**3.** *H. pylori*

In 1982 *Helicobacter pylori* was isolated by Barry Marshall and Robin Warren [1]. Their research changed the long-standing view that the stomach is as a sterile organ, being naturally hostile to bacterial survival. Today, it is known that *H. pylori* infects more than 50% of the world's population with the only significant reservoir for the infection appearing to be humans. Possible routes of infection include oral-oral, fecal-oral, and iatrogenic spread (e.g., by unsterile endoscopic interventions). In developing countries, infection is usually acquired early in childhood, unlike in industrialized countries, where it develops more commonly in adulthood [9].

*H. pylori* is a Gram-negative, spiral-shaped, motile, and flagellated bacteria that is uniquely adapted to colonizing the gastric niche. Hence, it comes with no surprise that when present, *H. pylori* has the highest relative abundance among all gastric microbial communities in both adults and children [10–12]. Upon infection, *H. pylori* utilizes urease and α-carbonic anhydrase to generate ammonia and HCO3 −. This neutralizes H+ and locally increases the pH, facilitating the bacteria's passage through the acidic gastric fluid and the pH-sensitive mucous layer. Using chemotaxis, the bacteria navigates the pH gradient to their niche near the host's epithelium [13, 14]. Once established in the inner mucus layer, *H. pylori* can utilize diverse adhesins (e.g., SabA and BabA) to attach to epithelial cells. Once attached, bacterial

**55**

*Gastric Microbiota: Between Health and Disease DOI: http://dx.doi.org/10.5772/intechopen.86926*

**4. Other non-***H. pylori* **microbiota**

stomach estimated at >103

(evolution).

• Targeted qPCR [27]

**4.1 Culture-dependent identification of gastric microbiota**

**4.2 Culture-independent identification of gastric microbiota**

A variety of 16S rRNA based methods exist, including:

• Dot-blot hybridization with rRNA-targeted probes [26]

• Fluorescent in situ hybridization (FISH) [25]

to those which are culture-dependent. These include:

• 16S rRNA is present in almost all bacteria.

effector molecules, such as the vacuolating cytotoxin (VacA) and the cytotoxin-associated gene A (CagA), modulate the gastric epithelial cell behavior, leading to loss of cell polarity, release of nutrients and chemokines, and regulation of acid secretion via control of gastrin and H+/K+ ATPase [9, 15, 16]. In response to the *H. pylori* infection, the host mounts a complex inflammatory response, which ultimately leads to active chronic gastritis and subsequent gastroduodenal diseases. Therefore, the host's attempts to eradicate *H. pylori* increase gastric immunopathology (gastritis, epithelial damage such as atrophy and intestinal metaplasia), which alters the gastric compartment and its microbiota and may subsequently progress to gastric cancer.

Initial studies on the bacteria present in the stomach, using culture-based techniques, such as gastric juice cultures and mucosal biopsies were reported even before the isolation of *H. pylori*. In 1977 Savage DC [17] isolated bacteria from the

*Lactobacillus*, *Streptococcus*, *Clostridium*, and *Veillonella*), *Actinobacteria* (genus *Bifidobacterium*), and *Proteobacteria* (*coliforms*). However, due to the fact that these bacteria are prevalent along the whole GI tract, they were considered transient bacteria, which form small colonies that exist for short periods of time, rather than true gastric colonizers. Later culture-based studies [18–23] find that the most prevalent phylum, regardless of *H. pylori* status, is *Firmicutes*, followed by *Proteobacteria* and *Bacteroidetes*. *Actinobacteria* varies in studies as the second or third most prevalent phylum. The most commonly found genera were *Streptococcus*, *Lactobacillus*, *Bacteroides*, *Staphylococcus*, *Veillonella*, *Corynebacterium*, and *Neisseria*. However, given that culturing conditions for the majority of microbes colonizing the GI tract are not established, culture-based methods are considered to underestimate the gastric microbial diversity and are largely replaced by culture-independent methods.

Culture-independent studies use a variety of molecular methods based on 16S rRNA gene sequencing. A multitude of reasons define these methods as far superior

• The function of the 16S rRNA gene has remained unchanged over time, suggesting that random sequence changes are a more accurate measure of time

• The 16S rRNA gene is large enough for computational purposes [24].

CFU/g. The predominant phyla were *Firmicutes* (genera

*Gastric Microbiota: Between Health and Disease DOI: http://dx.doi.org/10.5772/intechopen.86926*

*Gastrointestinal Stomas*

**2. The hostile gastric environment**

tal bile reflux and the gastric peristalsis.

**3.** *H. pylori*

This neutralizes H+

between resident and transient microbiota and its role in health and disease remains controversial. Nevertheless, the potential of understanding the structure and dynamics of the gastric microbiota for the pathogenesis, diagnosis, and treatment of gastroduodenal diseases remains. Hence, this review aims to underline current knowledge on gastric microbiota and its relation to gastroduodenal pathology.

Compared to other gastrointestinal (GI) segments, the stomach has a physiological environment that is significantly more hostile to bacterial colonization and is a crucial part of the dynamics of the gastric microbiota. Primary reason for this is the gastric juice, which is composed of two main components—proteolytic enzymes and hydrochloric acid (HCl). The hydrochloric acid creates a strong acidic environment by maintaining a pH of 1–2 in the gastric lumen, which together with the proteolytic features of the gastric enzymes creates an intragastric environment that serves both digestive and protective roles. This environment facilitates the denaturation of proteins and nutrient absorption but also severely limits bacterial colonization and survival, preventing infection by pathogens [4]. The low pH value is the main restrictive component of the gastric juice [5]. To prevent damage to the mucosa from the acid and enzymes, neck cells of the gastric glands secrete mucus on the surface of the gastric epithelium. This mucus layer establishes a pH gradient that increases the pH up to 6–7 at the surface of the mucosa [6]. This is due to the unique properties of the mucus which permit acid to flow from parietal cells into crypts which communicate with the lumen, but do not allow acid at pH <4 from penetrating the mucus layer [6]. The mucus layer consists of several different mucin molecules, including MUC1, MUC5AC, MUC5AB, and MUC6, and forms two sublayers, an inner mucus layer that is firmly attached to the epithelia and a loose mucus layer, which is in direct contact with the lumen [7, 8]. Additional factors that contribute to the strong antimicrobial environment of the stomach are the acciden-

In 1982 *Helicobacter pylori* was isolated by Barry Marshall and Robin Warren [1]. Their research changed the long-standing view that the stomach is as a sterile organ, being naturally hostile to bacterial survival. Today, it is known that *H. pylori* infects more than 50% of the world's population with the only significant reservoir for the infection appearing to be humans. Possible routes of infection include oral-oral, fecal-oral, and iatrogenic spread (e.g., by unsterile endoscopic interventions). In developing countries, infection is usually acquired early in childhood, unlike in industrialized countries, where it develops more commonly in adulthood [9].

*H. pylori* is a Gram-negative, spiral-shaped, motile, and flagellated bacteria that is uniquely adapted to colonizing the gastric niche. Hence, it comes with no surprise that when present, *H. pylori* has the highest relative abundance among all gastric microbial communities in both adults and children [10–12]. Upon infection, *H. pylori* utilizes urease and α-carbonic anhydrase to generate ammonia and HCO3

through the acidic gastric fluid and the pH-sensitive mucous layer. Using chemotaxis, the bacteria navigates the pH gradient to their niche near the host's epithelium [13, 14]. Once established in the inner mucus layer, *H. pylori* can utilize diverse adhesins (e.g., SabA and BabA) to attach to epithelial cells. Once attached, bacterial

and locally increases the pH, facilitating the bacteria's passage

−.

**54**

effector molecules, such as the vacuolating cytotoxin (VacA) and the cytotoxin-associated gene A (CagA), modulate the gastric epithelial cell behavior, leading to loss of cell polarity, release of nutrients and chemokines, and regulation of acid secretion via control of gastrin and H+/K+ ATPase [9, 15, 16]. In response to the *H. pylori* infection, the host mounts a complex inflammatory response, which ultimately leads to active chronic gastritis and subsequent gastroduodenal diseases. Therefore, the host's attempts to eradicate *H. pylori* increase gastric immunopathology (gastritis, epithelial damage such as atrophy and intestinal metaplasia), which alters the gastric compartment and its microbiota and may subsequently progress to gastric cancer.
