MICROBIOMES OF HUMAN, LIVESTOCK ANIMAL GASTROINTESTINAL TRACT, FOOD PRODUCTS AND COMPOUND FEEDS: CONNECTIONS AND IMPACTS. PART 2

. Research on the human gut microbiome began long ago and currently uses the latest modern methods and creates new insights and understanding. The human gut microbiome contains billions of microbial cells per 1 g of intestinal contents. These microbes include members of all superkingdoms: prokaryotes (kingdoms Bacteria and Archaea), eukaryotes (Fungi), and viruses. The taxonomic composition includes hundreds of bacterial species, dozens of archaeal and fungal species, and dozens of viral families. They are constantly in close connection and interaction with each other and with host cells and tissues. Methanogenic archaea have been shown to potentially impact the development of certain diseases, and fungi and bacteria are beneficial symbionts that have a significant impact on host health. Viruses are mostly bacteriophages that modulate bacterial populations. The impact on human health occurs through complex molecular mechanisms: microbes secrete biologically active metabolites that modulate cellular and tissue biochemical activity and, hence, the functioning of the immune system and other organs, including the CNS. In turn, the human body responds using its nervous and immune systems and local intestinal tissues that produce certain substances that modify the activity of microorganisms. This results in formation of a gut-brain axis consisting of afferent (to the brain) and efferent (from the brain) pathways. A correlation between the composition of the microbiota and the development of some intestinal and non-intestinal diseases, including neurodegenerative and behavioral disorders, has been shown. The human gut microbiota varies throughout a person's life, and differs significantly by age (from infancy to the elderly) in terms of the taxonomic proportions. At the same time, food products contain hundreds of species of microbes, i


Introduction. Formulation of the problem
To date, a great deal of knowledge has been accumulated about the normal microbiota of the human gastrointestinal tract (GIT).It is well known that this microbiota consists of billions of bacterial cells belonging to many dozens of genera and hundreds of species, as well as non-bacterial microorganisms (archaea) or agents (viruses).
Similarly, a lot of information has been accumulated on the microbiota of food products, divided into different categories (manufacturing microbiota, spoilage microbiota, opportunistic or obligate pathogens).Under certain conditions (permissible content exceeded, certain species or strains present), this microbiota makes food unfit for consumption, both because of spoilage and the risk of poisoning, and because of the risk of foodborne infection.
At the same time, the impact of the food microbiota (without the presence of pathogenic species or strains and with a normal, unspoiled condition of the product) on the normal human gastrointestinal microbiota has not been studied and has to be revealed.
The objective of this review was to summarize the knowledge of the human gut microbiome, its role in Volume 18 Issue 1/2024 human physiology and health, and the food microbiota and its impact on human health, highlighting areas that could be investigated in the future.
The purpose of this study was to assess the current knowledge about the microbiomes of the human gastrointestinal tract and food products.
To achieve this goal, the following tasks were set: 1) to review the literature on human gut and food microbiomes and the role of the gut microbiome in human health; 2) to highlight unresolved issues for further research and development.
The figure shows that bacteria are the most abundant group (up to 1012 cells per 1 g of intestinal content), although the number of viruses and archaea is not much inferior to them (up to 1010 per 1 g of intestinal content), and the number of fungi is much lower (up to 106 per 1 g).
The microbiota in the human intestine appears very quickly after birth: its first representatives come from the mother's birth canal, then it begins to enter with food, and during the first decade of life, under the influence of dietary changes, the intestinal microbiome develops to a more mature state [2,3,4].
1.1.Bacteria According to the study [5], 461 existing species and 368 potential species (based on metagenomic and metataxonomic studies), as well as 416 potential taxa of superspecies ranks were identified.The existing 461 species include representatives of 198 genera in 10 phyla, the 368 potential species include 130 genera in 8 phyla, and the 416 superspecies taxa include 60 genera in 3 phyla.The researchers grouped all these species and other taxa into 1235 species-level phylotypes, i.e. morphologically and biochemically similar species, which potentially reflects their common evolution in the gut microbiome in the past.
Fig. 2 shows a diagram of proportional relationships between the main phylotypes according to the same study [5].A proportional relationship means that the phylotypes have proportional abundances of genetic markers.In the figure, pink lines indicate a direct proportionality, and green lines indicate an inverse proportionality.
In addition, not all taxa of microorganisms inhabiting the intestine are known to be equally active in biochemical processes aimed at maintaining microbiome homeostasis.Therefore, they make different contributions to it.Thus, the authors of the study [6] used the amount of RNA as an indicator of cell activity (intensive RNA synthesis indicates high metabolic activity and cell proliferation), the results of their study are shown in Fig. 3.
This indicates significant differences in the contribution of different groups of microorganisms to the functioning of the intestinal microbiome.Some phyla (groups) can be seen to be very abundantly represented in the active part of the microbiome, while others are almost absent there at all.
There is a considerable number of studies of the age-related dynamics of the gastrointestinal microbiome from infancy to old age.For example, the results of the study [7] are shown in Fig. 4. Volume 18 Issue 1/2024 1milk feeding, 2supplementary feeding, 3complete weaning, 4between 4 and 9 years, subsequent numberssegments of 9 years to the next point (10-19, 20-29, etc.) Fig. 4. Age-related changes in the human gastrointestinal microbiota (phyla) according to [7] The figure shows that Proteobacteria (gramnegative rods) had the highest abundance, and this does not change with age.Firmicutes are the second most abundant bacteria, and the contribution of this group decreased at the end of life.The content of Bacteroidetes (gram-negative anaerobes) also decreased, and the content of actinobacteria fell from almost 50% to almost 0%.The Proteobacteria phylum includes the Enterobacteriaceae family, as well as pseudomonads, campylobacters, and vibrios.The gram-positive Firmicutes phylum includes two common spore-forming genera, Bacillus and Clostridium, as well as lactobacilli and gram-positive cocci (in particular, staphylococci, streptococci, and enterococci).The Bacteroidetes phylum includes, among others, the widespread genera Bacteroides, Prevotella, Flavobacterium, Porphyromonas.The Actinobacteria phylum includes, among others, bifidobacteria and mycobacteria [7].
Other studies confirm this picture.Table 1 shows data from a study [8] on the main groups of bacteria in the human gastrointestinal tract.
As can be seen from the table, the greatest diversity in the human gastrointestinal tract is demonstrated by representatives of the Firmicutes phylumgram-positive rods, including spore-forming, and cocci.This phylum includes lactic acid rods (lactobacilli), clostridia, and streptococci.The second place is held by representatives of the Bacteroidetes phylum -gram-negative obligate anaerobic rods.The Actinobacteria and Proteobacteria phyla are represented by only one major genus each: bifidobacteria and Escherichia, respectively.

. Archaeome
Archaea are prokaryotic microorganisms morphologically very similar to bacteria, but with significant biochemical and molecular differences in cell structure, which allowed them to be distinguished into a separate kingdom (domain).They play an important role in the human (and animal) gastrointestinal tract, being in metabolic symbiosis with bacteria and contributing to the host's digestive processes.The aggregate of archaea in the human or animal gastrointestinal tract is called an archaeome, the archaeome consists of a large number of taxa (Fig. 5) [9].
The figure shows that the human gastrointestinal microbiome contains representatives of most taxa (order level) of archaea.The majority of the representatives belong to methanogens (orders Methanobacteriales and Methanomassilicoccales), i.e. those that produce methane as a metabolite by assimilating hydrogen and carbon dioxide produced by bacteria.In addition to the gut, methanogens are also found in the oral cavity.
It is known that archaea in the normal microbiota of the human body live not only in the intestines, but also in the nasal cavity and on skin [10], as well as in the oral cavity [11].. At the same time, there is evidence of the potential role of archaea in reducing the risk of certain human diseases (in particular, atherosclerosis), and thus the possibility of their use as probiotics [12].

Mycobiome
Fungi are eukaryotic heterotrophic decomposing organisms.They occupy an important place in the microbiomes of humans and animals: they are present in the microbiota of the gastric rumen in ruminants and on the skin of humans and animals, as well as in the intestines.Both yeast and mycelial fungi are present on human skin (including the ear canals and genitalia) and in the intestines (Table 2) [13].

hansenii Trichosporon
Among the fungi in this table, the genera Cryptococcus, Malassezia, and Trichosporon belong to the division Basidiomycota, and the rest of the genera belong to Ascomycota.In other words, only higher fungi are present in the intestinal mycobiome, while representatives of other orders are also present in the mycobiomes of the stomach and intestines of animals (see Part 1).However, there is also evidence of fungi of the genus Mucor (Zygomycota) in human intestinal contents, and in vegetariansrepresentatives of Agaricus (mushrooms) and epiphytic-phytopathogenic genera Alternaria and Epicoccum [14].
Studies show that fungi in the gut microbiome are in constant connection with bacteria and demonstrate a correlation in numbers [15,16], and at the same time play an important role: they modulate immune activity and the development of inflammatory processes, promoting the activation of certain groups of T-helper cells [17].

Virome
A virome is a collection of viruses that inhabits a particular biome (in which their hosts live).Viruses of both eukaryotes and prokaryotes (bacteriophages) are found in the normal microbiomes of animal and human organisms.At the same time, bacteriophages make up about 90% of the virome, and viruses of eukaryotesless than 10% (Table 3) [18].
As can be seen from the table, the diversity of viruses in the human gut is quite large and variable throughout life: it differs significantly between infants and adults.The number of viruses associated with diseases increases significantly with age.Studies show that the infant's intestinal virome depends on the feeding method: during breastfeeding, some viruses (bacteriophages and others) enter the baby's organism with milk [19].Bacteriophages modulate the activity of the bacterial part of the microbiome by lysing (killing) some cells and changing the properties of others through the appearance of prophages in them, and this balance is influenced by various factors, such as diet, the state of health of the intestines and the whole organism, taking certain medications, etc.It has been shown that bacteriophages of human intestinal virome can not only cause antibiotic resistance in bacteria by introducing new genetic material, but also modify their genome by interfering with CRISPR sequences [21].

The role of the gastrointestinal microbiota in shaping human health
The role of the intestinal microbiota in human life is well researched and shows a huge contribution to the majority of physiological processes and the formation of most mechanisms that underlie the vital activity of the human body.
Fig. 6 shows a diagram of the impact of human intestinal microecology on the health according to [22].
A positive effect of supporting microbiota with probiotics on the course of a number of diseases was shown, the diseases include non-intestinal disorders: diarrhea of various etiologies, necrotizing enterocolitis, respiratory infections, urinary system infections, asthma, eczema, fungal infections, Crohn's disease, cystic fibrosis, type II diabetes, depressive mental disorders, and chronic periodontitis [24].

Gut-brain axis
The neuroregulatory influence of the microbiota has attracted the attention of scientists in the 21st century and has been studied to some extent.These studies have shown the existence of what is known as gut-brain axis, i.e., the pathway of physiological influence of the gut microbiota on human brain activity.A diagram of this axis is shown in Fig. 7 [25].As can be seen from the figure, the gut-brain axis represents the reciprocal influence between the gastrointestinal microbiota and the central nervous system.The microbiota produces metabolites and biologically active substances that trigger impulses that reach the brain in various ways: directly via the vagus nerve, through the bloodstream, or through the spinal canal.In turn, the central nervous system sends impulses that activate secretory cells in the intestinal mucosa (goblet cells, Paneth cells, and others), which produce mucus with biologically active substances (e.g., lysozyme and defensins).
Medical studies have shown the influence of the gut microbiota (through the gut-brain axis) on the risk of stroke and its consequences and complications [26], as well as the development and course of Alzheimer's disease [27].In addition, certain correlations have been observed between the gut microbiome and the course of other diseases: autism spectrum disorders, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, and depressive disorders [28].

Food microbiota and its impact on the human gastrointestinal microbiota
The microbiota of food products is not uniform and depends entirely on the composition of the product, its manufacturing and storage conditions.Below (Table 4) is a summary of the most important groups of microorganisms in food products according to [29].
The microorganisms listed in the table include both saprophytic microbiota (most bacteria, fungi, yeasts), which can cause food spoilage, and pathogenic forms (protozoa, viruses, some bacteria), which cause food poisoning and infectious diseases.Fungi can also cause poisoning due to the release of mycotoxins, which are their toxic metabolites.
Another publication [30] pays great attention to the microbiota of meat and meat products (Table 5).
These data indicate a huge diversity of food microbiota, even within the same food group.The publication of the International Commission on Microbiological Specifications for Foods (ICMSF) [31] defines the most important (by the degree of risk to human health) microbiological indicators (Table 6) and methods and ways to control them.

Impact of food microbiota on human intestinal microbiota
This issue has not been studied to date.According to the authors of [32], only the effect of probiotic preparations used to correct intestinal microbiome disorders is well covered, and the role of the general non-pathogenic microbiota of foods is unknown.It can be assumed that this impact will be strongest on the health of infants and preschool children due to an unstable, underdeveloped microbiome, and in the elderly due to the decline of their own normal microbiome.

Table 1 -The most important groups of bacteria in the human gastrointestinal tract according to [8]
Enterobacteriaceae EscherichiaVolume 18 Issue 1/2024 1.2

Table 3 -Composition of intestinal viromes in infants under 1 year of age and adults according to [18] Viral group Genome Viral taxa in infants under 1 year of age Viral taxa in adults
* Viruses associated with human diseases Volume 18 Issue 1/2024