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.

Aquaculture is the most rapidly growing branch of animal production. The efficiency and quality of the produced food depends on sustainable management, water quality, feed prices and the incidence of diseases. Micro- (MP < 5 mm) and nanoplastic (NP < 1000 nm) particles are among the current factors causing serious water pollution. This substance comes solely from products manufactured by humans. MP particles migrate from the terrestrial to the aquatic environment and adversely affect, especially, the health of animals and humans by being a favorable habitat and vector for microbial pathogens and opportunists. More than 30 taxa of pathogens of humans, aquacutural animals and plants, along with opportunistic bacteria, have been detected in plastic-covering biofilm to date. The mobility and durability of the substance, combined with the relatively closed conditions in aquacultural habitats and pathogens’ affinity to the material, make plastic particles a microbiological medium threatening the industry of aquaculture. For this reason, in addition to the fact of plastic accumulation in living organisms, urgent measures should be taken to reduce its influx into the environment. The phenomenon and its implications are related to the concept of one health, wherein the environment, animals and humans affect each other’s fitness.

Nowadays, there is a growing interest in environmental pollution; however, knowledge about this aspect is growing at an insufficient pace. There are many potential sources of environmental contamination, including sex hormones—especially estrogens. The analyzed literature shows that estrone (E1), estradiol (E2), estriol (E3), and synthetic ethinyloestradiol (EE2) are the most significant in terms of environmental impact. Potential sources of contamination are, among others, livestock farms, slaughterhouses, and large urban agglomerations. Estrogens occurring in the environment can negatively affect the organisms, such as animals, through phenomena such as feminization, dysregulation of natural processes related to reproduction, lowering the physiological condition of the organisms, disturbances in the regulation of both proapoptotic and anti-apoptotic processes, and even the occurrence of neoplastic processes thus drastically decreasing animal welfare. Unfortunately, the amount of research conducted on the negative consequences of their impact on animal organisms is many times smaller than that of humans, despite the great richness and diversity of the fauna. Therefore, there is a need for further research to help fill the gaps in our knowledge.

Ruminants are an important part of world animal production. The main factors affecting their production rates are age, diet, physiological condition and welfare. Disorders related to low level of welfare can significantly affect the microbiological composition of the digestive system, which is essential to maintain high production rates. The microbiology of the ruminant gastrointestinal tract may be significantly affected by inappropriate keeping system (especially in juveniles), psychological stress (e.g. transport), or heat stress. This results in an increased risk of metabolic diseases, reduced fertility and systemic diseases. Therefore, the paper focuses on selected disorders i.e., aforementioned inappropriate maintenance system, psychological stress, heat stress and their effects on the microbiome of the digestive system.

The development of research methods and tools related to microbiome investigation, as well as widened knowledge and awareness concerning the significance of microorganisms inhabiting mammalian organisms, has led to an increasing popularity of studies in this field. This review paper presents some issues related to the swine microbiome, its development starting from an early age of life and its status in adult animals, as well as factors affecting the microbiome in pigs. Attention is paid to the role of probiotics and prebiotics as alternatives to antibiotics in the context of post-weaning diarrhea treatment, and to the role of microorganisms inhabiting the digestive tract of pigs in performance indices formation. In veterinary and pork production practice, understanding of the swine microbiome and its relationships with the host organism may be useful in the prevention of some diseases and also in improvement of performance results of animals.

In recent years, a boost in the ruminant population has been observed, and consequently, an increase in the animals’ demand for nutrients and methane emissions. Methane emission is generated during the microbial fermentation of feed in the rumen, and a percentage even up to 12% of the energy obtained by this process can be wasted. In addition, the use of antibiotics in animal husbandry is being increasingly restricted. restricted. As a result, there is a continuous search for innovative feed additives that can serve as alternatives to antibiotics, and will also be safe for both people and the environment. In the present review article, additives were selected on basis that, according to studies conducted so far, may positively affect the microbiome of the digestive system by improving indicators and/or reducing methane production. Among them, probiotics, prebiotics or their combination—synbiotics are at the forefront of research. However, additives in the form of algae or plant origin are also gaining ground in popularity, such as essential oils, fermented wheat straw or Gelidium amansii, due to their general recognition as safe (GRAS) for both humans and environment.