10.5061/DRYAD.JDFN2Z37N
Stoffel, Martin Adam
0000-0003-4030-3543
University of Edinburgh
Acevedo-Whitehouse, Karina
Autonomous University of Queretaro
Morales-Durán, Nami
Autonomous University of Queretaro
Grosser, Stefanie
Ludwig Maximilian University of Munich
Chakarov, Nayden
Bielefeld University
Krüger, Oliver
Bielefeld University
Nichols, Hazel J.
Bielefeld University
Elorriaga-Verplancken, Fernando R.
Instituto Politécnico Nacional
Hoffman, Joseph I.
Bielefeld University
Early sexual dimorphism in the developing gut microbiome of northern
elephant seals
Dryad
dataset
2020
Microbial Biology
Life History Evolution
Deutsche Forschungsgemeinschaft
https://ror.org/018mejw64
HO 5122/5-1
Liverpool John Moores University
https://ror.org/04zfme737
PhD studentship
Genetics Society
https://ror.org/03d21k332
Heredity Fieldwork Grant
Autonomous University of Queretaro
https://ror.org/00v8fdc16
142908
Bielefeld University
https://ror.org/02hpadn98
Department of Animal Behaviour
2020-03-06T00:00:00Z
2020-03-06T00:00:00Z
en
https://doi.org/10.1111/mec.15385
2719395 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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 .
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.