Urinary Tract Microbiome Association with Diseases and Autoimmunity: Plausible Potential for Therapeutics and Accompanying Challenges

1. Introduction

The establishment of the Human Microbiome Project (HMP) in 2008 marked the beginning of a new chapter in our knowledge of the microbial populations that live inside of us. [1]. The population of bacteria that thrives in the urinary system, encompassing kidneys, ureters, bladder, and urethra, constitutes the urinary tract (UT) microbiome[2,3]. Although the urinary system was once thought to be sterile, advances in molecular biology techniques have shown that a wide variety of bacteria, fungi, and viruses may be present there [4]. The UT microbiome preserves the integrity of the associated epithelium, protect against infections and foster the appropriate operation of the immune system[5]. It maintains the urinary tract homeostasis through various mechanisms, including the regulation of pH levels, production of antimicrobial peptides, and competition for resources, which collectively help to establish and preserve a balanced urinary tract environment[6]. The human immune system and the epithelial cells lining the UT interact with the microbiota, which may impact the inflammatory and immunological responses[7]. Stimulation of host defense by modulating immune system can play crucial roles in defending against pathogens and maintaining tissue integrity.

The microbial composition of the urinary tract microbiota is influenced by various factors, including host genetics, anatomy, immune function, and external factors such as diet and antibiotic use[8]. The microbiota typically includes bacteria, but fungi and viruses may also be present in smaller quantities[9]. Roughly 90% of samples with no growth by normal urine culture contain live bacteria, according to studies using both 16S rRNA amplicon sequencing and advanced urine culture [10]. In healthy individuals, the urinary tract microbiota is often dominated by a few bacterial species, primarily from the genera Lactobacillus[11]. Numerous urological conditions, including UT infections, incontinence, bladder pain syndrome and urinary stone formation have been related to changes in the microbial community composition[12,13]. Several bacteria and fungi can cause UT infections, but the most frequent culprits are uropathogenic bacteria Escherichia coli, Klebsiella pneumoniae, Proteus mirabili,s Staphylococcus saprophyticus, Enterococcus faecalis, Proteus mirabilis [14] and fungus Candida sp.[15,16]. The urinary tract microbiota is dynamic and can change in response to various factors, such as hormonal fluctuations, sexual activity, urinary tract infections, and antibiotic treatment[17,18]. These changes can affect the balance of beneficial and potentially pathogenic microorganisms. Overall, urobiota contributes to the maintenance of the bladder homeostasis[19] and dysbiosis in it leads to health issues[20]. The diversity of the UT microbiota communities and their impact on health, namely the distinction between eubiosis and dysbiosis, are the subject of ongoing research. The present goal of scientific study on the UT microbiota is to comprehend the potential function that it may play in the development of UTIs as well as other medical conditions including cancer and other UIs [4]. Understanding the urinary tract microbiota has important clinical implications for the diagnosis and management of urinary tract infections and other urinary tract disorders[18,21]. For example, changes in the urinary microbiota may influence susceptibility to infections, treatment outcomes, and recurrence rates.

2. Methods to Study the Microbiome

While conventional urine culture methods primarily targeted aerobic microorganisms and pathogens like Escherichia coli, molecular techniques offer a more comprehensive view of the urinary microbiota[22,23]. Advent of cutting-edge molecular techniques have helped us get a better picture of the microbial population in the UT system. Urine microbiome can now be studied by two major methods; microbial culturing and metagenomic sequencing[24].

2.1. Microbial Culturing

To study UT microbiota, urine samples are usually tested for the presence of urinary pathogens using culture-dependent techniques. Standard urine culture, which includes plating urine onto agar plates containing 5% sheep blood agar as well as MacConkey agar plates and incubation aerobically at 35°C for 24 hours to produce quantitative colony counts, is the primary approach used to diagnose UTIs [25]. Nevertheless, the detection of bacteria in urine is severely limited by this approach, as the diagnostic criteria are ≥105. This traditional method for diagnosing urinary tract infections (UTIs), often misses low bacterial counts. Enhanced quantitative urine culture (EQUC) offers a more sensitive approach by utilizing larger urine volumes, multiple incubation durations, diverse culture media, varied incubation atmospheres (CO₂-enriched, aerobic, anaerobic, microaerobic)[26]. Compared to standard culture, EQUC can detect 88% of non-E. coli uropathogens and 67% of all uropathogens missed by standard culture[27]. However, it still has limitations and this can lead to misdiagnosis and inappropriate treatment.

2.2. Metagenomic Sequencing

The entire range of persistent microbial communities in the human UT and UGT is undetectable, even by EQUC[28]. With next generation sequencing (NGS) based metagenomic sequencing techniques, researchers have evaluated the entire microbial composition without bias. Currently, 16S rRNA amplicon sequencing and shotgun metagenomic sequencing are the two main methods of metagenomic sequencing [29]. 16S rRNA Amplicon Sequencing involves deep sequencing of amplicons encompassing variable regions of the 16S rRNA gene, enabling ecological structure assessment, community profiling, and sequence identification through subsequent bioinformatics analyses [30]. While this method offers sensitive detection of low-abundance microbial DNA with minimal host contamination, it suffers from inherent bias in primer binding, limiting its application to taxonomic analysis and relative abundance assessments [31,32]. Conversely, shotgun metagenomics sequences all DNA molecules present in a sample, providing an in-depth analysis of the entire sequence space. Despite its potential for detailed examination, it often encounters host contamination, necessitating sufficient sequencing depth to discern microbial populations accurately[33]. Strategies to enhance microbial DNA enrichment through refined sample preparation and DNA extraction methods are crucial for minimizing host contamination. The comprehensive analysis of the metagenome facilitates the determination of taxonomic composition, community structure, and functional attributes of the local microbiota's genetic potential. Nonetheless, 16S rRNA sequencing remains prevalent in human urine microbiome studies, primarily due to its utility in community taxonomic profiling[34].

3. Variability of UT Microbiome

Variability in the composition and diversity of the microbiome stems from a myriad of factors encompassing age, gender, diet, lifestyle, and overall health status[35]. Predominantly, bacterial infections of the UT afflict adults, with microbial analyses revealing distinct microbial profiles across age and gender cohorts[17,36]. In individuals around 18 years old, prevalent taxa include Lactobacillus, Corynebacterium, Escherichia, and Streptococcus sp., whereas 28-year-old males exhibited Lactobacillus, Sneathia, Veillonella, Corynebacterium, and Prevotella. Females aged 27–67 years showcased a microbial landscape dominated by Lactobacillus, Prevotella, Gardnerella, Peptoniphilus, and Dialister[4]. Notably, both healthy males and females spanning various age ranges exhibit diverse bacterial taxa in midstream urine samples, including Lactobacillus, Klebsiella, Corynebacterium, and Staphylococcus, among others[37,38]. Gender-specific differences are discernible, likely influenced by physiological and hormonal variations, alongside differential excretion of urinary chemicals such as creatinine, citrate, calcium, and oxalate, which may modulate microbial colonization patterns [39]. Studies indicate that midstream urine samples from females demonstrate greater bacterial diversity compared to those from males, with Lactobacillus species prominently represented in fertile women alongside Actinobacteria and Bacteroidetes phyla[40]. Despite gender-specific distinctions, core genera such as Lactobacillus, Corynebacterium, and Streptococcus persist in the UT microbiome across genders and life stages, albeit in varying abundances [41,42]. Women bear a disproportionate burden of urinary tract infections (UTIs), with about 50% experiencing UTIs at some point in their lives, with heightened risks among postmenopausal and elderly individuals[43,44]. Conditions like interstitial cystitis/bladder pain syndrome (IC/BPS) and UT obstructions also influence UT microbiome dynamics, with pathogenic bacteria associated with UTIs and structural abnormalities disrupting microbial composition[45].

Beyond host-related factors, medications, dietary patterns, hygiene practices, and environmental variables exert substantial influence on the UT microbiome. Medications like antibiotics and cancer treatments, dietary habits, fluid intake, hygiene practices, and environmental exposures all shape microbial ecology and colonization patterns[46,47]. Comprehensive understanding of these multifaceted influences is crucial for elucidating the urinary microbiome's implications in health and disease and devising strategies for UT health maintenance.

4. Role in Health and Disease

The UT microbiome serves a pivotal role in maintaining health by contributing to protective mechanisms akin to those observed in the gut microbiome. Through niche occupation and resource competition, beneficial bacteria inhibit the colonization of pathogenic counterparts, thereby preventing microbial imbalances and UT infections [21]. Additionally, interactions between the UT microbiome and the local immune system are instrumental in modulating immune activity, crucial for preserving immunological homeostasis and averting inflammation or autoimmune responses[48,49,50]. Metabolic versatility allows microbes to metabolize various substances, including host-produced molecules and dietary components, affecting the nutritional and chemical landscape of the surrounding environment. The composition of the UT microbiome can influence the body response to treatments, such as medications for UT infections, suggesting the potential for developing more effective therapeutic interventions by elucidating microbiota functions in treatment outcomes[51]. Alterations in UT microbiome composition may serve as biomarkers for specific diseases or conditions, offering insights into personalized treatment strategies and providing valuable diagnostic or prognostic information[52]. The UT microbiome exhibits lower pH levels in a healthy state, which can rise in disease states. Presence of various probiotic strains like Lactobacillus rhamnosus, Lactobacillus fermentum, and Lactobacillus reuteri are beneficial and exert their antibacterial activity primarily through the production of lactic acid during carbohydrate metabolism in the epithelium's glycosaminoglycan layer. The resulting decrease in pH (≤4.5) creates an inhospitable environment for many pathogenic bacteria (Figure 1)[53]. Additionally, they produce other antibacterial substances like hydrogen peroxide and bacteriocin. Hence, probiotics and prebiotics represent promising avenues for UT illness management alongside personalized antibiotic therapies, informed by a deeper understanding of urine microbiome dynamics and composition [53].

Changes in the composition of the UT microbiome, known as dysbiosis, have been linked to various diseases, including UTIs, interstitial cystitis or bladder pain syndrome (IC/BPS), overactive bladder syndrome (OAB), urinary incontinence (UI), and kidney stones[28]. Additionally, the gut microbiota plays a significant role in regulating the development of certain UT illnesses through a mechanism known as the gut-bladder axis[54,55]. NGS studies have revealed a strong causal relationship between these disorders and the influence of the microbiome on both the bladder and gut. Consequently, dysbiosis of both the gut and urine microbiota may represent a significant contributing factor in the development of diseases affecting the urinary system [56]. Some of these have been elaborated below to highlight the role of microbiota in disease.

UTIs

UTIs can generally be classified as higher UTIs or lower UTIs. Upper UTIs involve infections in the kidneys or ureters, while lower UTIs refer to infections in the bladder or urethra[57]. E. coli bacteria are the main cause of UTIs[58]. Although this bacterium is naturally occurring in human bodies, it intermittently finds a way into the UT through the urethra and begins to proliferate in the bladder and ureters, leading to UT infections[59]. Another concept, referred to as the gut-vaginal bladder axis, suggests that when UTI causing strains enter the bladder by the gastrointestinal tract or vagina, they engage in polyinfection and quorum sensing [60]. Further evidence supports the role of vaginal microbiota in regulating UTI as well, because women with vaginosis caused by anaerobic G. vaginalis overgrowth have a higher risk of UTI than women with healthy microbial communities dominated by Lactobacillus [61]. In every age group, women are more likely than males to get an uncomplicated UTI. Age-matched men report an incidence rate of roughly 0.01 per person/year, whereas young, sexually active women report incidence rates ranging from 0.5 to 0.7 per person/year[62]. There is now a lot of research being done on the connection between the compositional dynamics of the urinary microbiome and the prevalence of UTIs [63].

Exposure to G. vaginalis leads to the outflow of latent intracellular reservoirs of E. coli in the bladder, hence increasing the risk of potentially fatal E. coli infections[64,65]. Exposure to G. vaginalis is sufficient to induce renal damage that persists after the microbe is eliminated from the urine system, as well as bladder epithelial apoptosis and exfoliation[64]. Therefore, UTI-associated disease in humans cannot be explained by a single invasion of an exogenous pathogenic bacterium. The complexity of UTI-associated diseases in humans underscores the need to consider both urinary microbiota imbalance and polymicrobial pathogenic causes for a comprehensive understanding of UTIs [45,66]. Thus, addressing UTIs requires a multifaceted approach that acknowledges the interplay between host physiology, microbial communities, and infectious agents.

Interstitial Cystitis or Bladder Pain Syndrome (IC/BPS)

Interstitial cystitis or bladder pain syndrome (IC/BPS) is a perplexing urological illness characterized by urgency of urine and discomfort in the bladder[67]. While the exact cause of IC/BPS remains unknown, recent research suggests a potential link between the UT microbiome and the development of the condition[68,69,70]. While traditionally, the microbiological diagnosis of UTIs relied on culture techniques, which may not adequately capture the diverse microbial communities present in patients with IC/BPS, recent advancements in metagenomic analysis have provided insights into the role of the urinary microbiome in this condition [71,72]. Xu et al. investigating the microbiome of individuals with IC/BPS have revealed significant correlations between urinary microbiota composition (upregulation of four opportunistic pathogenic genera, i.e. Serratia, Brevibacterium, Porphyromonas, and Citrobacter) and symptomatology[71]. Utilizing metagenomic techniques, Zheng et al. have identified alterations in the urinary microbiome of females (abundance of Lactobacillus and Escherichia-Shigella; decreased Bacteroides and Acinetobacter) vs males with IC/BPS compared to healthy controls[73]. Ceprnja et al. have further elaborated the contributing role of Gammaproteobacteria in IC by metagenomics and prediction through generalized Lotka-Volterra modeling[74].

Overactive Bladder Syndrome (OAB)

Overactive bladder syndrome (OAB) is a chronic medical disorder that significantly impacts the quality of life for both men and women, characterized by urgency of urination, frequency, and nocturia, with or without urgent incontinence, in the absence of obvious illness[75]. The multifactorial nature of OAB complicates its understanding, as the underlying causes may vary among individuals[76]. Previously, it was allied with neurological factors impacting bladder but now research has revealed that low-grade bacterial colonization or dysbiosis (imbalance) in the urinary tract might contribute to OAB symptoms in some individuals. The microbiomes of healthy women without OAB symptoms and those with OAB have revealed significant differences in the microbial composition of the bladder. Siddiqui et al. have used 16s rRNA technique to identify Streptococcus, Atopobium, Ureaplasma, Prevotella, Bacteroides in the OAB impacted patient[77]. Hilt et al.[78] have shown presence of Lactobacillus, Corynebacterium, Streptococcus, Actinomyces, Staphylococcus, Aerococcus, Gardnerella, Bifidobacterium, and Actinobaculum by using culture dependent techniques alongside 16s rRNA sequencing study of four women suffering from OAB. While Lactobacillus was less prevalent in the urine of women with OAB compared to healthy controls, the presence of Proteus was more frequently observed in OAB patients[79]. Bacterial presence may trigger inflammation in the bladder, leading to hypersensitivity and OAB symptoms. Certain bacteria might alter nerve signaling pathways involved in bladder control[75]. Using 70 patients, Li et al. identified certain bacterial genera (e.g., Porphyromona and Prevotella) to be significantly correlated with severity of OAB sub-symptoms[80]. A systematic review analysis by Sze et al. shows that no study reveals identical microbiota abundance, even among healthy individuals[81]. OAB patients exhibit a reduced bacterial diversity compared to controls and overall microbiome composition depends on the specimen collection method and the metagenomic sequencing technique used. OAB urine microbiome is more susceptible to alterations from gut or vaginal influences compared to controls[81,82]. Not all OAB cases are linked to changed UT microbiota and studies have identified a connection between OAB and the gastrointestinal tract microbiota as well[61]. Alterations in the gut microbiome composition have been linked to OAB and daily urine urgency, with individuals experiencing OAB symptoms exhibiting less microbial diversity compared to non-OAB groups. Specifically, the abundance of Bifidobacteriaceae was significantly lower in individuals with OAB and daily urine urgency.

Urinary Incontinence (UI)

UI refers to the involuntary loss of urine, a prevalent condition affecting millions worldwide[83]. While the causes of UI are diverse, a growing body of research suggests a complex interplay between the urinary tract microbiome and the development of UI, particularly urgency urinary incontinence (UUI)[84]. UUI has symptoms that resemble those of a urinary infection, including increased frequency and urgency of urination. Significant changes in the quantity and frequency of urinary microbiota have been discovered by both high-throughput sequencing and extended culture techniques [85]. A control cohort showed a decrease in Lactobacillus and an increase in Gardnerella in the UUI microbiome after using EQUC procedures to extract live bacteria from urine collected via transurethral catheter from women with UUI[86]. Culture revealed the presence of Actinobaculum, Actinomyces, Aerococcus, Arthrobacter, Corynebacterium, Gardnerella, Oligella, Staphylococcus, and Streptococcus in patients. Lactobacillus gasseri was more frequently detected in the UUI cohort, while Lactobacillus crispatus was most commonly found in controls[86]. Lactobacillus abundance was also allied with resistance to anticholinergic treatment for this condition[84]. Several investigations have suggested a potential connection between intestinal dysbiosis and UUI[61].

Kidney Stones

Kidney stones, also known as nephrolithiasis or renal calculi, are mineral deposits that form in the kidneys and can cause significant pain and discomfort when they obstruct urinary flow[87]. Nanobacteria have been linked to kidney stone formation, with 97.2% of the stones tested yielding positive results for nanobacteria[88]. Notably, only struvite stones exhibited the presence of common bacteria alongside nanobacteria. While apatite stones exhibited the highest nanobacteria antigen signals, the overall presence of nanobacteria was not affected by the stone type. In vitro experiments revealed that the isolated nanobacteria could indeed generate apatite stones, as demonstrated by the incorporation of calcium and strontium-85. Urease-producing bacteria, such as Proteus mirabilis, Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, Providentia stuartii, Serratia, and Morganella morganii, are consistently associated with the formation and recurrence of struvite stones[89]. These bacteria produce urease, which breaks down urea, resulting in the formation of ammonia and carbon dioxide. This process leads to urine alkalinization and the subsequent formation of phosphate salts, contributing to stone formation in the kidneys. Moreover, there is a concurrent increase in acid-tolerant pathobionts among individuals with recurrent stone formation[90]. Additionally, specific enzymes involved in oxalate metabolism have been found to be elevated in those who suffer from kidney stones chronically.

Furthermore, the presence of biofilms, microbial communities encased in a protective matrix, on the surface of kidney stones may contribute to stone growth and recurrence. These biofilms can harbor bacteria and facilitate the adherence of crystals, promoting stone formation and providing a reservoir for recurrent infections [91]. When the urinary microbiome of kidney stone patients was investigated using 16S rRNA gene sequencing, it was found that the patients urine contained a different representation of bacteria linked to inflammation, such as Acinetobacter, and that the diversity of the urinary microbiota was significantly lower in these patients than in healthy controls. Thus, dysbiosis in the urinary and stomach microbiota appears to be a major factor in kidney stone formation, mediated by the rate at which oxalate is consumed or the control of the kidney's inflammatory response [92]. Certain bacteria in the gut and potentially the urinary tract may influence the breakdown and absorption of substances like oxalate, a major component of some kidney stones[93]. Clinical trials exploring the potential of using O. formigenes or its enzymes to decrease hyperoxaluria have exhibited encouraging findings. In vivo studies have demonstrated that Lactobacillus and Bifidobacterium species possess the capability to reduce oxalate levels[93].

Benign Prostatic Hyperplasia

Benign Prostatic Hyperplasia (BPH) is a condition characterized by the non-cancerous enlargement of the prostate gland, which can lead to urinary symptoms such as difficulty urinating, frequent urination, weak urine flow, and incomplete bladder emptying[94]. While BPH is primarily considered a condition related to changes in hormone levels and age, there is growing evidence suggesting a potential role for the microbiota in the development or exacerbation of BPH[95,96,97]. Propionibacterium acnes, commonly found in the skin microbiota and implicated in various inflammatory conditions like acne, has shown an association with BPH in some studies, suggesting a potential role in prostatic inflammation[98]. Okada et al. have also identified Burkholderia as a culprit for BPH[99]. Sarkar et al.[100] have also reported Kocuria palustris and Cellvibrio mixtus to be notably enriched in samples from patients with BPH. Jain et al. [101]revealed a unique microbial composition within BPH tissues, characterized by the notable presence of E. coli among other species such as Micrococcus spp, coagulase-positive Staphylococcus, Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria. This finding suggests a potential role of these bacteria, particularly E. coli, in the inflammation and tissue damage associated with BPH. In vitro studies further demonstrated that E.coli associated with BPH can activate NF-κB signaling and induce DNA damage in prostate epithelial cells. Bajic et al. (2020) expanded the research, utilizing both mid-stream urine and transurethral catheterization samples. They utilized urine culture and 16S rRNA gene sequencing analysis, identifying Streptococcus, Veillonella, Gardnerella, Staphylococcus, and Candida as relevant microbiota[102]. They also found that an increase in the International Prostate Symptom Score (IPSS) was associated with significantly higher odds of detectable bacteria in catheterized urine, indicating the adequacy of catheterized urine in sampling the bladder microbiome

Glomerulonephritis

Glomerulonephritis, a condition characterized by inflammation in the kidney's glomeruli, can be triggered or exacerbated by certain microbial infections, particularly in cases of post-infectious glomerulonephritis[103]. Among the microbial agents responsible for this condition, Group A Streptococcus (Streptococcus pyogenes) is the most common culprit, often associated with throat or skin infections such as strep throat or impetigo, leading to what is known as post-streptococcal glomerulonephritis (PSGN)[103]. Although its incidence is now decreased in developed countries, it still occurs with notable frequency in densely populated and economically disadvantaged communities worldwide, where group A β-haemolytic streptococcal infections are prevalent[104]. Among children, PSGN remains the most common cause of acute glomerulonephritis. Bateman et al. [105]have stated that postinfectious glomerulonephritis represents an immune-mediated form of acute glomerulonephritis typically observed several weeks after an infection with Streptococcus pyogenes. Koyama et al.[106] have also reported its association with MRSA infection. It is hypothesized that post-MRSA glomerulonephritis may be induced by superantigens, leading to the production of high levels of cytokines and polyclonal activation of IgG and IgA. The formation of immune complexes containing IgA and IgG in the circulation subsequently contributes to the development of glomerulonephritis. Other bacteria, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae, have also been linked to cases of post-infectious glomerulonephritis, albeit less frequently[107,108,109]. In post-infectious glomerulonephritis, the immune response elicited by these microbial infections results in the deposition of immune complexes within the glomeruli, leading to inflammation and kidney tissue damage. However, not all cases of glomerulonephritis are directly linked to microbial infections, as various forms of the disease have different underlying causes.

Urinary Tract Cancer

Urinary tract cancer encompasses a range of malignancies that can affect different parts of the urinary system, including the kidneys, bladder, ureters, and urethra. While the role of the microbiota in urinary tract cancer is an area of ongoing research, there is growing evidence suggesting that alterations in the urinary microbiota may be associated with the development or progression of certain types of urinary tract cancer[110,111,112,113,114]. These differences include alterations in the abundance of specific bacterial species or taxa, as well as changes in overall microbial diversity can lead to cancer. Certain microbial metabolites produced by dysbiotic urinary microbiota may have carcinogenic properties or influence tumor progression. For example, metabolites such as nitrosamines and aromatic amines, which can be derived from dietary sources or microbial metabolism, have been implicated in bladder carcinogenesis [115]. Three key components have been identified to represent the tumor-promoting effect of E. coli in this context[116]. Firstly, the contamination of bladder tissues by E. coli increases the carcinogenic potential of nitrosamine precursors, potentially due to an elevation in nitrite production by the bacteria and sustained synthesis of nitrosamine through in-situ nitrosamine formation. Secondly, E. coli contamination accelerates urothelial cell proliferation, which may enhance the mutagenic effects of the carcinogenic agent. Thirdly, prolonged exposure to oxidative and nitrosative stress leads to DNA damage and mutation. These findings highlight the multifaceted mechanisms through which E. coli contamination in bladder tissues can contribute to the progression of cancer.

Heidler et al. [117]studied kidney cancer microbiota using amplicon metagenomics and found Aeromonas salmonicida, Pseudoalteromonas haloplanktis, Parageobacillus toebii, Trachelomonas volvocinopsis, Mycoplasma mycoides, and Halomicrobium mukohataei as common in the cancerous parts. Bacteria like Cyanophora paradoxa, Spirosoma navajo, Phaeocystis antarctica, Euglena mutabilis, and Mycoplasma vulturii were only found in the cancerous tissue. These bacteria can produce carcinogenic metabolites, induce chronic inflammation, or promote DNA damage, potentially contributing to carcinogenesis. However, the most extensively studied types of urinary tract cancer in relation to the microbiota is bladder cancer, where differences in the composition of the urinary microbiota between individuals with bladder cancer and healthy controls[118,119]. Increased abundance of certain bacteria, like Proteobacteria and Fusobacteria, has been linked to bladder cancer, while others like Lactobacillus may have protective effects. E. coli and other members of the Enterobacteriaceae family, have also been associated with bladder cancer[120].

Autoimmune Diseases

The urinary tract system organs are also affected by autoimmune diseases (Table 1). Although not all of them have been allied with impaired microbiota of urinary tract, there is evidence supporting role of bacteria in infection and autoimmunity trigger in some of the diseases, such as pyelonephritis.

Acute pyelonephritis is characterized by fever, back-pain, pus and foul smell of urine. Its primary culprits have been identified as E. coli and K. pneumoniae [133]. G. vaginalis abundance also exposes women to pyelonephritis[134]. Research has also shown that P. mirabilis and uropathogenic E. coli cooperate through metabolic interactions, allowing them to better colonize and persist within the urinary tract, potentially increasing the risk of pyelonephritis[135,136]. Keogh et al. (2016) revealed that in iron-limited environment, E. faecalis secretes L-ornithine to aid uropathogenic E. coli in acquiring iron, a nutrient crucial for bacterial growth and worsen infection during UTI, leading to pyelonephritis[137]. This suggests that these bacterial interactions can worsen infections. Staining of glomerular structures has revealed presence of H. pylori antigens in 100% of kidney samples from IgA vasculitis patients[138]. Haemophilus parainfluenzae has been detected in 35% of IgA vasculitis kidney biopsies, with a much lower prevalence (4%) in biopsies from patients with other kidney diseases[139]. Nephritis-associated plasmin receptor (NAPI-r), a group A streptococcal antigen has been detected in some patients with IgA vasculitis[140] as well as IgA nephropathy[141]. Kidney biopsies of some IgA nephropathy patients have also shown evidence of E. coli and H. influenza. This suggests that a direct bacterial infection with these species might contribute to IgA nephropathy and the exposure might trigger an autoimmune response that mistakenly attacks the glomeruli (filtering units) in the kidneys, leading to IgA nephropathy. H. pylori has also been implicated in the membranous nephropathy in almost two third of patients and some patients in Lupus nephritis [138]. However the pathogenic nature of the H. pylori presence remains yet to be elucidated in Lupus nephritis[142].

Aerobic culture of the seminal fluid of prostatitis patients revealed Enterobacteriaceae, enterococci and Staphylococcus aureus inpatients and absent from control group[143]. Nickel et al. [144]reported Burkholderia cenocepacia over represented in chronic prostatitis, using initial and mid-stream urine. Shoskes et al. [145]used urine DNA to identify higher counts of Clostridia compared with controls in prostatitis patients. Mandar et al. [146]further revealed that men with prostatitis had lower levels of health-promoting lactobacilli and a more diverse bacterial community (including proteobacteria) compared to healthy men[147].