3.1 | Summary of the Sable Island Horse Microbiome
We used a 16S amplicon sequencing approach to characterize the bacterial microbiome of faecal samples collected from 86 adult females of the Sable Island feral horse population. Sequencing resulted in an average of 51,480 quality assembled reads per sample (rarefied to 34,280 reads for all analyses other than those which used centred-log ratio transformed count tables). A total of 3,767 ASVs were detected in the population, although the average horse hosted 817 ± 11 SE ASVs, and only 2 ASVs were observed in all 86 horses.
The average Sable Island horse microbiome was comprised of Ruminococcaceae (15% ± 4% SD mean relative abundance), Lachnospiraceae (13% ± 3%), Prevotellaceae (10% ± 2%), Spirochaetaceae (9% ± 3%), Fibrobacteriaceae (9% ± 4%), Rikenellaceae (8% ± 3%), and three Bacteroidales families (p-251-o5: 9% ± 4%, F082: 3% ± 2%, RF16: 2% ± 1%). An additional 56 families comprised 13% ± 3% of rarefied reads, while the remaining 9% ± 2% of sequences could not be assigned to family; almost half of these unassigned reads were identified as members of the order WCHB1-41 within the newly described class, Kiritimatiellae (Figure S2, Supporting information). Alpha diversity (ASV richness) decreased by 45 ± 12 SE with every 1 standard deviation increase in longitude (p < 0.01). Horses with access to sandwort also had 137 ± 35 SE fewer ASVs than those without access to sandwort (p < 0.01), while mares without foals had 52 ± 20 SE fewer ASVs than mares with foals (p = 0.01; Figure 3). The full model averaging output can be found in Table S1 of the Supporting information.