
The human microbiome is currently being studied with increasing interest. Millions of microorganisms live in the human body and affect its homeostasis in several ways. The terms microbiome and microbiota are universally described to literally mean all living organisms in an area. The term ‘microbiome’, which was first used by Lederberg and McCray [1], is a combination of microbes living in the body and the biome (ecosystem). The microbiome, therefore, refers to the microorganisms living in the body and their genetic information. Conversely, microbiota refers to groups of microorganisms [2,3]. Understanding the complex microbial community that inhabits our bodies is recognized as a determinant of the pathogenesis of various diseases and profound pathogen-host interactions [4,5].
The Human Microbiome Project (HMP) was started in 2007 to characterize the human microbiome and analyze its role in human health and diseases. The project initiated large-scale studies on the microbial ecosystems of the human gut, skin, mouth, or vaginal microbiota [6-8]. Unfortunately, the urinary tract (UT) was not formerly explored in the HMP since it was considered unethical to obtain bladder biopsies or suprapubic aspirates from healthy individuals to characterize the bladder microbiome while avoiding sample contamination with microorganisms from the urethra [9,10]. Moreover, since the 1950s, with the establishment of the standard urine culture, until approximately 10 years ago, the UT had been considered sterile under normal conditions, and hence microbial communities inhabiting the UT have been less extensively studied [4,7-11]. It is well known that the gut microbiome plays an important role in several body functions, including nutrient processing and assimilation, defense against pathogenic microbes, and even stimulation of angiogenesis [5]. The ecosystem changes are linked to the causes of several gut diseases in children. Based on the recent microbiome literature, alterations in the microbiome have been associated with the causation of several non-urological diseases in pediatrics, such as infantile colic, necrotizing enterocolitis, asthma, atopy, obesity, type-1 diabetes, autism, atopic dermatitis, psoriasis, bronchial asthma, caries, periodontitis, and chronic rhinosinusitis [5].
With the advent of modern molecular high throughput DNA sequencing techniques such as 16S ribosomal RNA (rRNA) gene or whole metagenome sequencing, slowly or fastidiously growing aerobic and anaerobic bacteria have been detected as part of a unique commensal flora colonizing the UT [4,12]. Recently, there has been a shift in the outdated concept of sterile urine in healthy individuals, and interest in the role of the urinary microbiome (UM) is growing. While some UM studies such as prostate cancer, bladder cancer, interstitial cystitis (IC), urinary urge incontinence (UUI), overactive bladder (OAB), urinary stone disease, and urinary tract infection (UTI) have been conducted in adults [6,9,11], there are still very few UM studies in children. Therefore, based on the recent literature on the UM in the UT, this review focuses on the role of the UM from a pediatric urological perspective.
The urine collection methods employed in clinical practice are clean-catch midstream urine, first-void urine, suprapubic aspiration, or intermittent transurethral catheterization. The techniques used characterize the UM and determine the microbial diversity detected [9]. Urine sampling methods are frequently debated in any study related to UM. Most studies investigating the UM were based on collecting clean-catch midstream urine into a sterile container or through a transurethral catheter. These collection methods have potential urethral or perineal contamination since contamination by bacteria inhabiting the lower genitourinary tract, such as the distal urethra or perineum, might not be completely avoidable [4]. Wolfe et al. [13] compared different urine collection methods to discern bacteria present in the bladder. They concluded that due to minimal genitourinary contamination, the best methods are suprapubic aspiration and transurethral catheterization. However, although suprapubic aspiration is less vulnerable to genitourinary contamination, it is a more invasive procedure.
Additionally, consideration should be given to laboratory reagents contaminated by the bacterial genera
Traditionally, the detection of microorganisms in the UT was based on standard urine cultures in clinical microbiology laboratories. These methods only allow the detection of aerobic and fast-growing bacteria such as
To date, the human microbiome in the urological field has been less extensively reported in adults as well as pediatrics. The microbiome studies recently reported for UT diseases in adults include chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), IC/bladder pain syndrome (IC/BPS), UUI/OAB, urinary stone disease, sexually transmitted infections (STI), UTI, prostate cancer, bladder cancer, and renal cancer [6]. However, unlike microbiome studies in gastrointestinal and non-gastrointestinal disorders as well as in UT disease in adults, few pediatric studies in the urological field have been conducted to assess the role of UM in health and disease. Therefore, this study examines and compares how and to what extent UM studies are different in children compared to adults.
Several studies in benign urological diseases have investigated the UM in relation to UTI, urinary stones, UUI, OAB, neurogenic bladder (NB), lower urinary tract symptoms, STI, IC/BPS, and CP/CPPS in adults. However, literature reviews have revealed that there are very few studies on UM in pediatric urological benign diseases.
(1) UTI: Since the establishment of the standard urine culture in the 1950s until approximately 10 years ago, the UT had been considered sterile under normal conditions [7-11]. This perspective is now altered with the discovery of the genitourinary microbiome and the demonstration that most urinary bacteria identified by 16S sequencing can be cultured under expanded conditions [10,12]. As symptomatic UTI is the outcome of an altered UM makeup, some researchers have suggested that the terms “UTI” and “asymptomatic bacteriuria” be replaced by the term “dysbiosis” [14].
The relationship between UM and UTI is obvious and relatively well-studied. Several studies suggest that the microbial composition and diversity of the UM are related to the development of a UTI, with an association between decreased microbial diversity and the incidence of UTI [10,15-17]. Studies analyzing the UM reported that the UT is inhabited by a diverse bacterial community, with the predominant genera being
A study of patients with indwelling urinary catheters suggested that microbial diversity plays a protective role in the development of UTIs, which are caused by dysbiosis of the commensals [16]. However, the benefits of the HU2117
Yoo et al. [19] conducted a human bladder microbiome study to investigate the effect of
The majority of UM studies have focused on adult subjects, and pediatric reports are scarce. Mapping the UM in the pediatric population has just begun [12]. Kinneman et al. [20] assessed the UM in 85 children younger than 48 months, with and without UTI. They demonstrated that UM was identified in every child, and altered microbiome diversity and composition were observed in subjects with a standard culture-positive UTI. They also observed that antibiotic administration was effective in the UM only for a short time. Kassiri et al. [21] examined the UM in 20 prepubertal boys (aged 3 months-8 years; median age 15 months) with and without prior antibiotic exposure. The majority of patients presented with
(2) UUI and OAB: OAB is a poorly understood disorder, but is thought to be multifactorial and is believed to originate from abnormal neuromuscular signaling and functioning of the detrusor muscle [10,22]. In the pediatric population, OAB not only burdens the child’s development but also negatively impacts the family [12]. OAB is a condition where frequent urination is required, which often leads to UUI. The mechanisms of OAB are not fully elucidated, but there are potential links to the involvement of the microbiome. Since anticholinergics or beta-3 agonists that inhibit detrusor contraction and promote bladder relaxation are ineffective in many patients, this indicates other etiologies besides neuromuscular dysfunction, including UM [22,23].
Several studies of the UM in adults have been conducted in patients with UUI and OAB, and have reported significant differences in bacterial urine compositions between adult female UUI and healthy controls. These differences are reported to affect the symptom severity and treatment responses [15,23-25]. Compared to controls, patients with UUI exhibit higher
Other studies have investigated the clinical associations between UM and different UUI treatments. In 40% of UUI women treated with anticholinergics, there was minimal or no response [26]. The diversity of UM has been associated with the response to solifenacin for the treatment of UUI. The presence and number of cultivatable bacteria are directly correlated with the presence and severity of UUI [24,27]. Thomas-White et al. [24] found that a lower diversity of cultivatable bacteria is associated with a positive response to a low dose of solifenacin.
In summary, the studies published to date have demonstrated a clear role of the UM in adults with UUI/OAB, and in the response to UUI/OAB treatment. However, there is uncertainty about the possible associations between UM and OAB symptoms in the pediatric population due to a lack of reports concerning UM in pediatric UUI/OAB.
(3) Urinary stone: The role of the microbiome in urolithiasis is relatively well-established. Recently, numerous culture-independent UM studies have been published in an attempt to elucidate whether the UM contributes to urinary stone formation [28]. More recently, several studies have suggested that UM may play an important role in urinary stone formation [10]. Stern et al. [29] presented that compared to 6 controls, 23 patients with kidney stones had higher levels of
Up to 32% of calcium oxalate stones demonstrate bacterial growth when cultured. However, the cultured bacteria may be unique to the stone. Calcium oxalate stones have been shown to harbor a microbiome that is independent of the UM in children with urolithiasis [10]. Barr-Beare et al. [31] demonstrated significant bacterial diversity in children with calcium oxalate stones, including
Several studies revealed an inverse relationship between intestinal colonization with
However, there are still uncertainties about differences obtained in the results between studies due to experimental factors (such as sample collection, storage, DNA extraction, sequencing, or data analysis) or biological factors (such as geography, ethnicity, stone phenotype, or some other regional factors) [28].
Taken together, several studies proposed that bacteria present in calcium oxalate deposits contribute to calcium oxalate renal disease. Furthermore, the UM may play an important role in urinary stone formation in both children and adults.
(4) NB: It is well known that patients, especially children with NB, have a high risk of recurrent UTIs. UM variations were observed using 16S rRNA sequencing analysis for patients with NB and normal bladder function. Urine in the healthy control bladders was significantly predominant in
Groah et al. [36] demonstrated that the UM in patients with NB comprised uropathogenic bacteria, including
Dysbiosis of the microbiome contributes to carcinogenesis through several mechanisms, including DNA damage, production of carcinogenic metabolites, and stimulation of inflammation [38]. Numerous studies have focused on the relationship between the host microbiome and cancer susceptibility in systems other than the UT, such as gastric, colorectal, or hepatobiliary cancer [9,39]. However, the role of UM in UT cancers has yet to be elucidated. According to the reports of a few studies on urological cancers in adults thus far, UM is mainly associated with prostate cancer, bladder cancer, and renal cancer.
(1) Prostate cancer: Many pathogenic microorganisms including endogenous
However, unlike studies in adults, to date there are no reports on the relationship between UM and any prostate disease (including benign diseases and malignant tumors such as sarcoma) in children.
(2) Bladder cancer: Some studies have demonstrated that the UM is associated with bladder cancer transformation and metastatic progression. It has further been suggested that dysbiosis of the UM produces a chronically inflammatory urothelial microenvironment which leads to bladder cancer [45]. However, it remains unknown whether the UM affects the development or progression of bladder cancer, or whether bladder cancer is responsible for the alternation of the UM [6]. Some studies indicate that the bladder microbiome may change the extracellular matrix (ECM) to promote or inhibit urothelial carcinogenesis. The ECM regulates tissue homeostasis and maintains the onset and progression of cancer, including bladder cancer [6]. Conversely, Hayatsu and Hayatsu [46] reported that the
There is a well-documented association between chronic schistosomiasis and bladder squamous cell carcinoma [6,50,51]. Adebayo et al. [50] demonstrated that certain UM, such as
In terms of urothelial cell carcinoma (UCC), Xu et al. [52] studied the changes in the UM community of UCC patients in comparison to healthy individuals. They presented an enrichment of Streptococcus in urine in a preliminary study of the UM involving a small number of patients with UCC.
Unfortunately, unlike studies in adults, there has been no research in children to study the relationship between UM and bladder cancer or UCC.
(3) Renal cancer: Unlike UM studies in prostate cancer and bladder cancer in adults, very few studies have been conducted for renal cancer. In a recent study about the microbiome in 5 benign renal and malignant renal tissues in adults, Heidler et al. [53] are the first to demonstrate a plethora of microorganisms with significant differences between the two groups. They isolated 3 domains, 15 phyla, 16 classes, 19 orders, 27 families, 28 genera, and 30 species of microorganisms.
Unfortunately, there are no reports on the association between UM and renal cancer, especially Wilms’ tumor, in children.
(4) Other genitourinary cancers: There have been no studies associating UM and other genitourinary cancers, such as testis cancer, penile cancer, urethral cancer, etc., in both adults and children. Therefore, there needs to be an escalated interest in the UM study of these genitourinary cancers.
There have been recent attempts for the therapeutic application of probiotic microorganisms as a treatment of disease in clinical practice. Probiotics have also been applied to modify the intestinal microbiome. Various clinical trials, including fecal microbiota transplantation, have been performed to study the role of certain beneficial strains in UTI, bladder cancer, and urinary stone formation [9].
To date, antibacterial therapy is the primary basic management for UTIs in children. However, it is inevitable that the UM undergoes alterations during UTI and antibiotic therapy. Long-term use of broad-spectrum antibiotics negatively affects the beneficial bacterial flora in the host, with the consequential selective overgrowth of pathogenic bacteria, eventually resulting in bacterial resistance [54]. Therefore, probiotics such as
Recently, the relationship between dysbiosis and UTI suggests that altering the UM through the use of probiotics may impart therapeutic effects. Probiotics using commensal bacteria could serve as either alternatives or adjuvant options to antibiotics for preventing antibiotic resistance [10]. Trials of bacterial interference with probiotics of the HU2117
According to recent cancer studies in adults, probiotics such as the oral
Siener et al. [32] demonstrated that
Dietary factors such as cranberry, D-Mannos, and fermented milk products are also known to reduce the risk or incidence of recurrent UTIs by altering the properties of the genitourinary bacterial flora [57-60]. Therefore, dietary habits that may change the UM may be important factors associated with urological disorders, especially UTIs in children.
We are still in the early stages of understanding the role of UM in human health and genitourinary diseases, especially in pediatric patients. It is important for us to expand our knowledge of the impact of UM in urological areas, especially in children. New diagnostic technologies and therapeutic avenues on the UM in pediatric urological diseases will continue to advance our understanding of the impact of UM on pediatric health and disease. The newly elucidated role of UM in the pediatric urological area suggests that both probiotics and dietary modification probably exert a therapeutic influence on pediatric urological diseases, including recurrent UTI, UUI/OAB, NB, and urolithiasis.
Previous microbiome studies in the gut and non-urological, non-gut diseases in pediatrics (such as infantile colic, necrotizing enterocolitis, asthma, atopy, obesity, type-1 diabetes, autism, atopic dermatitis, psoriasis, bronchial asthma, caries, periodontitis, and chronic rhinosinusitis) can expose new strategies for the prevention and management of these diseases by several applications such as immunomodulatory, anti-inflammatory, or growth-promoting action and antibacterial substances production [5]. More prospective research unearthing the characterization of the human microbiome in the pediatric urological area might help to develop new microbiome-based biomarkers to provide information about the diagnosis, disease severity, or treatment response, and also utilize these bacterial derivatives as therapeutic or preventive agents to control various pediatric urological diseases [9].
The UM and its relationship to UT diseases are currently under comprehensive investigation. Recently, improved techniques such as EQUC and high throughput molecular DNA sequencing of bacterial 16S rRNA genes have resulted in the discovery of a significant and diverse microbiome. However, there are insufficient studies evaluating the role of UM in the pediatric urological area. It is also important to consider the variations observed in the bacterial, fungal, and viral genera described for the UM in different studies; this could be attributed to differences in the gender, sample size, and urine collection methods and techniques used to study the UM [9].
Since initiation of the HMP, it is now known that urine is not sterile. The differences in the UM between healthy individuals and urological patients suggest that urinary dysbiosis may constitute an etiological factor in several urological disorders in both children and adults, with potential diagnostic and therapeutic implications in the near future.
Further larger scale, well-designed, prospective investigations to characterize the pediatric urological UM are required. This will enable the development of new microbiome-based biomarkers for the diagnosis and treatment, and also new microbiome-based-bacterial derivatives as therapeutic or preventive agents to control various pediatric urological diseases.
This study was supported by a 2-year basic research grant from Pusan National University (Mar. 2021 - Feb. 2023), Busan, Korea.
No potential conflict of interest relevant to this article was reported.
S.D.L. participated in data collection and analysis and wrote the manuscript. J.M.C. participated in the study design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.