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This review aims to explain the influence and characterization of the microbiome in the ruminant digestive system by presenting the knowledge collected so far. The knowledge presented in this work is focused on the main factors affecting the microbiome and the main dependencies that have been found in it so far. The microbiome in the rumen is the first to come into contact with the biomass of the forage and its main purpose is to decompose into smaller particles or compounds. With the gradual increase in knowledge about the microbiome, there is a chance to manipulate it so that the animal continues to live in a symbiotic relationship with it, while reducing greenhouse gas emissions to the environment as well as increasing feed efficiency. Therefore, understanding the influence of the ruminant microbiome is the main step to achieve such results. However, learning the relationship between microorganisms is only at an early stage, because research focuses mainly on taxonomy. Future research should focus on interactions in the ecosystem which is the microbiome, on explaining individual functions and on influence of environmental factors. [ABSTRACT FROM AUTHOR]

Simple Summary: The skin is one of the largest surface organs for animals. The microbiome of the skin plays an important role in protecting the host. The study showed that the environment in which the animals lived and their size could affect the bacterial composition of their skin. Additionally, individual differences between the bacterial composition of the skin were observed, which may indicate the existence of a factor called "individual influence". For decades, skin has been assigned the main role of an insulator of the inside of the body from the external environment, but it also plays a role in maintaining homeostasis. In this study, the level of selected bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) was assessed in three sheep breeds (Świniarka sheep, Uhruska sheep and BCP line (synthetic sheep breed; n = 6) and in two breeds of goats (Boer, Saenian; n = 6) living in the same environment and fed on the same feed, where the aim was to identify differences in terms of race, species and individual differences. Significant differences were found in Firmicute, Actinobacteria and Proteobacteria phyla (p ≤ 0.05). Statistically significant and positive correlations were demonstrated between Actinobacteria and Proteobacteria, Proteobacteria and Bacteroidetes or Firmicutes and Bacteroidetes. The obtained results suggest that the species and racial differences in the level of the studied bacterial phyla may also result from the physicochemical differences of the skin surface, as they could exacerbate the variations in humidity, temperature, composition of antimicrobial peptides (AMP) and lipid content. In addition, individual differences were observed, which indicate a similar effect of an individual on the microbiological composition of its organism. [ABSTRACT FROM AUTHOR]

Simple Summary: The ruminant microbiome is considered a specific ecosystem found within the gastrointestinal tract. A balanced intestinal microbiota is important not only for maintaining gut homeostasis, but also for regulating immune function and has a direct impact on the gut–brain axis. Factors, such as pregnancy, age, or genetics, can influence the microbial composition of the digestive system. The results of the study suggest that the parity, as well as the age of the animals, may affect the level of microorganisms in the digestive system. During pregnancy and parturition, the homeostasis of the body is disturbed, and the immune system is undermined, which is associated with hormonal changes within the body. Recently, it has also been suggested that physiological and hormonal changes associated with pregnancy may affect the composition of the gastrointestinal microbiome. Therefore, the aim of this study was to determine the composition of the microbiome in the third month of pregnancy in sheep in their first and second parity. Eighteen females in total were selected for the experiment, and they were divided into two groups: primiparous (aged 1 year) and multiparous ones (aged 2 years). The animals were fed the same fodder, and did not show any disease symptoms. Fecal samples were collected individually from each female (n = 20), and then bacterial DNA isolation and real-time PCR were performed for the main bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) and families (Lactobacillaceae and Clostridia). The obtained results showed the differentiation in the microbiome between the primiparous and multiparous ewes with respect to the following groups: Bacteroidetes, Proteobacteria, and Actinobacteria—the level was higher in the case of the primiparas. These results suggest that the parity and age of the females may affect the gastrointestinal microbiome, but further studies are recommended. [ABSTRACT FROM AUTHOR]

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". 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. [ABSTRACT FROM AUTHOR]

Simple Summary: The microbiome plays an important role in the digestive system of ruminants. It affects the health status of animals and their development and production rates. However, its composition may be influenced by factors such as diet, age, gender, and health condition. The study was conducted on three breeds of sheep that were kept in one environment and fed with the same feed. The microbiological analysis showed that the animal microbiome is also influenced by breed. Studies carried out so far have indicated the effect of the microbiome on the composition of ruminant products. Recent studies have shown that not only diet, but also genetic factors can affect the microbiological composition of the digestive system. The aim of the study was to determine the differences in the levels of selected bacterial phyla in terms of breed differences. Three sheep breeds, i.e., Olkuska, Romanov, and old-type Polish Merino, differing in their use (meat–wool, meat, prolificacy) and country of breed origin were included in the study. Sheep at the same age and of the same sex were kept for a period of 3 months in the same environmental conditions and fed the same feed in the same proportions. The study included real-time PCR (polymerase chain reaction) analysis of feces collected before the slaughter and measurements of body weight and chilled carcasses. The obtained results showed significant differences between the breeds in the levels of bacterial populations tested. There were also differences in body weight between the breeds during the first weight measurements, however, the final results did not show any differences—after three months of maintenance all of them reached similar body weights, despite differences in fecal microbiological composition. The study suggests that in addition to diet and environmental conditions, the microbiology can also be influenced by breed. [ABSTRACT FROM AUTHOR]