**4.1 Structure and function**

Body surfaces facing the external environment, namely the skin and all mucosal surfaces (nasal, oral, gastrointestinal, etc.) are colonized by a huge number of microorganisms, collectively called microbiota. Most of them reside in the gut, in a *continuum* of extremely dynamic microbial communities. In terms of microbial density, it is estimated that approximately 1012 microorganisms per gram of content are present in colon and feces. These microorganisms belong to all three domains of life: Bacteria, which predominate, Archaea (methanogens, essentially belonging to *Methanobrevibacter* and *Methanosphaera* genera), and Eukarya (fungi and protists) [23]. The evolution of the intestinal microbiota starts at birth and is completed during the first years of life until it stabilizes in the adult phase. Immediately after birth, the gastrointestinal tract is rapidly colonized by a microbial consortium whose composition varies depending on several factors, such as the mode of delivery (vaginal or caesarian), the diet during infancy (breast or formula milk), and during adulthood (for example, vegetable or meat-based), the use of antibiotics. In particular, breastfeeding stimulates the maturation of the intestinal microbiota, as breast milk contains bifidogenic oligosaccharides (HMO, human milk oligosaccharides), which have a prebiotic action [24]. The maturation is then completed within the first years of life and occurs in parallel and synergistically with the development of the immune system. Perturbations of gut microbiota composition are associated with aging, and these changes favor the growth of pathogens and increase the susceptibility to gut-related diseases [25]. In this complex ecosystem, the collective genomes of bacteria and other microorganisms have been the focus of increasing interest over the past two decades, facilitated by the rapid development of culture-independent genomic approaches and advanced computational technologies. The gut microbiota is characterized by an enormous phylogenetic diversity, with more than 1000 bacterial species found in the entire human population, among which about 150 are present in a single individual. At higher phylogenetic levels this biodiversity is reduced, in fact, the human gut microbiota is composed of two main populations belonging to the Firmicutes and Bacteroidetes phyla, which collectively constitute over 90% of the known phylogenetic taxa. Other less abundant, but not less important phyla, such as Actinobacteria, Proteobacteria, and Verrucomicrobia, whose relative abundances are often below 1%, are also present. The advent of culture-independent methods, although detecting a high inter-individual variability in the composition of the intestinal microbiota, has allowed to identify a common "microbial core", with shared metabolic activities, characterizing healthy individuals [26]. Indeed, the relative proportions of the various phyla are maintained in balance under physiologic conditions (eubiosis), whereas changes in microbial composition and function, termed dysbiosis, associated to a lower overall microbial diversity, often occur in immune-mediated and metabolic disorders, thus proving the important role of the gut microbiota in maintaining host health status, which goes far beyond the initial experimental observations about relevance in regulating body fat tissue accumulation and energy balance [27]. The microbiome, defined as the collective genome of the gut microbiota, contains approximately 3.3 million genes, a number about 150-fold higher than that of the genes of the human genome, most of which are involved in both the metabolism of carbohydrates, amino acids, cofactors, and vitamins, and the biosynthesis of secondary metabolites. Thanks to this enormous genetic heritage, intestinal microorganisms exert a profound influence on the nutritional, metabolic, and immune responses of the host, so that the intestinal microbiota is considered an "accessory organ" and the higher organisms, with their associated microbial communities, are defined as "holobionts" [28]. As mentioned, the main function of the gut microbiota concerns metabolic activity. Intestinal bacteria are, in fact, able to produce essential nutrients such as vitamins and, mostly, to extract energy from complex polysaccharides, which are not digestible by the human enzymes present in the gastrointestinal tract. Indeed, the microbiota possesses the metabolic capacity to degrade a wide range of substrates that reach the colon. In particular, the fermentation of complex polysaccharides

### *Immune System, Gut Microbiota and Diet: An Interesting and Emerging Trialogue DOI: http://dx.doi.org/10.5772/intechopen.104121*

produces, among other substances, the short-chain fatty acids (SCFA), essentially acetate, propionate, and butyrate, which play a key and multifactorial role in the physiology of the host. Microbiota also contributes to the barrier effect, counteracting colonization by enteropathogens and opportunistic pathogens. The main mechanisms involved are both direct, such as competition for nutrient resources and adhesion sites to the intestinal mucosa, the inhibition of bacterial growth through the creation of microenvironments at acidic pH, and the production of bacteriocins (such as colicins, microcins, and nisin), and indirect, through stimulation of the host immune system and of maturation and growth of enterocytes [29]. Moreover, it is now universally recognized the existence of a gut-brain axis that envisages an active contribution of the intestinal microbiota in the regulation of anxiety, pain, and behavior by acting on the synthesis of neurotransmitters, and a possible contribution to the pathophysiology of disorders of the central nervous system. Finally, the gut microbiota is also able to interact and modulate the endocrine system, strongly influencing the levels of stress-related hormones and insulin, as well as appetite [30].

### **4.2 Influence of gut microbiota on the immune system**

The intestinal microbiota is recognized as an effective integral component of the host immune system, capable of finely tuning the immune responses, innate and adaptive, in the different phases of life. Indeed, the close relationship established between bacteria and immune cells in the gut is crucial for the maintenance of immunological homeostasis and, mostly, for the "education" of the immune system during the early stages of life [2]. In fact, according to the most recent theories, the interaction between microbiota and the immune system is necessary to "train," first, and "keep trained," then, the various functions of the latter. Thanks to the continuous contact with the gut microorganisms, with the molecules they synthesize, with those they produce from undigested food components, the immune system satisfies two apparently conflicting needs: to defend the organism from real threats, and to tolerate microbes and molecules not harmful to the organism. Indeed, the large variety of microorganisms constituting the microbiota can be functionally distinguished into symbionts and pathobionts, also referred to as opportunistic pathogens, both fundamental, as the former educate the immune system to tolerance, while the latter train it to pathogen recognition and attack [31]. In the physiological condition of eubiosis, symbionts and pathobionts are present in equilibrium. If this balance is altered, for example, due to an excessive antibiotic treatment, one of the two groups becomes predominant, leading to the onset of one of two possible extreme conditions: hyperstimulation of the immune system (inflammation) or hypostimulation (immunosuppression) [32] (**Figure 3**). It is worth noting that pathobionts, that are not harmful and are even necessary to educate the immune system in physiological conditions, become dangerous when the equilibrium is altered, as in dysbiosis. The immunological surveillance of the intestinal microorganisms involves the abovementioned TLRs, which recognize MAMPs and PAMPs [9, 33]. These receptors differently act in distinct cellular compartments. Indeed, recognition of these receptors on the apical surface of the epithelium (i.e., the one in contact with the intestinal lumen) generally promotes tolerance towards commensal bacteria and foodborne antigens, and low (basal) inflammatory tone; conversely, activation of these same receptors on the basolateral side, in contact with the underlying mucosa, promotes strong inflammatory responses. Numerous microbial stimuli activate inflammatory cascades through signal transduction pathways that essentially involve the nuclear

transcription factor NF-κB, with consequent production of pro-inflammatory cytokines, such as IL-1 and IL-6, or anti-inflammatory factors more directly related to the extinguishing of inflammation/immune response, such as IL-10, thus playing a crucial role in maintaining intestinal homeostasis [10]. The different communities of the intestinal microbiota, characterized by metabolic specialization, complementarity, and cooperation, constitute a very complex network of microbe-microbe and microbe-host interaction, in the form of a symbiotic or mutualistic relationship, resulting in a continuous cross-talk. The host derives substantial immunological and metabolic benefits from the physical proximity of microbial populations in the gut and underlying tissues, but at the same time, this proximity poses an ongoing threat to health. In fact, although the immune system is designed to establish the proper balance between tolerance to the gut microbiota, maintaining a low level of basal inflammation and surveillance against infectious agents and opportunistic pathogens, the disruption of this balance, for example, due to inflammatory diseases or following the excessive use of antibiotics, induces a malfunction of the intestinal barrier with consequent opening of the junctions between enterocytes. The assembly and maintenance of tight junctions are regulated by several signaling pathways, that can be altered by pro-inflammatory cytokines, in particular TNF-α, IFN-γ, and IL-1β. Thus, an increase of these cytokines due to an inflammatory status can induce a decrease in the expression of tight junction proteins, or alter their phosphorylation status, causing a "loosening" of tight junctions [34]. This condition, referred to as a leaky gut syndrome, facilitates the translocation of pathogenic bacteria or harmful antigens from the intestinal lumen to the underlying mucosa (**Figure 3**). This process determines the establishment of endotoxemia, i.e., the presence of LPS in the circulation. The LPS, present on the cell wall of Gram-negative bacteria, is one of the microbial components able to act as an immune activator, therefore, representing a MAMP that

### **Figure 3.**

*Schematic representation of eubiosis and dysbiosis conditions. Gut immunological homeostasis is the result of a continuous cross-talk between microbiota and immune system. In eubiosis, the commensals predominate over pathobionts, maintaining the integrity of the intestinal barrier and an anti-inflammatory milieu. In dysbiosis, pathobionts take over and cross epithelial barrier inducing inflammation. AMPs, antimicrobial peptides; B, B lymphocyte; DC, dendritic cell; M, macrophage; Treg, regulatory T cell.*

### *Immune System, Gut Microbiota and Diet: An Interesting and Emerging Trialogue DOI: http://dx.doi.org/10.5772/intechopen.104121*

binds to TLR4 and triggers an inflammatory response, which from local becomes systemic. The polysaccharide A of *Bacteroides fragilis*, on the other hand, triggers an anti-inflammatory response, by stimulating IL-10 production and Treg proliferation [35]. Other bacteria, such as segmented filamentous bacteria (SFB), is pathobionts present exclusively during the first years of life, and play an important role in the immune system training, by inducing IL-17 secretion in the intestine and stimulating the production of IgA in the mucosal membranes of the oral and respiratory cavity [36]. Moreover, some evidence shows that SBF can promote IL-22 production by ILCs [37]. Fundamental to the maintenance of intestinal homeostasis is the proper balance of the different T lymphocyte subpopulations, mentioned in the 2.2.1 paragraph of the present chapter. In particular, the Th17/Treg balance appears crucial, and this balance is also modulated by the microbiota. It is worth noting that the interactions between microbiota and the immune system can have different outcomes, depending on the context of eubiosis or dysbiosis. Recently, the advent of high throughput molecular sequencing techniques has allowed the isolation from the human intestine of some bacteria with anti-inflammatory activity, which are of particular interest, especially for their possible applications in counteracting obesity and inflammatory bowel diseases, such as Crohn's disease and ulcerative colitis. Among the most important are *Akkermansia muciniphila* and *Faecalibacterium prausnitzii*, which have been defined as "next generation probiotics," as they are not yet commercially available, but candidates to be used as "biotherapeutics" [38].
