Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-throughput Sequencing of the V4 Region of the 16S rRNA Gene

Abstract

The hindgut of horses is an anaerobic fermentative chamber for a complex and dynamic microbial population, which plays a critical role in health and energy requirements. Research on the gut microbiota of Mongolian horses has not been reported until now as far as we know. Mongolian horse is a major local breed in China. We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions from gut fecal material to characterize the gut microbiota of Mongolian horses and compare them to the microbiota in Thoroughbred horses. Fourteen Mongolian and 19 Thoroughbred horses were used in the study. A total of 593,678 sequence reads were obtained from 33 samples analyzed, which were found to belong to 16 phyla and 75 genera. The bacterial community compositions were similar for the two breeds. Firmicutes (56% in Mongolian horses and 53% in Thoroughbred horses) and Bacteroidetes (33% and 32% respectively) were the most abundant and predominant phyla followed by Spirochaete, Verrucomicrobia, Proteobacteria, and Fibrobacteres. Of these 16 phyla, five (Synergistetes, Planctomycetes, Proteobacteria, TM7, and Chloroflexi) were significantly different (p<0.05) between the two breeds. At the genus level, Treponema was the most abundant genus (43% in Mongolian horses vs 29% in Thoroughbred horses), followed by Ruminococcus, Roseburia, Pseudobutyrivibrio, and Anaeroplasma, which were detected in higher distribution proportion in Mongolian horses than in Thoroughbred horses. In contrast, Oscillibacter, Fibrobacter, Methanocorpusculum, and Succinivibrio levels were lower in Mongolian horses. Among 75 genera, 30 genera were significantly different (p<0.05) between the two breeds. We found that the environment was one of very important factors that influenced horse gut microbiota. These findings provide novel information about the gut microbiota of Mongolian horses and a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in horses.

Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments of Mongolian horses

“…As mentioned above, Firmicutes and Bacteroidetes were the dominant bacteria at a ratio of 1:1 in the LG of the horses, the result contradicted the observations using fecal samples (Costa et al, 2012; Costa, Stampfli, et al, 2015; Schoster, Mosing, Jalali, Staempfli, & Weese, 2016; Zhao et al, 2016). However, this result is consistent with studies on microbial communities in different parts of the intestine (Costa, Silva, et al, 2015; Ericsson, Johnson, Lopes, Perry, & Lanter, 2016).…”

“…This bacterium is an appealing candidate to become a human probiotic because of negative correlation with the incidence of obesity, diabetes, inflammation, and metabolic disorders (Everard et al, 2013; Hansen et al, 2012; Png et al, 2010; Wang, Bose, Kim, Han, & Kim, 2015). Only four previous studies (Costa, Stampfli, Allen‐Vercoe, & Weese, 2016; Costa, Stampfli, et al, 2015; Rodriguez et al, 2015; Zhao et al, 2016) described the genus Akkermansia in the equine intestinal microbiota, which was only found in stool samples. In this study, for the first time, we found the ventral colon had the highest content of Akkermansia in the gastrointestinal tract of Mongolian horses, which supports further study of this bacterium.…”

“…The Mongolian horse is one of the most ancient grassland horse bred in the world and found in Inner Mongolia, China. At present, studies of the intestinal microorganisms of Mongolian horses have been limited in feces (Zhao et al, 2016). Horse feces can only represent the microbial changes in the distal regions of the posterior intestine (Costa, Silva, et al, 2015; Dougal et al, 2012) rather than the whole gastrointestinal microflora, and this had been demonstrated by studies of human intestinal microflora (Durban et al, 2011; Eckburg et al, 2005).…”

Transcriptome analysis of fasting caecotrophy on hepatic lipid metabolism in New Zealand rabbits

“…It is speculated that there may be two main reasons for this phenomenon, one is that soft feces is rich in vitamins and microbial proteins, with the same feed intake, rabbits that were fasted to eating feces would consume 15% to 22% less protein. The other one reason is that soft feces of rabbits contain a large number of microorganisms, when forbid the rabbits from eating soft feces, resulting in changes in the microflora in their digestive tract and the reduction of bacterial populations [38, 39].…”

Evaluation of DNA Extraction Methods of Mule Dung

“…These studies have employed many methods for DNA extraction from equine fecal samples, which has been predominantly used to analyse the equine hind gut microbial profile. Although most of the studies have used fecal DNA kits [5][6] , many have also used soil microbe DNA kits [7][8] or total DNA isolation kits 9 . The DNA extraction method is a critical step in microbial community profiling as apart from its effect on sequencing output and microbial community profiling 10 , it adversely affects the result comparison across studies, especially in physiological and pathological studies [11][12] .…”