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Simple Summary  The microbiome of the digestive system of both animals and humans is affected by many factors including diet, environment, age, physical condition, and genetic factors, as well as the “host effect”. Physical effort, as a factor influencing the physiological state of an animal, can affect the microbial composition of the digestive system. The research so far is largely based on human and laboratory animals, but not enough research has been done on the effect of physical effort on horse digestive system. The study conducted suggests that effort has a significant impact on the studied bacterial phyla level and that there is also variation in the proportions of the studied phyla between individual horses, as well as “reacting” to changes in different ways, which also suggests the occurrence of a phenomenon called “host influence”.    Abstract  Exercise significantly affects the body of both animals and humans, including the composition of the digestive microbiome. This study aimed to determine the changes in the composition of the most numerous bacterial phyla (Firmicutes and Bacteroidetes, as well as the level of the  Lactobacillaceae  family) in the digestive system of horses under the influence of physical effort. The study included a group of 17 Thoroughbred racehorses at the age of 3 years, fed the same forage, from whom feces samples were collected individually before and 48 h after physical effort. The obtained samples were subjected to DNA isolation and RT-PCR analysis. The results showed a significant increase in the level of both phyla after exercise compared to the state before physical effort; there were no such differences in the level of facultative aerobes, i.e., the  Lactobacillaceae  family (although a decreasing tendency was found after exercise). In addition, the analysis of the level of the studied phyla indicates individual differences in horses’ response to the effort.

Effect of Intense Exercise on the Level of Bacteroidetes and Firmicutes Phyla in the Digestive System of Thoroughbred Racehorses