**2. Human intestinal microbiota**

Colonization of the human body occurs after birth, and possibly before birth, with a diverse microbial community of archaea, bacteria, fungi, viruses, and protozoa. This diverse community is referred to as the HIM. The prokaryote organisms colonizing the human body encompass nearly 90% of all HIM [13, 14]. Resident microbiota of the human GI tract, the one that colonizes permanently, is one of the most densely populated communities, even more so than the soil, the subsoil, and the oceans [15].

Colonization of GI tract is influenced by many factors like mode of birth delivery, infant feeding method, and the environment (stress, frequency of exercise, hygiene habits, infections, pharmaceuticals use, and type of feeding) [16, 17]. Within the human intestinal microbiota, there are both types of microorganisms: those who are essential, and even indispensable, for the survival of the host, and those who are potentially pathogenic. The vast majority have beneficial rather than detrimental effects on the host's health [15].

The importance of the GI microbiota was overlooked for a long time, and efforts to determine its composition and functions were unsuccessful; on the one hand, cultures from stool samples are unproductive, and on the other hand, according to estimations, 80% of the GI microbiota are anaerobe uncultivable organisms [10]. Anaerobic bacteria outnumber aerobic and facultative anaerobic bacteria by 100- to 1000-fold [16, 17]. Calculations of microbial counts in the colon of adult humans reach a mean of 1011 organisms/gram of wet stool, a quantity updated that is similar to the total number of human cells [18]. Estimated HIM composition comprise up to 1800 genera representing 7000–40,000 bacterial strains belonging to 500–1000 resident species [17, 18].

Taking into account the presence of gene content and metabolic products, along with the microbiota organisms contained within a particular body site, we must refer to it as a microbiome [15]. Studies on composition and function of uncultured microbial communities, more specifically by sequencing-based assays, are referred to as metagenomics. First, community DNA is extracted from a sample containing

**221**

*Interplay between Human Intestinal Microbiota and Gut-to-Brain Axis…*

multiple microbial members. Second, bacterial taxa present in the community are then defined by amplification of the 16S rRNA gene followed by sequencing. Highly similar sequences are grouped into operational taxonomic units (OTUs) or phylotypes, which can be compared to 16S rRNA databases to identify them as accurately as possible. An alternate method identifies community taxa after the total DNA is metagenomically sequenced and compared to reference genomes or gene catalogs. The OTUs can be described in terms of their relative abundance and/or their phylogenetic relationships, while sequenced genomes can be described as relative

The human intestinal microbiome is mainly defined by the high abundance of two bacterial phylotypes: Bacteroidetes and Firmicutes. Other phylotypes present at lesser amounts are Proteobacteria, *Actinomyces*, Fusobacterium, and Verrucomicrobia [14]. The gut microbiome is conformed with nearly 470 phylotypes, more than 1000 bacterial species representing more than 5000 strains, which in turn encode between 5 and 10 million of nonredundant genes (150-fold the number of genes identified in the human genome) [16, 17]. Studies on intestinal microbiome in health and disease revealed two microbiome subpopulations, one with high-gene counts and the other with low-gene counts; the first one seems to be

Every person has a unique microbiome profile; still there is a reduced number of species shared between persons. The aforesaid feature allowed to classify individuals into one of three enterotypes, each one based on the proportions of the three predominant intestinal genera, based on their abundance, *Bacteroides*, *Prevotella*, and *Ruminococcus*. The first two genera represent the Bacteroidetes, and the last one represents the Firmicutes. Enterotype 1 shows predominance of *Bacteroides*, while enterotypes 2 and 3 were defined by predominance of *Prevotella* and *Ruminococcus*,

Alterations of the typical GI microbiota, in number and abundance distribution

There are two ongoing multi-group projects on human microbiome, the Europebased Metagenomics of the Human Intestinal Tract (MetaHIT) and the US-based Human Microbiome Project (HMP). Both of them will allow to define to its finest details the microbiome diversity, at least to species level, their genetic load, and how

The intestinal microbiota maintains a symbiotic relationship with the host. Studies in both humans and mammals have implicated the intestinal microbiome in several physiological processes that are pivotal to the host health, from food digestion and energy homeostasis to immune and neurobehavioral development [25]. The single layer of intestinal epithelial cells, connected by tight junctions, constitutes itself a physical and biochemical barrier that segregates the commensal microbiota organisms to maintain intestinal homeostasis. This occurs through regulation of nutrients, electrolytes, and water absorption, as well as through release of mucins, antimicrobial peptides, and IgA for the prevention of the entry of pathogenic microorganisms [26–28]. The interaction between the microbiota and intestinal epithelial cells also promotes tissue restoration in the setting of injury or acute inflammation, thus supporting epithelium integrity. Besides the above statement, the microbiota provides protection against exogenous pathogenic organisms, either through competition for common nutrients and niches or by prompting

of distinctive types of microorganisms, and the host's adverse response to such changes have been called as dysbiosis. Thus, dysbiosis with low diversity has been linked particularly with obesity, inflammatory bowel disease, and ASD [16].

*DOI: http://dx.doi.org/10.5772/intechopen.89998*

abundances of its genes and pathways [19].

associated with a healthy digestive status [20, 21].

microbiota interacts with the host [23, 24].

**2.1 Biological role of GI microbiota**

respectively [22].

#### *Interplay between Human Intestinal Microbiota and Gut-to-Brain Axis… DOI: http://dx.doi.org/10.5772/intechopen.89998*

*Microorganisms*

The abovementioned psychiatric disorders frequently co-occur with each other, but interestingly they also occur in comorbidity with metabolic disorders, such as diabetes, cardiovascular disease, and metabolic syndrome [6–8], and are associated with adverse outcomes including higher mortality [6]. The insights of how those disorders are linked remain unclear. One likely explanation is that gut microbiota can trigger and guide the communication network of GBA and subsequently alter

ASD are a heterogeneous set of lifelong neurodevelopmental diseases, whose incidence increased significantly over the past decades [9]. No unique etiology of ASD has been identified, though both genetic and environmental factors have been suggested [9, 10]. However, findings of candidate genes do not conclusively explain the etiopathology of ASD; thus, scientific research has been redirected to GI comorbidities of ASD, under the premise that the high frequency of gut microbiota alterations seen in these patients may be associated with autism symptoms severity [10]. Indeed, the independent observations of Rodakis [10] and Sandler et al. [11] about improvements in autism clinical manifestations after antibiotic treatments prompted intense research around the issue, including therapeutic interventions such as diet modification, supplementation with biotics (prebiotics, probiotics, synbiotics, and/or postbiotics), alternative antibiotic treatments, and fecal micro-

Colonization of the human body occurs after birth, and possibly before birth, with a diverse microbial community of archaea, bacteria, fungi, viruses, and protozoa. This diverse community is referred to as the HIM. The prokaryote organisms colonizing the human body encompass nearly 90% of all HIM [13, 14]. Resident microbiota of the human GI tract, the one that colonizes permanently, is one of the most densely populated communities, even more so than the soil, the subsoil, and

Colonization of GI tract is influenced by many factors like mode of birth delivery, infant feeding method, and the environment (stress, frequency of exercise, hygiene habits, infections, pharmaceuticals use, and type of feeding) [16, 17]. Within the human intestinal microbiota, there are both types of microorganisms: those who are essential, and even indispensable, for the survival of the host, and those who are potentially pathogenic. The vast majority have beneficial rather than

The importance of the GI microbiota was overlooked for a long time, and efforts to determine its composition and functions were unsuccessful; on the one hand, cultures from stool samples are unproductive, and on the other hand, according to estimations, 80% of the GI microbiota are anaerobe uncultivable organisms [10]. Anaerobic bacteria outnumber aerobic and facultative anaerobic bacteria by 100- to 1000-fold [16, 17]. Calculations of microbial counts in the colon of adult humans reach a mean of 1011 organisms/gram of wet stool, a quantity updated that is similar to the total number of human cells [18]. Estimated HIM composition comprise up to 1800 genera representing 7000–40,000 bacterial strains belonging to 500–1000

Taking into account the presence of gene content and metabolic products, along with the microbiota organisms contained within a particular body site, we must refer to it as a microbiome [15]. Studies on composition and function of uncultured microbial communities, more specifically by sequencing-based assays, are referred to as metagenomics. First, community DNA is extracted from a sample containing

metabolic and psychological equilibrium [3, 5, 7, 8].

biota transplantation, among others, with variable outcomes [12].

**2. Human intestinal microbiota**

detrimental effects on the host's health [15].

the oceans [15].

resident species [17, 18].

**220**

multiple microbial members. Second, bacterial taxa present in the community are then defined by amplification of the 16S rRNA gene followed by sequencing. Highly similar sequences are grouped into operational taxonomic units (OTUs) or phylotypes, which can be compared to 16S rRNA databases to identify them as accurately as possible. An alternate method identifies community taxa after the total DNA is metagenomically sequenced and compared to reference genomes or gene catalogs. The OTUs can be described in terms of their relative abundance and/or their phylogenetic relationships, while sequenced genomes can be described as relative abundances of its genes and pathways [19].

The human intestinal microbiome is mainly defined by the high abundance of two bacterial phylotypes: Bacteroidetes and Firmicutes. Other phylotypes present at lesser amounts are Proteobacteria, *Actinomyces*, Fusobacterium, and Verrucomicrobia [14]. The gut microbiome is conformed with nearly 470 phylotypes, more than 1000 bacterial species representing more than 5000 strains, which in turn encode between 5 and 10 million of nonredundant genes (150-fold the number of genes identified in the human genome) [16, 17]. Studies on intestinal microbiome in health and disease revealed two microbiome subpopulations, one with high-gene counts and the other with low-gene counts; the first one seems to be associated with a healthy digestive status [20, 21].

Every person has a unique microbiome profile; still there is a reduced number of species shared between persons. The aforesaid feature allowed to classify individuals into one of three enterotypes, each one based on the proportions of the three predominant intestinal genera, based on their abundance, *Bacteroides*, *Prevotella*, and *Ruminococcus*. The first two genera represent the Bacteroidetes, and the last one represents the Firmicutes. Enterotype 1 shows predominance of *Bacteroides*, while enterotypes 2 and 3 were defined by predominance of *Prevotella* and *Ruminococcus*, respectively [22].

Alterations of the typical GI microbiota, in number and abundance distribution of distinctive types of microorganisms, and the host's adverse response to such changes have been called as dysbiosis. Thus, dysbiosis with low diversity has been linked particularly with obesity, inflammatory bowel disease, and ASD [16].

There are two ongoing multi-group projects on human microbiome, the Europebased Metagenomics of the Human Intestinal Tract (MetaHIT) and the US-based Human Microbiome Project (HMP). Both of them will allow to define to its finest details the microbiome diversity, at least to species level, their genetic load, and how microbiota interacts with the host [23, 24].

#### **2.1 Biological role of GI microbiota**

The intestinal microbiota maintains a symbiotic relationship with the host. Studies in both humans and mammals have implicated the intestinal microbiome in several physiological processes that are pivotal to the host health, from food digestion and energy homeostasis to immune and neurobehavioral development [25].

The single layer of intestinal epithelial cells, connected by tight junctions, constitutes itself a physical and biochemical barrier that segregates the commensal microbiota organisms to maintain intestinal homeostasis. This occurs through regulation of nutrients, electrolytes, and water absorption, as well as through release of mucins, antimicrobial peptides, and IgA for the prevention of the entry of pathogenic microorganisms [26–28]. The interaction between the microbiota and intestinal epithelial cells also promotes tissue restoration in the setting of injury or acute inflammation, thus supporting epithelium integrity. Besides the above statement, the microbiota provides protection against exogenous pathogenic organisms, either through competition for common nutrients and niches or by prompting

development and functional maturation of the gut immune system, including gut-associated lymphoid tissue, T-helper 17 cells, inducible regulatory T cells, IgAproducing B cells, and innate lymphoid cells [13].

The HIM microbiota has a considerable input on the metabolomic profile, the complete set of intestinal metabolites, of the host [29]. Specifically, the microbiota is a major source of both circulating organic acids and tryptophan metabolites, which have beneficial effects on the host health (**Table 1**) [30–53].

Fermentative processes of nondigestible complex carbohydrates, from dietary fiber, by Firmicutes and Bacteroidetes, result in the production of various shortchain fatty acids (SCFAs), such as acetate, propionate, butyrate, isobutyrate, valerate, and isovalerate. These bacteria-derived SCFAs, in a physiological context, may serve as an energy source for enterocytes, stimulate water and sodium absorption, decrease colonic pH, etc. [30].

Hyperproduction or deficiency of SCFAs may also affect the pathogenesis of a diverse range of diseases, from allergies and asthma to neurological diseases [17, 29, 30]. For example, a diet high in fat and digestible saccharides provokes that majority of nutrients be absorbed in the duodenum, leaving very few substrates for the colonic bacteria, leading to dysbiosis. Higher levels of SCFAs can also alter the intercellular spaces between the cells, resulting in a leaky gut that allows for more metabolites and bacteria to pass through the epithelial barrier, where bacterial endotoxins and other microbial-derived metabolites can gain entry into the bloodstream [17] Furthermore, dysbiosis can affect host immunity and neurobehavioral responses [17, 29]. Among SCFAs, butyrate is a promoter of colonic functionality and physical integrity, via cholesterol-rich membrane microdomain, as well as the preferred metabolic substrate for the colonocytes' energy requirements [54].

Essential vitamins such as folate, vitamin K, and vitamin B12, for the host's growth, are synthesized by gut microbiota, which in turn may affect DNA and histone protein methylation [55–57]. Certain hormones and vitamins also participate in drug and poison removal [58].

Apart from carbohydrates, GI bacteria also metabolize complex lipids and proteins that are indigestible by the host [59–61]. Expression of colipase, a critical protein factor for lipid metabolism, and subsequent stimulation of the release of pancreatic lipases appear to be regulated by *Bacteroides thetaiotaomicron* [59].

The metabolism of tryptophan by the HIM and/or gut and immune cells follows three alternative pathways: (a) the transformation to ligands of the aryl hydrocarbon receptor (AhR), (b) the kynurenine pathway (via indoleamine 2,3-dioxygenase 1), and (c) the serotonin (5-HT) production pathway. These pathways are performed by HIM, enterocytes/immune cells, and enterochromaffin cells, respectively. The HIM pathway yields several molecules, indole-3-aldehyde, indole-3-acid-acetic, indole-3-propionic acid, indole-3-acetaldehyde, and indoleacrylic acid. AhR signaling is crucial for gut epithelium renewal and barrier integrity and acts over many immune cell types for responsiveness [62].

Microbial metabolism of tryptophan is very important for intestinal AhR activity, since the absence or imbalance of tryptophan-metabolizing organisms generate deficiency of AhR agonists [46]. The production of AhR ligands have been determined among few HIM species, *Peptostreptococcus russellii* and *Lactobacillus* ssp. Many GI and neuropsychiatric diseases have been related to dysbiotic impairment of tryptophan metabolism or to accumulation of the end products [62].

Several HIM species not only can synthesize but respond as well to hormones and neurotransmitters of bacterial and human origin, which impact their growth and virulence. Beneficial *Lactobacillus* spp. are able to synthesize acetylcholine and gammaaminobutyric acid (GABA), while *Bifidobacterium* spp. produce GABA. *Escherichia* spp*.* produce norepinephrine, serotonin, and dopamine; other Firmicutes species

**223**

**Table 1.**

*Interplay between Human Intestinal Microbiota and Gut-to-Brain Axis…*

Butyrate Clostridia (clusters IV and IVa)

> *Faecalibacterium. Prausnitzii*

*Roseburia inulinivorans*

tryptophanaseproducing bacteria

such as *Lactobacillus* spp.

Indole Various

IPA *Clostridium* 

*sporogenes*

*Bifidobacterium*

*I3A, indole-3-aldehyde; IPA, indole-3-propionate; HYA, 10-hydroxy-cis-12-octadecoate (linoleic acid derivative);* 

*Examples of intestinal microbiota-derived metabolites and their beneficial effects on human health.*

spp.

**Pathway Metabolite Microbial agent Health benefits Refs.**

Increased intestinal barrier function [30, 31]

[32]

[35]

[33, 34]

[33, 34]

[40]

[41]

[42]

[43]

[43, 46]

[47, 48]

[49, 50]

Modulate intestinal macrophage

cells that polarize naive CD4+ T cells toward IL-10–producing regulatory

*Coprococcus catus* Suppression of colonic inflammation [36, 37] *Anaerostipes hadrus* Improvements in insulin sensitivity [38]

cell homeostasis

*C. catus* Decreased innate immune responses

inflammation

*P. copri* Improvements in insulin sensitivity

IL-22

I3A *Lactobacillus* spp*.* Maintenance of mucosal homeostasis

HYA *Lactobacillus* spp*.* • Maintenance of intestinal barrier

*Blautia obeum* Suppression of colonic inflammation [39]

to microbial stimulation

Protection from allergic airway

and weight control in obese mice

Maintenance of host–microbe homeostasis at mucosal surfaces via

and intestinal barrier function Protection against mouse intestinal

• Increased production of

• Decreased inflammation • Increased intestinal IgA

• Maintenance of intestinal barrier function and mucosal homeostasis

antioxidant and neuroprotectant

Reduced adiposity [52]

*B. longum* Increased barrier function [44] *B. fragilis* Modulation of host metabolism [45]

inflammation.

molecules

function

production

*F. prausnitzii* Improved insulin sensitivity [53]

CLA *Lactobacillus* spp. Decreased inflammation [51]

function

*Eubacterium* spp*.* Regulation of colonic regulatory T cell homeostasis

*Roseburia* spp*.* Induction of tolerogenic dendritic

T cells

Propionate *Bacteroides* spp. Regulation of colonic regulatory T

*DOI: http://dx.doi.org/10.5772/intechopen.89998*

Carbohydrate metabolism

Tryptophan metabolism

Llipid metabolism

*CLA, conjugated linoleic acid. Modified from [29].*


*Interplay between Human Intestinal Microbiota and Gut-to-Brain Axis… DOI: http://dx.doi.org/10.5772/intechopen.89998*

*Microorganisms*

development and functional maturation of the gut immune system, including gut-associated lymphoid tissue, T-helper 17 cells, inducible regulatory T cells, IgA-

which have beneficial effects on the host health (**Table 1**) [30–53].

The HIM microbiota has a considerable input on the metabolomic profile, the complete set of intestinal metabolites, of the host [29]. Specifically, the microbiota is a major source of both circulating organic acids and tryptophan metabolites,

Fermentative processes of nondigestible complex carbohydrates, from dietary fiber, by Firmicutes and Bacteroidetes, result in the production of various shortchain fatty acids (SCFAs), such as acetate, propionate, butyrate, isobutyrate, valerate, and isovalerate. These bacteria-derived SCFAs, in a physiological context, may serve as an energy source for enterocytes, stimulate water and sodium absorption,

Hyperproduction or deficiency of SCFAs may also affect the pathogenesis of a diverse range of diseases, from allergies and asthma to neurological diseases [17, 29, 30]. For example, a diet high in fat and digestible saccharides provokes that majority of nutrients be absorbed in the duodenum, leaving very few substrates for the colonic bacteria, leading to dysbiosis. Higher levels of SCFAs can also alter the intercellular spaces between the cells, resulting in a leaky gut that allows for more metabolites and bacteria to pass through the epithelial barrier, where bacterial endotoxins and other microbial-derived metabolites can gain entry into the bloodstream [17] Furthermore, dysbiosis can affect host immunity and neurobehavioral responses [17, 29]. Among SCFAs, butyrate is a promoter of colonic functionality and physical integrity, via cholesterol-rich membrane microdomain, as well as the preferred metabolic substrate for the colonocytes' energy requirements [54]. Essential vitamins such as folate, vitamin K, and vitamin B12, for the host's growth, are synthesized by gut microbiota, which in turn may affect DNA and histone protein methylation [55–57]. Certain hormones and vitamins also participate

Apart from carbohydrates, GI bacteria also metabolize complex lipids and proteins that are indigestible by the host [59–61]. Expression of colipase, a critical protein factor for lipid metabolism, and subsequent stimulation of the release of pancreatic lipases appear to be regulated by *Bacteroides thetaiotaomicron* [59].

three alternative pathways: (a) the transformation to ligands of the aryl hydrocarbon receptor (AhR), (b) the kynurenine pathway (via indoleamine 2,3-dioxygenase 1), and (c) the serotonin (5-HT) production pathway. These pathways are performed by HIM, enterocytes/immune cells, and enterochromaffin cells, respectively. The HIM pathway yields several molecules, indole-3-aldehyde, indole-3-acid-acetic, indole-3-propionic acid, indole-3-acetaldehyde, and indoleacrylic acid. AhR signaling is crucial for gut epithelium renewal and barrier integrity and

acts over many immune cell types for responsiveness [62].

of tryptophan metabolism or to accumulation of the end products [62].

The metabolism of tryptophan by the HIM and/or gut and immune cells follows

Microbial metabolism of tryptophan is very important for intestinal AhR activity, since the absence or imbalance of tryptophan-metabolizing organisms generate deficiency of AhR agonists [46]. The production of AhR ligands have been determined among few HIM species, *Peptostreptococcus russellii* and *Lactobacillus* ssp. Many GI and neuropsychiatric diseases have been related to dysbiotic impairment

Several HIM species not only can synthesize but respond as well to hormones and neurotransmitters of bacterial and human origin, which impact their growth and virulence. Beneficial *Lactobacillus* spp. are able to synthesize acetylcholine and gammaaminobutyric acid (GABA), while *Bifidobacterium* spp. produce GABA. *Escherichia* spp*.* produce norepinephrine, serotonin, and dopamine; other Firmicutes species

producing B cells, and innate lymphoid cells [13].

decrease colonic pH, etc. [30].

in drug and poison removal [58].

**222**

*I3A, indole-3-aldehyde; IPA, indole-3-propionate; HYA, 10-hydroxy-cis-12-octadecoate (linoleic acid derivative); CLA, conjugated linoleic acid. Modified from [29].*

#### **Table 1.**

*Examples of intestinal microbiota-derived metabolites and their beneficial effects on human health.*

belonging to *Streptococcus* and *Enterococcus* produce serotonin, and *Bacillus* produce norepinephrine and dopamine [17]. Those bacteria-derived neurotransmitters released directly to the intestinal lumen may either induce epithelial cells to in turn release molecules that modulate neural signaling within the enteric nervous system (ENS) or, after passing through the gut wall, gain entry into the portal circulation to exert direct effects on afferent axons [63, 64]. Indeed, several reports documented elevated levels of noradrenaline and adrenaline in the plasma of subjects coursing with systemic infections by gram-negative Proteobacteria, like *Escherichia coli*. (Reviewed in [64]).
