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Early sexual dimorphism in the developing gut microbiome of northern elephant seals

Citation

Stoffel, Martin Adam et al. (2020), Early sexual dimorphism in the developing gut microbiome of northern elephant seals, Dryad, Dataset, https://doi.org/10.5061/dryad.jdfn2z37n

Abstract

The gut microbiome is an integral part of a species’ ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups stay ashore without feeding. We found substantial sex-differences in the early-life gut microbiome, even though males and females could not yet be distinguished morphologically. Sex and age both explained around 15% of the variation in gut microbial beta diversity, while microbial communities sampled from the same individual showed high levels of similarity across time, explaining another 40% of the variation. Only a small proportion of the variation in beta diversity was explained by health status, assessed by full blood counts, but clinically healthy individuals had a greater microbial alpha diversity than their clinically abnormal peers. Across the post-weaning period, the northern elephant seal gut microbiome was highly dynamic. We found evidence for several colonisation and extinction events as well as a decline in Bacteroides and an increase in Prevotella, a pattern that has previously been associated with the transition from nursing to solid food. Lastly, we show that genetic relatedness was correlated with gut microbiome similarity in males but not females, again reflecting early sex-differences. Our study represents a naturally diet-controlled and longitudinal investigation of how intrinsic factors shape the early gut microbiome in a species with extreme sex differences in morphology and life history.

Methods

Here, we studied the gut microbiome of northern elephant seals across the post-weaning period. We sampled rectal swabs to quantify the microbiome communities using 16S rRNA sequencing (please have a look at our Molecular Ecology paper for details). The processed 16S raw reads were assembled into amplicon sequence variants (ASVs). In this repository, we store these ASV tables alongside other sampling data (Sex, age, clinical health status) in phyloseq objects (ps0 and ps3). These are used in the R-scripts and make it possible for the interested scientist to reproduce our analyses and figures. The raw reads are stored in the European Nucleotide Archive (ENA) under study accession PRJEB36555 and we also provide the relevant scripts used for bioinformatics processing. More information can be found in README.txt . 

Usage Notes

The full repository can also be found at https://github.com/mastoffel/nes_microbiome . The README file and comments in the R-scripts contain all relevant information to reproduce the analyses in the paper.

Funding

Deutsche Forschungsgemeinschaft, Award: HO 5122/5-1

Liverpool John Moores University, Award: PhD studentship

Genetics Society, Award: Heredity Fieldwork Grant

Universidad Autónoma de Querétaro, Award: 142908

Universität Bielefeld, Award: Department of Animal Behaviour