## 2 Human Microbiome
### Microbiome Types
#### 2.1.5 Urogenital Tract  
The urinary tract and the genital tract are intrinsically linked, so they are often referred to as the urogenital tract. The urinary tract is usually considered a sterile space and exhibits resistance to bacterial colonization, even though the distal urethra often encounters frequent contamination. However, recent technological advancements have allowed us to gain new insights into this topic. It is now known that there is also a resident microbiome in the bladder, which, when in balance, has no negative impact on the body [85; 86]. The main defense against urinary tract infections is the flow of urine, especially during complete bladder emptying, where bacteria invading the bladder are eliminated through urination. Additionally, urine possesses other antimicrobial defense mechanisms such as a high concentration of urea, acidic pH, and various immune barriers. Besides this defense, the protection of the upper organs of the urinary system against colonization by bacteria from the vagina or penile surface is ensured by the action of a sphincter in the urethral area, which acts as a barrier to the entry of microorganisms [85; 87]. It is estimated that the diversity of the urinary microbiome is very comparable to the diversity of the vaginal microbiome, being mostly composed of _Lactobacillus_, but also some _Staphylococcus_, _Streptococcus_, and possibly, a residual amount of _E. coli_, mainly present in the distal urethra. However, there may also be transient colonization by fecal microorganisms such as enterobacteria, which can lead to infections of the upper urinary tract [88; 89]. Just like in the intestinal microbiome, the urinary microbiome plays an important role in maintaining the balance of the urinary system. Some of the most-important functions include the degradation of toxic compounds, the maintenance of mucosal integrity, the activation of the immune system, and the production of antimicrobial compounds [87; 90]. \begin{table}
\begin{tabular}{c c c} \hline \hline
**Region** & **Luminal Concentration** & **Main Composition** \\ \hline  & & _Lactobacillus_ \\  & & _Candida_ \\ Stomach & 0–\(10^{2}\) & _Streptococcus_ \\  & & _Helicobacter pylori_ \\  & & _Peptostryptococcus_ \\ Duodenum & \(10^{2}\) & _Lactobacillus_ \\ Jejuno & \(10^{2}\) & _Streptococcus_ \\ Proximal ileum & \(10^{2}\) & _Lactobacillus_ \\  & & _Streptococcus_ \\  & & _Cosridium_ \\  & & _Steptococcus_ \\ Distal ileum & \(10^{7}\)–\(10^{8}\) & _Bacteroides_ \\  & & _Actinomycine_ \\  & & _Corynebacteria_ \\  & & _Bacteroides_ \\ Colon & \(10^{11}\)–\(10^{12}\) & _Cosridium_ \\  & & _Bifidobacterium_ \\  & & _Enterobacteriaceae_ \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Composition and luminal concentrations of important microbial species in gastrointestinal tract regions [79; 80; 81; 82]. As concerns the genital tract, the vaginal microbiome has long been considered an important defense mechanism against infections in women. Subject to various modifications due to age and hormonal factors in women, the vagina exhibits a great microbial diversity. Before puberty, this microbiome consists mostly of _Streptococcus_, _Staphylococcus_, and _Escherichia coli_. Upon puberty and with the production of estrogen, _Lactobacillus_ becomes the predominant species, and the continuous production of lactic acid is responsible for vaginal acidification, preventing the colonization of new microorganisms, whether bacteria, fungi, or viruses. Simultaneously, these microorganisms will produce antimicrobial substances such as hydrogen peroxide, which inhibits the spread of viruses and the growth of bacteria and fungi. They will also stimulate the vaginal immune system, enhancing local defense mechanisms, and form a biofilm that prevents pathogenic agents from accessing the vaginal mucosa. During this phase, it is common for the microbiome to include _Lactobacillus_, _Corynebacterium_, _Staphylococcus_, _Streptococcus_, and _Bacteroides_[1].