Despite an increasing appreciation of the importance of host-microbe interactions in ecological and evolutionary processes, the factors shaping microbial communities in wild populations remain poorly understood. We therefore exploited a natural experiment provided by two adjacent Antarctic fur seal (Arctocephalus gazella) colonies of high and low social density and combined 16S rRNA metabarcoding with microsatellite profiling of mother-offspring pairs to investigate environmental and genetic influences on skin microbial communities. Seal-associated bacterial communities differed profoundly between the two colonies, despite the host populations themselves being genetically undifferentiated. Consistent with the hypothesis that social stress depresses bacterial diversity, we found that microbial alpha diversity was significantly lower in the high-density colony. Seals from one of the colonies that contained a stream also carried a subset of freshwater-associated bacteria, indicative of an influence of the physical environment. Furthermore, mothers and their offspring shared similar microbial communities, in support of the notion that microbes may facilitate mother-offspring recognition. Finally, a significant negative association was found between bacterial diversity and heterozygosity, a measure of host genetic quality. Our study thus uncovers a complex interplay between environmental and host genetic effects, while also providing empirical support for the leash model of host control, which posits that bacterial communities are driven not only by bottom-up species interactions, but also by top-down host regulation. Taken together, our findings have broad implications for understanding host-microbe interactions as well as prokaryotic diversity in general.
AFSmicrobiome_SI_OTUprocessingPipelineScripts_DatasetS1
Collection of scripts for the OTU processing pipeline
AFSmicrobiome_SI_OTUprocessingPipelineStatistics_DatasetS2
Summary statistics for the OTU processing pipeline
AFSmicrobiome_SI_Rmarkdown_DatasetS3_html
R Markdown file in .html format containing all the R code used for the analyses of the Antarctic fur seal microbiome
AFSmicrobiome_SI_Rmarkdown_DatasetS3_Final_revision.html
AFSmicrobiome_SI_Rmarkdown_DatasetS3_Rmd
R Markdown file in Rmd format containing all the R code used for the analyses of the Antarctic fur seal microbiome
AFSmicrobiome_SI_Rmarkdown_DatasetS3_Final_revision.Rmd
AFSmicrobiome_SI_SequencingStatsFile_Rinput_DatasetS4
R markdown input file containing sequencing statistics
AFSmicrobiome_SI_MicrosatelliteGenotypes50_P22removed_colnames_Rinput_DatasetS5
R markdown input file containing genotypes at 50 microsatellite loci for 95 fur seal individuals (pup P22 was removed due to large number of missing genotypes). Contains table header with loci names.
AFSmicrobiome_SI_MicrosatelliteGenotypes50_P22removed_colnames_Rinput_DatasetS5.1
R markdown input file containing genotypes at 50 microsatellite loci for 95 fur seal individuals (pup P22 was removed due to large number of missing genotypes). Header line removed.
AFSmicrobiome_SI_relatednessWang50Msats_Rinput_DatasetS6
R markdown input file containing pairwise relatedness estimates
AFSmicrobiome_SI_otuRDPclassification_Rinput_DatasetS7
R markdown input file containing the OTU RDP classifications obtained with the USEARCH sintax command
AFSmicrobiome_SI_otuRDPclassification_phyloseqIn_Rinput_DatasetS8
R markdown input file containing the OTU RDP classifications prepared for phyloseq input
AFSmicrobiome_SI_OTUtable_final_trimmed_allSamples_Rinput_DatasetS9
R markdown input file containing the trimmed OTU table for all samples
AFSmicrobiome_SI_OTUtable_final_trimmed_raref10000_Rinput_DatasetS10
R markdown input file containing the trimmed and rarefied OTU table for 94 samples
AFSmicrobiome_SI_Metadata_allSamples_Rinput_DatasetS11
R markdown input file containing metadata for all samples
AFSmicrobiome_SI_alphaDiversity_Rinput_DatasetS12
R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated from the non-normalised and rarefied OTU tables in USEARCH for all sampled individuals
AFSmicrobiome_SI_alphaDiversity_MainPhyla_Rinput_DatasetS13
R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated for OTUs belonging to the main phyla
AFSmicrobiome_SI_outgroup_pynastAligned_filtered_Rinput_DatasetS14
R markdown input file containing a phylogenetic tree needed for UniFrac distance calculations (created with FastTree in QIIME).
AFSmicrobiome_SI_PuppingLocations_Rinput_DatasetS15
R markdown input file containing pupping locations at SSB
AFSmicrobiome_SI_alphaDiversityMultiRaref_Rinput_DatasetS16
R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated for 100 rarefied OTU tables in USEARCH for all sampled individuals
AFSmicrobiome_SI_NSTIvalues_filteredTrimmed_rarefied_Rinput_DatasetS17
R markdown input file containing NSTI values calculated from PICRUSt
AFSmicrobiome_SI_Categorize_by_FunctionL3_FilteredTrimmed_rarefied_Rinput_DatasetS18
R markdown input file containing read counts for KEGG functional predictions calculated with PICRUSt