22 Evaluating the core bacterial microbiome of 1,787 horses

Abstract

The core bacterial microbiome can be defined as the bacteria that are consistently prevalent within a given population. Determining the core microbiome of the equine gastrointestinal tract would allow for the development of probiotics, prebiotics, and management techniques to promote the growth of these taxa and subsequently support horse health. The Microbiome Quotient project (MQ; Purina Animal Nutrition, Gray Summit, MO) aims to determine the core bacterial microbiome from a repository of rectal swabs obtained from thousands of horses across various locations, breeds, ages, and diets, among other factors. To this end, the bacterial DNA of 2,057 rectal swabs were extracted using the Quick-DNA Fecal/Soil Microbe Miniprep kit (Zymo Research, Irvine, CA) and the V3-V4 hypervariable region of the 16S rRNA gene was sequenced by following the Illumina 16S Protocol (San Diego, CA). Data were initially filtered with DADA2 within the QIIME2 pipeline. The data were filtered again in R (4.2.2) to remove samples with missing data points as well as samples with low sequencing depth (<1,000 sequences). In total, 1,787 samples were considered for downstream analysis. The core microbiome was determined by using the Microbiome and qiime2R packages in R to aggregate taxa at the genera level across allsamples with the criteria that the taxa must exceed 0.1% relative abundance in over 70% of the samples (prevalence ≥ 0.7). The data were then analyzed within the following top 5 breeds: Quarter Horse (n = 567), Thoroughbred (n = 314), Warmblood (n = 177), Paint (n = 105), and Arabian (n = 79). The top 15 genera across all samples consisted of Rikenellaceae RC9 gut group (12.58%), uncultured genus (6.79%), Erysipelotrichaceae UCG-004 (4.80%), Ruminococcaceae UCG-002 (4.09%), Akkermansia (3.89%), Ruminococcaceae UCG-010 (3.62%), Arcanobacterium (2.84%), Phascolarctobacterium (2.33%), Streptococcus (1.90%), Treponema 2 (1.75%), Prevotellaceae UCG-001 (1.71%), Mycoplasma (1.64%), Prevotellaceae UCG-004 (1.63%), Clostridium sensu stricto 1 (1.57%), and Alloprevotella (1.56%). Three unique genera were observed between the top 5 breeds and were Campylobacter (Warmblood), Bacteroides (Arabian), and Ruminococcaceae UCG-004 (Paint). Further investigation of this growing database within and between other variables related to health (e.g., age, Body Condition Score, and history of disease) is necessary to fully characterize and understand the function of the equine gastrointestinal core microbiome and to determine the best practices for supporting gastrointestinal health.