Abstract
The Sealcentre Pieterburen, the Netherlands, rehabilitates stranded harbour (Phoca vitulina) and grey seals (Halichoerus grypus). Most of the seals stranded on the Dutch coast are orphaned pups or juvenile seals with parasitic pneumonia and are admitted in the Sealcentre with critical health status. Some of the seals receive antibiotic (AB) therapy during rehabilitation to treat bacterial infections, like infected wounds, umbilical cord infections and pneumonia. Rehabilitation and treatment may affect the gut microbiome of the seals.1,2 Therefore, we investigated the microbiome of the seals before and during rehabilitation using 16S amplicon sequencing.
During summer 2015 and winter 2015–2016, rectal swabs were collected from 200 harbour seals. The samples were collected at admission, during rehabilitation (days 8 and 15) and before release. In case the seal received AB treatment, samples were taken before and one day after finalizing treatment. From all swabs collected, DNA was isolated and amplicon sequencing was performed using Illumina Miseq 2x300 bp on 460 bp of the 16S V3–V4 region. Reads were analyzed using Mothur. Alpha and beta diversity were determined using Shannon and Unifrac, respectively. Statistical analyses were performed using Wilcoxon signed rank. Random Forest analysis of AB microbiomes was performed using the Bioconductor random Forest package.4,6-10
The microbiome of harbor seals at the rehabilitation center is primarily composed of species of Escherichia, Fusobacterium, Bacteroides, Psychrobacter, Anaerobiospirillum, Clostridium and a novel species of Campylobacter. We observed differences in microbiome between the sampled time points which may be a consequence of maturation of the seals. Our results indicate that AB treatment has a severe but short-lived effect on both alpha and beta diversity and that the seal microbiome returns to untreated within approximately four days. Interestingly, animals with or without an antimicrobial treatment have a similar microbiome at release.
The microbiomes of AB treated and non-treated harbour seals are indistinguishable at release. The effect of AB treatment on the seal gut microbiome is extensive, however it is short-term and appears to restore within few days. Further studies are needed to compare the microbiome of rehabilitated seals to those of free-ranging wild seals.
Acknowledgements
The authors wish to thank the staff and volunteers of the Sealcentre Pieterburen that helped with the sample collection and Erwin Raangs for his help in generating the 16S data.
* Presenting author
Literature Cited
1. Nelson TM, Rogers TL, Carlini AR, Brown MV. 2013. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ Microbiol. 15:1132–1146.
2. Stoddard RA, Atwill ER, Conrada PA, Byrne BA, Spencer J, Lawrence J, McCowanc B, Gulland FMD. 2009. The effect of rehabilitation of northern elephant seals (Mirounga angustirostris) on antimicrobial resistance of commensal Escherichia coli. Vet Microbiol. 133(3):264–271.