Table 1.
Diets of the 21 mammals sampled from Shubenacadie Wildlife Park.
Presented is the animal common name, the daily diet, and the speciality food stuffs required to meet dietary requirements.
Table 2.
List of oligonucleotides used for 16S rDNA amplification.
Table 3.
Summary of profiled species and 16S rRNA sequencing details.
Presented is the common animal name, the scientific animal name, the total number of sequences, the number of OTUs per sample, number of unique OTU’s per sample, and the number of remaining sequences after stitching and quality filtering.
Fig 1.
A 3-dimensional principal component analysis plot of the weighted UniFrac beta-diversity for 21 profiled species.
The mammals belonging to a taxonomic order, indicated with bold font, are encircled to show the order’s space on the plot. The zoomed-in black box depicts a section of the graph rotated in 3D space to show the slight, but present separation between the two taxonomic orders Rodentia and Artiodactyla.
Fig 2.
Microbiome analysis of all sequenced mammals shows great bacterial diversity between samples with some overlap in taxonomic orders.
Taxonomic relative abundances of 16S rRNA data collapsed to sequences of indicated bacterial orders were identified from fecal samples of 21 mammals. All sequences under 0.01% abundance were clustered into the Other category.
Table 4.
Taxonomic assignments for replicate sequencing of the Arctic wolf, coyote, beaver and porcupine.
The 16 most abundant taxonomic assignments are shown for each mammal. All taxonomic assignments are average percent abundance. Standard deviation (StDev) is shown in brackets of each calculation.
Table 5.
Summary of profiled species and sequences from shotgun metagenomic sequencing.
Presented is the number of reads in total, after stitching with PEAR, and after screening to remove human and PhiX reads.
Fig 3.
Metagenomic taxonomic summary of select Rodentia (porcupine and beaver) and Carnivora mammals (coyote and Arctic wolf).
Each dot represents a node in the phylogenetic tree, whose size indicates the prevalence of representatives of that node in the sample. Colours are used to group bacteria into orders, indicated in each panel. Species identified with high abundance are labelled (A through W, and A through K in Panels A and B, respectively), while some with low abundance are not. Both the Rodentia mammals (A) and the Carnivora mammals (B) are represented.
Table 6.
The 13 most abundant gene pathways identified using HUMAnN1 (metagenomic sequencing) in the Arctic wolf, coyote, porcupine, and beaver.
Units are relative abundance of gene pathway sequences expressed as a percentage average. Standard deviation (StDev) is shown in brackets.
Fig 4.
Summary functional heat-map of select enzymes in the starch and sucrose metabolism KEGG pathway.
Functional assignment of the metagenomic sequencing was done using HUMAnN and the KEGG database. Generation of the above heatmap was done using Morpheus (see methods) using only genes in the starch and sucrose metabolism pathway, which has been simplified for clarity. Transport and degradation genes in the starch and sucrose metabolism pathway are labelled with black lines. Rows and columns were clustered using the hierarchal clustering tool in Morpheus, using the one minus Pearson correlation matrix and the average linking method. AR, Arctic wolf replicate; CR, coyote replicate; BR, beaver replicate; PR, porcupine replicate.
Fig 5.
The comparison between the predicted (PICRUSt) and actual (HUMAnN1) mean sequence proportion of genes encoding particular enzymes in selected mammalian microbiomes.
Box plots of predicted (A; PICRUSt) or identified (B; HUMAnN1) mean sequence proportion of genes encoding the indicated enzymes are shown for feces of four indicated mammals. Predicted data were obtained via PICRUSt analysis from 16S rRNA sequencing, in triplicate. Mean sequence proportions were obtained via HUMAnN1 analysis from shotgun metagenomic sequencing, in triplicate. Statistical significance was determined using ANOVA with Benjamini-Hochberg FDR correction for multiple tests.
Fig 6.
HUMAnN2 analysis gene family abundance and these gene families contributing taxa.
Whisker plots for the relative abundance (measured in reads mapped per kilobase) were generated from HUMAnN2 functional analysis for endoglucanase (K01179) and beta-glucosidase (K05349). A two-way ANOVA using Holm-Sidak multiple test correction we used to test significance (A, p = 0.0137; B, not significant). The taxonomic breakdown for each gene family was also generated using HUMAnN2 output and presented at the genus level (C).
Table 7.
Average percent abundances of bacterial genus’ contributing beta-glucosidase (K05349) in the Arctic wolf, coyote, beaver and porcupine microbiomes as analyzed by HUMAnN2.
Average percent abundances were obtained by calculating the percentage of each organism in each run (relative abundance divided by total abundance) and then taking the average of these means. Each sample was sequenced in biological triplicate times, except the porcupine which was sequenced in biological quadruplicate.
Table 8.
Average percent abundances of bacterial genus’ contributing to endoglucanase (K01179) in the Arctic Wolf, Coyote, Beaver and Porcupine microbiomes as analyzed by HUMAnN2.
Average percent abundances were obtained by calculating the percentage of each organism in each run (Relative abundance divided by total abundance) and then taking the average of these means. Each sample was sequenced in biological triplicate.