Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene

Abstract

The intestinal tract houses one of the richest and most complex microbial populations on the planet, and plays a critical role in health and a wide range of diseases. Limited studies using new sequencing technologies in horses are available. The objective of this study was to characterize the fecal microbiome of healthy horses and to compare the fecal microbiome of healthy horses to that of horses with undifferentiated colitis. A total of 195,748 sequences obtained from 6 healthy horses and 10 horses affected by undifferentiated colitis were analyzed. Firmicutes predominated (68%) among healthy horses followed by Bacteroidetes (14%) and Proteobacteria (10%). In contrast, Bacteroidetes (40%) was the most abundant phylum among horses with colitis, followed by Firmicutes (30%) and Proteobacteria (18%). Healthy horses had a significantly higher relative abundance of Actinobacteria and Spirochaetes while horses with colitis had significantly more Fusobacteria. Members of the Clostridia class were more abundant in healthy horses. Members of the Lachnospiraceae family were the most frequently shared among healthy individuals. The species richness reported here indicates the complexity of the equine intestinal microbiome. The predominance of Clostridia demonstrates the importance of this group of bacteria in healthy horses. The marked differences in the microbiome between healthy horses and horses with colitis indicate that colitis may be a disease of gut dysbiosis, rather than one that occurs simply through overgrowth of an individual pathogen.

Figure 1. Rarefaction curves.

Rarefaction curves comparing the number of reads with the number of phylotypes found in the DNA from feces of healthy horses (Healthy 1–6) and horses affected by colitis (Colitis 1–10).

Figure 2. Fecal bacterial population.

Overall percentages of bacterial populations at the phylum level (Fig. A) and intra-phylum variation (Fig. B) present in feces of healthy horses and horses affected by colitis.

Figure 3. Phylogenetic trees – OTUs approach.

Phylogenetic tree demonstrating the similarity of OTUs found in feces of healthy horses (Healthy 1–6) and horses affected by colitis (Colitis 1–10). Results were obtained using the Yue & Clayton measure (A) and the Jaccard index (B).

Figure 4. PCoA and NMDS.

PCoA (Fig. A and B) and MNDS (Fig. C and D) showing the representation of vectorial analysis of sequences found in feces of healthy horses (blue dots) and horses affected by colitis (red dots). Results were obtained using the Yue & Clayton measure (Fig. A and C), the Jaccard index (Fig. B and D).

Figure 5. Phylogenetic trees – Phylotypes approach.

Phylogenetic tree demonstrating the similarity of Phylotypes found in feces of healthy horses (Healthy 1–6) and horses affected by colitis (Colitis 1–10). Results were obtained using the Yue & Clayton measure (A) and the Jaccard index (B).