Early functional and community development of the equine hindgut microbiome in semi-feral- and domestic conventionally managed foals including cases of foal diarrhea
Date
2018
Authors
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Journal ISSN
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Publisher
University of Delaware
Abstract
The early development of the gut microbiome has been proven to be an essential part in maintaining a healthy neonate in both humans and animals. During this time, the foal is more susceptible to gut dysbiosis. As a result, gastrointestinal abnormalities such as foal heat diarrhea can occur. Foal diarrhea is a common non- infectious digestive issue that usually occurs in the foal in their first few weeks of life. Currently, no studies have been conducted analyzing foal diarrhea in non- conventionally managed foals. In the first study conducted, ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were studied for analysis of the early development of their hindgut microbiomes to determine changes as the foals aged as well as the effects of different management techniques. In the second study conducted, seven diarrheic foals and seven age- and domestication management-matched (semi-feral- or domestic conventionally-managed) healthy foals were sampled for analysis of their hindgut microbiome to determine the effects of foal diarrhea. In both studies, rectal swab microbial communities were determined using next generation sequencing and a total of 25 different phyla were found with the most abundant phylum present being Firmicutes followed by Bacteroidetes in both foals and dams. ☐ Dams were found to have a significantly higher mean diversity than foals (PD whole tree, nonparametric t-test, p<0.001). When comparing foals by week of age, week 1 foals had a significantly lower mean diversity than week 2, week 3, week 4, week 5 and week 6 foals (PD whole tree, nonparametric t-test, p<0.01). Significant differences were also found between semi-feral managed and domestic conventionally managed foals (ANOSIM, p<0.01, PERMANOVA, p<0.05, nsamples=116, ngroups=2) as well as well as between different foal ages (ANOSIM, PERMANOVA, p<0.001, nsamples=116, ngroups=6), showing that management type and age have notable effects on the horse at an early stage in their life. Lactobacillus spp. and Lactobacillaceae gen., bacteria associated with lactic acid production and starch-induced laminitis, were found to be enriched only in DCM foals, specifically during their second and third week of life (Kruskal-Wallis, LDA score>2.0, p<0.05). Predicted function of the microbiome was also analyzed and SFM foals were found to have a significantly higher mean sequence count in the OTUs contributing to lipid, general carbohydrate, complex carbohydrate, simple carbohydrate and protein digestion (p<0.001, Kruskal- Wallis). DCM foals were also found to have a microbiome more similar to their dams in their fifth and sixth week of life than were SFM foals to their dams in their sixth week of life. ☐ There were significant differences found between diarrheic and non-diarrheic foals in specific OTUs but not when analyzing their gut communities as a whole. This may suggest that the bacteria found to be significantly different are those contributing to mild diarrhea, but these changes are not drastic enough to cause serious illness in the foal. Bacteroides fragilis, Prevotella spp., Veillonella spp., Lachnospiraceae gen. and Clostridiales fam. are some of the taxa found to be significantly higher in diarrheic foals. Ruminococcaceae gen., Bacteroides spp., Butyricimonas spp., Odoribacter spp., Oscillospira spp., Fusobacterium spp. and Escherichia coli were some of the taxa found to be significantly higher in non-diarrheic foals. The function of the microbiome was also analyzed and non-diarrheic foals were found to have a significantly higher abundance of the OTUs responsible for starch digestion, general carbohydrate digestion, simple carbohydrate digestion, complex carbohydrate digestion and protein digestion when compared to diarrheic foals (p<0.05, Kruskal-Wallis). ☐ These studies provide insight into how management and foal diarrhea can affect the foal’s hindgut microbiome as well as gives a detailed description of the function and community of this microbial community in the foal’s first six weeks of life.
Description
Keywords
Biological sciences, Early development, Foal diarrhea, Foals, Hindgut, Management, Microbiome