehabilitation had only minor effects on the gut microbiome of seal pups and seal weaners.
Acknowledgements
We thank the staff and volunteers of the Sealcentre Pieterburen who helped with the sample collection. The authors would also like to thank Maarten van Putten (University Medical Center Groningen, Groningen, The Netherlands) for his great help with the DNA extraction and 16S rRNA sequencing and John O´Connor for his help with the figures.
*Presenting author
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