Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection

Comparison of the urinary microbiome in men who have sex with men with and without Chlamydia trachomatis infection

PURPOSE

The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.

METHODS

This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.

RESULTS

Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385).

CONCLUSION

Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.

Metagenome-based microbial community analysis of urine-derived fertilizer

Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH3PO4.6H2O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture.

From Awareness to Action: Pioneering Solutions for Women's UTI Challenges in the Era of Precision Medicine

This article aims to bring clinicians' awareness to the widespread impact of urinary tract infection (UTI) on the lives of women and to the advances that offer hope for future improvements in the diagnosis and management of UTI. Thanks to physiological, anatomical, and lifestyle factor differences, women face heightened vulnerability to UTIs compared to men. In fact, women are four times more likely than men to develop a UTI and around half of these women encounter UTI recurrence, which is a significant source of both physical and psychosocial burdens. Despite the current shortcomings in diagnosis and management, emerging diagnostic technologies promise to identify UTIs more accurately and rapidly, offering women hope for a revolution in UTI management. Meanwhile, clinicians have the opportunity to reduce the psychosocial burden by recognizing the value of patients' lived experiences and ensuring their care plan is in alignment with their patients' goals and expectations for medical care.

Association between Urinary Flora and Urinary Stones

BACKGROUND

Urinary system stones are a common clinical disease, with significant differences in incidence and recurrence rates between different countries and regions. The etiology and pathogenesis of urinary system stones have not been fully elucidated, but many studies have found that some bacteria and fungi that are difficult to detect in urine constitute a unique urinary microbiome. This special urinary microbiome is closely related to the occurrence and development of urinary system stones. By analyzing the urinary microbiome and its metabolic products, early diagnosis and treatment of urinary system stones can be carried out.

SUMMARY

This article reviews the relationship between the urinary microbiome and urinary system stones, discusses the impact of the microbiome on the formation of urinary system stones and its potential therapeutic value, with the aim of providing a reference for the early diagnosis, prevention, and treatment of urinary system stones.

KEY MESSAGES

(i) Urinary stones are a common and recurrent disease, and there is no good way to prevent them. (ii) With advances in testing technology, studies have found that healthy human urine also contains various types of bacteria. (iii) Is there a potential connection between the urinary microbiota and urinary stones, and if so, can understanding these connections offer fresh perspectives and strategies for the diagnosis, treatment, and prevention of urinary stones?

Insights into the Interplay between the Urinary Microbiome and Bladder Cancer: A Comprehensive Review

New insights in the urinary microbiome have led to a better understanding being built of the shifts in bacterial representations from health to disease; these hold promise as markers for diagnosis and therapeutic responses. Although several efforts have been made to identify a "core urinary microbiome", different fingerprints have been identified in men and women that shift with age. The main bacterial groups overall include Firmicutes, Actinobacteria, Fusobacteria, and Bacteroidetes. Although patients with bladder cancer have a microbiome that is similar to that of healthy individuals, differences have been observed at the species level with Fusobacterium nucleatum and Ralstonia, and at the genus level with Cutibacterium. Different bacterial representations may influence extracellular matrix composition, affecting tumor metastatic spreading and tumorigenic metalloproteinase expression. Furthermore, gene expression affecting targets of immune therapy, such as PD-L1, has been associated with changes in bacterial representations and therapeutic response to BCG. This comprehensive review aims to examine the influence of the urinary microbiome in bladder cancer.

Navigating the microbial maze: unraveling the connection between gut microbiome and pediatric kidney and urinary tract disease

The gut microbiome is made up of trillions of bacteria, viruses, archaea, and microbes that play a significant role in the maintenance of normal physiology in humans. Recent research has highlighted the effects of the microbiome and its dysbiosis in the pathogenesis and maintenance of kidney disease, especially chronic kidney disease (CKD) and its associated cardiovascular disease. While studies have addressed the kidney-microbiome axis in adults, how dysbiosis may uniquely impact pediatric kidney disease patients is not well-established. This narrative review highlights all relevant studies focusing on the microbiome and pediatric kidney disease that were published between 7/2015 and 7/2023. This review highlights pediatric-specific considerations including growth and bone health as well as emphasizing the need for increased pediatric research. Understanding microbiome-kidney interactions may allow for novel, less invasive interventions such as dietary changes and the use of probiotics to improve preventive care and ameliorate long-term morbidity and mortality in this vulnerable population.

Resident Microbiome of Kidney Tumors

Emerging research has uncovered the significance of microbiota in carcinogenesis, with specific bacterial infectious agents linked to around 15% of malignant tumors. This review is focused on the resident kidney microbiome, its composition, and alterations in various diseases. Recent studies have shown that bacteria can infiltrate the kidney, with differences between normal and tumor tissue. These studies have identified distinctive microorganisms unique to both conditions, hinting at their potential clinical relevance. Research into the kidney microbiome diversity reveals differences in tumor tissue, with specific taxa associated with different histological types. Notably, the alpha diversity indices suggest variations in bacterial content between tumor and normal tissue, offering insights into potential diagnostic and prognostic use of these markers. Better studied is the impact of the gut microbiome on therapy efficacy in malignant kidney tumors. Antibiotics, which can alter the gut microbiome, have been linked to survival outcomes in patients receiving targeted therapy and immunotherapy. The findings suggest that the uncontrolled use of antibiotics may not only contribute to bacterial resistance but also disrupt the normal microbiome, potentially influencing the development of oncological diseases. In-depth investigation into the resident kidney microbiome is essential for addressing fundamental and practical aspects of kidney tumor development.

Characterization of Neisseria gonorrhoeae colonization of macrophages under distinct polarization states and nutrients environment

Neisseria gonorrhoeae (Ng) is a uniquely adapted human pathogen and the etiological agent of gonorrhea, a sexually transmitted disease. Ng has developed numerous mechanisms to avoid and actively suppress innate and adaptive immune responses. Ng successfully colonizes and establishes topologically distinct colonies in human macrophages and avoids phagocytic killing. During colonization, Ng manipulates the actin cytoskeleton to invade and create an intracellular niche supportive of bacterial replication. The cellular reservoir(s) supporting bacterial replication and persistence in gonorrhea infections are poorly defined. The manner in which gonococci colonize macrophages points to this innate immune phagocyte as a strong candidate for a cellular niche during natural infection. Here we investigate whether nutrients availability and immunological polarization alter macrophage colonization by Ng. Differentiation of macrophages in pro-inflammatory (M1-like) and tolerogenic (M2-like) phenotypes prior to infection reveals that Ng can invade macrophages in all activation states, albeit with lower efficiency in M1-like macrophages. These results suggest that during natural infection, bacteria could invade and grow within macrophages regardless of the nutrients availability and the macrophage immune activation status.

Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance

Random forests have emerged as a promising tool in comparative metagenomics because they can predict environmental characteristics based on microbial composition in datasets where β-diversity metrics fall short of revealing meaningful relationships between samples. Nevertheless, despite this efficacy, they lack biological insight in tandem with their predictions, potentially hindering scientific advancement. To overcome this limitation, we leverage a geometric characterization of random forests to introduce a data-driven phylogenetic β-diversity metric, the adaptive Haar-like distance. This new metric assigns a weight to each internal node (i.e., split or bifurcation) of a reference phylogeny, indicating the relative importance of that node in discerning environmental samples based on their microbial composition. Alongside this, a weighted nearest-neighbors classifier, constructed using the adaptive metric, can be used as a proxy for the random forest while maintaining accuracy on par with that of the original forest and another state-of-the-art classifier, CoDaCoRe. As shown in datasets from diverse microbial environments, however, the new metric and classifier significantly enhance the biological interpretability and visualization of high-dimensional metagenomic samples.

The microbiota and renal cell carcinoma

Renal cell carcinoma (RCC) accounts for about 2% of cancer diagnoses and deaths worldwide. Recent studies emphasized the critical involvement of microbial populations in RCC from oncogenesis, tumor growth, and response to anticancer therapy. Microorganisms have been shown to be involved in various renal physiological and pathological processes by influencing the immune system function, metabolism of the host and pharmaceutical reactions. These findings have extended our understanding and provided more possibilities for the diagnostic or therapeutic development of microbiota, which could function as screening, prognostic, and predictive biomarkers, or be manipulated to prevent RCC progression, boost anticancer drug efficacy and lessen the side effects of therapy. This review aims to present an overview of the roles of microbiota in RCC, including pertinent mechanisms in microbiota-related carcinogenesis, the potential use of the microbiota as RCC biomarkers, and the possibility of modifying the microbiota for RCC prevention or treatment. According to these scientific findings, the clinical translation of microbiota is expected to improve the diagnosis and treatment of RCC.

The elusive male microbiome: revealing the link between the genital microbiota and fertility. Critical review and future perspectives

There is a growing focus on understanding the role of the male microbiome in fertility issues. Although research on the bacterial communities within the male reproductive system is in its initial phases, recent discoveries highlight notable variations in the microbiome's composition and abundance across distinct anatomical regions like the skin, foreskin, urethra, and coronary sulcus. To assess the relationship between male genitourinary microbiome and reproduction, we queried various databases, including MEDLINE (available via PubMed), SCOPUS, and Web of Science to obtain evidence-based data. The literature search was conducted using the following terms "gut/intestines microbiome," "genitourinary system microbiome," "microbiome and female/male infertility," "external genital tract microbiome," "internal genital tract microbiome," and "semen microbiome." Fifty-one relevant papers were analyzed, and eleven were strictly semen quality or male fertility related. The male microbiome, especially in the accessory glands like the prostate, seminal vesicles, and bulbourethral glands, has garnered significant interest because of its potential link to male fertility and reproduction. Studies have also found differences in bacterial diversity present in the testicular tissue of normozoospermic men compared to azoospermic suggesting a possible role of bacterial dysbiosis and reproduction. Correlation between the bacterial taxa in the genital microbiota of sexual partners has also been found, and sexual activity can influence the composition of the urogenital microbiota. Exploring the microbial world within the male reproductive system and its influence on fertility opens doors to developing ways to prevent, diagnose, and treat infertility. The present work emphasizes the importance of using consistent methods, conducting long-term studies, and deepening our understanding of how the reproductive tract microbiome works. This helps make research comparable, pinpoint potential interventions, and smoothly apply microbiome insights to real-world clinical practices.

The Role of Metabolomics and Microbiology in Urinary Tract Infection

One of the common illnesses that affect women's physical and mental health is urinary tract infection (UTI). The disappointing results of empirical anti-infective treatment and the lengthy time required for urine bacterial culture are two issues. Antibiotic misuse is common, especially in females who experience recurrent UTI (rUTI). This leads to a higher prevalence of antibiotic resistance in the microorganisms that cause the infection. Antibiotic therapy will face major challenges in the future, prompting clinicians to update their practices. New testing techniques are making the potential association between the urogenital microbiota and UTIs increasingly apparent. Monitoring changes in female urinary tract (UT) microbiota, as well as metabolites, may be useful in exploring newer preventive treatments for UTIs. This review focuses on advances in urogenital microbiology and organismal metabolites relevant to the identification and handling of UTIs in an attempt to provide novel methods for the identification and management of infections of the UT. Particular attention is paid to the microbiota and metabolites in the patient's urine in relation to their role in supporting host health.

The urogenital microbiome in chronic kidney disease patients on peritoneal dialysis

INTRODUCTION AND OBJECTIVES

Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters.

MATERIALS AND METHODS

Mid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3-V4 region of the bacterial 16S rRNA gene. Correlations with the patients' clinical data and inflammatory profile were performed.

RESULTS

CKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups. Depletion of Gardnerella, Staphylococcus, Corynebacterium, Lactobacillus or Dermabacter populations correlated with CKD-PD patients with history of diabetes, history of peritonitis and altered levels of sCD14.

CONCLUSIONS

Our results highlight urogenital microbiome as a potential partner and/or marker in the overall health state of CKD-PD patients.

Characterization of Neisseria gonorrhoeae colonization of macrophages under distinct polarization states and nutrients environment

Neisseria gonorrhoeae (Ng) is a uniquely adapted human pathogen and the etiological agent of gonorrhea, a sexually transmitted disease. Ng has developed numerous mechanisms to avoid and actively suppress innate and adaptive immune responses. Ng successfully colonizes and establishes topologically distinct colonies in human macrophages and avoids phagocytic killing. During colonization, Ng manipulates the actin cytoskeleton to invade and create an intracellular niche supportive of bacterial replication. The cellular reservoir(s) supporting bacterial replication and persistence in gonorrhea infections are poorly defined. The manner in which gonococci colonize macrophages points to this innate immune phagocyte as a strong candidate for a cellular niche during natural infection. Here we investigate whether nutrients availability and immunological polarization alter macrophage colonization by Ng . Differentiation of macrophages in pro-inflammatory (M1-like) and tolerogenic (M2-like) phenotypes prior to infection reveals that Ng can invade macrophages in all activation states, albeit with lower efficiency in M1-like macrophages. These results suggest that during natural infection, bacteria could invade and grow within macrophages regardless of the nutrients availability and the macrophage immune activation status.

The Urinary Microbiome in Health and Disease: Relevance for Bladder Cancer

Bladder cancer (BC) constitutes one of the most diagnosed types of cancer worldwide. Advancements in and new methodologies for DNA sequencing, leading to high-throughput microbiota testing, have pinpointed discrepancies in urinary microbial fingerprints between healthy individuals and patients with BC. Although several studies suggest an involvement of microbiota dysbiosis in the pathogenesis, progression, and therapeutic response to bladder cancer, an established direct causal relationship remains to be elucidated due to the lack of standardized methodologies associated with such studies. This review compiles an overview of the microbiota of the human urinary tract in healthy and diseased individuals and discusses the evidence to date on microbiome involvement and potential mechanisms by which the microbiota may contribute to the development of BC. We also explore the potential profiling of urinary microbiota as a biomarker for risk stratification, as well as the prediction of the response to intravesical therapies and immunotherapy in BC patients. Further investigation into the urinary microbiome of BC patients is imperative to unravel the complexities of the role played by host-microbe interactions in shaping wellness or disease and yield valuable insights into and strategies for the prevention and personalized treatment of BC.

BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men

Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS), however, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65 to 90 years from the Osteoporotic Fractures in Men (MrOS) study. We identified significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis revealed complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome. By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.

Urinary tract infections: a review of the current diagnostics landscape

Urinary tract infections are the most common bacterial infections worldwide. Infections can range from mild, recurrent (rUTI) to complicated (cUTIs), and are predominantly caused by uropathogenic Escherichia coli (UPEC). Antibiotic therapy is important to tackle infection; however, with the continued emergence of antibiotic resistance there is an urgent need to monitor the use of effective antibiotics through better stewardship measures. Currently, clinical diagnosis of UTIs relies on empiric methods supported by laboratory testing including cellular analysis (of both human and bacterial cells), dipstick analysis and phenotypic culture. Therefore, development of novel, sensitive and specific diagnostics is an important means to rationalise antibiotic therapy in patients. This review discusses the current diagnostic landscape and highlights promising novel diagnostic technologies in development that could aid in treatment and management of antibiotic-resistant UTIs.

The urobiome in men and women: a clinical review

BACKGROUND

Antibiotic therapy alone is unable to control recurrent urinary tract infection (UTI); uropathogens have become multiresistant, and alternative strategies are needed. Far from sterile, the urinary tract contains various low-biomass microbiota, some of whose members appear to protect against clinical UTI.

OBJECTIVES

This narrative review summarizes (a) the current knowledge of male and female urobiomes in healthy and diseased states, as well as their interplay among sexual partners and (b) clinical trials to date assessing probiotic and other nonantibiotic measures to reduce UTI.

SOURCES

We used the PubMed interface to search Ovid Medline for articles describing urogenital flora, UTI, UTI dysbiosis, the effects of sexual intercourse on urogenital flora, and clinical trials of probiotics as UTI prophylaxis.

CONTENT

The healthy urobiome of women contains several Lactobacillus species, some of which may impede Escherichia coli growth in the urinary tract. Although Lactobacilli have been found in male urethral microbiota, their presence in male bladder microbiota is less certain. Distal male urethral and vaginal microbiomes of male and sexual female partners influence one another, but more research is needed on the direct interplay of their full urobiomes. Clinical trials assessing the therapeutic potential of Lactobacilli have been largely underpowered and highly varied in tested formulations and routes and frequencies of administration; as such, they have failed to show a clear benefit. Faecal microbiota transplantation for recurrent Clostridium difficile infection was shown, in a retrospective study of seven patients, to reduce recurrent UTI as a side effect.

IMPLICATIONS

The urobiome in men and women is complex, variable, and still understudied. Although there is hope that Lactobacilli and faecal microbial transplantation could be future nonantibiotic options for recurrent UTI, both require more pharmacologic and clinical research to identify optimal preparations and routes of administration.

Dissecting Microbiome-Derived SCFAs in Prostate Cancer: Analyzing Gut Microbiota, Racial Disparities, and Epigenetic Mechanisms

Prostate cancer (PCa) continues to be the most diagnosed cancer and the second primary cause of fatalities in men globally. There is an abundance of scientific evidence suggesting that the human microbiome, together with its metabolites, plays a crucial role in carcinogenesis and has a significant impact on the efficacy of anticancer interventions in solid and hematological cancers. These anticancer interventions include chemotherapy, immune checkpoint inhibitors, and targeted therapies. Furthermore, the microbiome can influence systemic and local immune responses using numerous metabolites such as short-chain fatty acids (SCFAs). Despite the lack of scientific data in terms of the role of SCFAs in PCa pathogenesis, recent studies show that SCFAs have a profound impact on PCa progression. Several studies have reported racial/ethnic disparities in terms of bacterial content in the gut microbiome and SCFA composition. These studies explored microbiome and SCFA racial/ethnic disparities in cancers such as colorectal, colon, cervical, breast, and endometrial cancer. Notably, there are currently no published studies exploring microbiome/SCFA composition racial disparities and their role in PCa carcinogenesis. This review discusses the potential role of the microbiome in PCa development and progression. The involvement of microbiome-derived SCFAs in facilitating PCa carcinogenesis and their effect on PCa therapeutic response, particularly immunotherapy, are discussed. Racial/ethnic differences in microbiome composition and SCFA content in various cancers are also discussed. Lastly, the effects of SCFAs on PCa progression via epigenetic modifications is also discussed.

Urogenital urobiome of healthy children does not differ from that of children with bladder and bowel dysfunction

INTRODUCTION

The pediatric urinary microbiome (urobiome) has been studied in the context of healthy children and children with genitourinary pathologies including neuropathic bladder, urinary tract infection (UTI) and nephrolithiasis. Little is known about the urobiome of children with bladder and bowel dysfunction (BBD), a condition that is an established risk factor of UTI. We hypothesized that the symptoms of a child with BBD may be related to urobiome composition.

OBJECTIVE

To evaluate the urogenital urobiome's role in BBD, we compared the urogenital urobiomes of children with and without BBD.

STUDY DESIGN

We performed a prospective case-control pilot study at a single large, academic children's hospital. Cases included toilet trained prepubertal females over 2 years of age with BBD established through a validated scoring system and controls included asymptomatic, presumably healthy, children. Children were excluded if they had symptoms or lab work consistent with a concurrent UTI or antibiotic course for any reason within the prior 14 days. We performed 16 S ribosomal RNA gene sequencing and expanded quantitative urine culture on clean catch urine samples. To compare within sample (alpha) diversity, we used the Kruskal-Wallis test. To compare between sample (beta) diversity, we calculated the Bray-Curtis distance and performed the PERMANOVA test.

RESULTS

Data from 25 children with BBD and 8 asymptomatic controls were analyzed. The demographic and clinical characteristics of the two comparison groups were similar, though a higher proportion of Black children were included in the asymptomatic control group. Neither alpha diversity nor beta diversity was significantly different between the two groups. The core microbiome of the BBD group included all the genera in the core urogenital urobiome of the controls, plus additional genera associated with opportunistic infection and/or UTI, including Escherichia, Campylobacter and Streptococcus.

DISCUSSION

The results of both the 16 S sequencing and expanded quantitative urine culture in this small study suggest that the urogenital urobiomes of children with BBD do not differ significantly from those of asymptomatic children. However, the core urogenital urobiome of children with BBD included genera associated with opportunistic infection and/or UTI. This study was limited by the sample collection method ("clean catch" midstream voided urine samples, which introduce the possibility of vulvovaginal contamination), small sample size, and unequal balance of patient characteristics between the two study groups.

CONCLUSION

The urogenital urobiomes of children with and without BBD do not appear to significantly differ. Larger studies are needed to confirm these findings.

Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study

BACKGROUND

Despite more than 60 years of research, the etiology of bacterial vaginosis (BV) remains controversial. In this pilot study, we used shotgun metagenomic sequencing to characterize vaginal microbial community changes before the development of incident BV (iBV).

METHODS

A cohort of African American women with a baseline healthy vaginal microbiome (no Amsel criteria, Nugent score 0-3 with no Gardnerella vaginalis morphotypes) were followed for 90 days with daily self-collected vaginal specimens for iBV (≥2 consecutive days of a Nugent score of 7-10). Shotgun metagenomic sequencing was performed on select vaginal specimens from 4 women, every other day for 12 days before iBV diagnosis. Sequencing data were analyzed through Kraken2 and bioBakery 3 workflows, and specimens were classified into community state types. Quantitative polymerase chain reaction was performed to compare the correlation of read counts with bacterial abundance.

RESULTS

Common BV-associated bacteria such as G. vaginalis , Prevotella bivia , and Fannyhessea vaginae were increasingly identified in the participants before iBV. Linear modeling indicated significant increases in G. vaginalis and F . vaginae relative abundance before iBV, whereas the relative abundance of Lactobacillus species declined over time. The Lactobacillus species decline correlated with the presence of Lactobacillus phages. We observed enrichment in bacterial adhesion factor genes on days before iBV. There were also significant correlations between bacterial read counts and abundances measured by quantitative polymerase chain reaction.

CONCLUSIONS

This pilot study characterizes vaginal community dynamics before iBV and identifies key bacterial taxa and mechanisms potentially involved in the pathogenesis of iBV.

In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract

The urogenital microbiota is the potential principal factor in the pathophysiology of urinary tract infection and the protection of urinary tract health. Little is known about the urogenital archaeome although several reports have indicated that the archaeomes of various regions of the human body are associated with health. Accordingly, we aimed to determine the presence and diversity of archaeomes in the human urogenital tract. To explore the urogenital archaeome, voided urine specimens from 373 asymptomatic Korean individuals were used. No difference was observed in body mass index, age, or gender, according to presence of archaea. Analysis of archaeal 16S rRNA gene amplicons of archaea positive samples consisted of simple community structures, including diverse archaea, such as the phyla Methanobacteriota, Thermoproteota, and Halobacteriota. Asymptomatic individuals showed high participant-dependent intervariability in their urogenital archaeomes. The mean relative archaeal abundance was estimated to be 0.89%, and fluorescence in situ hybridisation micrographs provided evidence of archaeal cells in the human urogenital tract. In addition, the urogenital archaeome shared partial taxonomic compositional characteristics with those of the other body sites. In this study, Methanobacteriota, Thermoproteota, and Halobacteriota were suggested as inhabitants of the human urogenital tract, and a distinct human urogenital archaeome was characterised. These findings expand our knowledge of archaea-host associations in the human urogenital tract and may lead to novel insights into the role of archaea in urinary tract health.

A Case of Urinary Tract Infection Caused by Multidrug Resistant Streptococcus mitis/oralis

S. mitis/oralis has been previously reported in isolated cases of bacterial endocarditis and liver abscesses. Its presence in urine is generally considered a contaminant. A 66-year-old male patient was admitted to the hospital due to recurrent chest tightness and four-year history of exertional dyspnea. On the second day of admission, the patient presented with urgent and frequent urination, as well as dysuria. Both initial and subsequent urine cultures showed S. mitis/oralis infection, with polymorphonuclear leukocyte phagocytosis observed in the second sample. MALDI-TOF results confirmed the isolated strain as S. mitis/oralis. Drug susceptibility testing revealed multidrug resistance to penicillin, ceftriaxone, cefepime, levofloxacin, ofloxacin, and tetracycline, but sensitivity to quinupristin/dalfopristin, vancomycin, and linezolid. The clinician then prescribed vancomycin for anti-infective treatment, which proved effective. Keywords: S. mitis/oralis, UTI, MDR, phagocytosis.

Urinary Tract Infection and Microbiome

Urinary tract infection is one of the most common bacterial infections and can cause major burdens, not only to individuals but also to an entire society. Current knowledge of the microbial communities in the urinary tract has increased exponentially due to next-generation sequencing and expanded quantitative urine culture. We now acknowledge a dynamic urinary tract microbiome that we once thought was sterile. Taxonomic studies have identified the normal core microbiota of the urinary tract, and studies on the changes in microbiome due to sexuality and age have set the foundation for microbiome studies in pathologic states. Urinary tract infection is not only caused by invading uropathogenic bacteria but also by changes to the uromicrobiome milieu, and interactions with other microbial communities can also contribute. Recent studies have provided insights into the pathogenesis of recurrent urinary tract infections and antimicrobial resistance. New therapeutic options for urinary tract infections also show promise; however, further research is needed to fully understand the implications of the urinary microbiome in urinary tract infections.

Insights into the Human Microbiome and Its Connections with Prostate Cancer

The human microbiome represents the diversity of microorganisms that live together at different organ sites, influencing various physiological processes and leading to pathological conditions, even carcinogenesis, in case of a chronic imbalance. Additionally, the link between organ-specific microbiota and cancer has attracted the interest of numerous studies and projects. In this review article, we address the important aspects regarding the role of gut, prostate, urinary and reproductive system, skin, and oral cavity colonizing microorganisms in prostate cancer development. Various bacteria, fungi, virus species, and other relevant agents with major implications in cancer occurrence and progression are also described. Some of them are assessed based on their values of prognostic or diagnostic biomarkers, while others are presented for their anti-cancer properties.

Sexual behavior shapes male genitourinary microbiome composition

The origin, composition, and significance of the distal male urethral microbiome are unclear, but vaginal microbiome dysbiosis is linked to new sex partners and several urogynecological syndromes. We characterized 110 urethral specimens from men without urethral symptoms, infections, or inflammation using shotgun metagenomics. Most urethral specimens contain characteristic lactic acid bacteria and Corynebacterium spp. In contrast, several bacteria associated with vaginal dysbiosis were present only in specimens from men who reported vaginal intercourse. Sexual behavior, but not other evaluated behavioral, demographic, or clinical variables, strongly associated with inter-specimen variance in urethral microbiome composition. Thus, the male urethra supports a simple core microbiome that is established independent of sexual exposures but can be re-shaped by vaginal sex. Overall, the results suggest that urogenital microbiology and sexual behavior are inexorably intertwined, and show that the male urethra harbors female urogenital pathobionts.

The Association of Prostate Cancer and Urinary Tract Infections: A New Perspective of Prostate Cancer Pathogenesis

Background and objectives: Microbiota of the urinary tract may be associated with urinary tract malignancy, including prostate cancer. Materials and Methods: We retrospectively collected patients with newly diagnosed prostate cancer and subjects without prostate cancer from the National Health Insurance Research Database (NHIRD) in Taiwan between 1 January 2000 and 31 December 2016. A total of 5510 subjects were recruited and followed until the diagnosis of a primary outcome (urinary tract infection, pyelonephritis, cystitis, and prostatitis). Results: We found that the patients with prostate cancer had a significantly higher risk of urinary tract infections than those without prostate cancer. The adjusted hazard ratios for pyelonephritis, prostatitis, and cystitis were 2.30 (95% CI = 1.36–3.88), 2.04 (95% CI = 1.03–4.05), and 4.02 (95 % CI = 2.11–7.66), respectively. We clearly identified the sites of infection and associated comorbidities in the prostate cancer patients with urinary tract infections. In addition, we found that the patients receiving radiotherapy and androgen deprivation therapy had a lower risk of urinary tract infections than the patients in corresponding control groups. Conclusions: Our study suggests that an abnormal urine microbiome could potentially contribute to the development of prostate cancer through inflammation and immune dysregulation. Furthermore, an imbalanced microbiome may facilitate bacterial overgrowth in urine, leading to urinary tract infections. These findings have important implications for the diagnosis and treatment of prostate cancer. Further research is needed to better understand the role of the urine microbiome in prostate cancer pathogenesis and to identify potential microbiome-targeted therapies for the prevention and treatment of prostate cancer.

Gut dysbiosis contributes to chlamydial induction of hydrosalpinx in the upper genital tract

Chlamydia trachomatis is one of the most common sexually infections that cause infertility, and its genital infection induces tubal adhesion and hydrosalpinx. Intravaginal Chlamydia muridarum infection in mice can induce hydrosalpinx in the upper genital tract and it has been used for studying C. trachomatis pathogenicity. DBA2/J strain mice were known to be resistant to the chlamydial induction of hydrosalpinx. In this study, we took advantage of this feature of DBA2/J mice to evaluate the role of antibiotic induced dysbiosis in chlamydial pathogenicity. Antibiotics (vancomycin and gentamicin) were orally administrated to induce dysbiosis in the gut of DBA2/J mice. The mice with or without antibiotic treatment were evaluated for gut and genital dysbiosis and then intravaginally challenged by C. muridarum. Chlamydial burden was tested and genital pathologies were evaluated. We found that oral antibiotics significantly enhanced chlamydial induction of genital hydrosalpinx. And the antibiotic treatment induced severe dysbiosis in the GI tract, including significantly reduced fecal DNA and increased ratios of firmicutes over bacteroidetes. The oral antibiotic did not alter chlamydial infection or microbiota in the mouse genital tracts. Our study showed that the oral antibiotics-enhanced hydrosalpinx correlated with dysbiosis in gut, providing the evidence for associating gut microbiome with chlamydial genital pathogenicity.

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.

Microbiota of female genital tract – functional overview of microbial flora from vagina to uterine tubes and placenta

Microorganisms and eukaryotic human cells coexist in synergistic relationships in nearly every niche of the human body. The female genital tract consisting of the vagina, uterus with its cervix and endometrium, uterine tubes and ovaries – harbors its own typical microbiota, which accounts for 9 % of the total bacterial population in females. To this organ system, we also assigned the microbiome of the placenta, which has not been studied much until now. Among the spectrum of microbial species, the female genital tract is mainly dominated by Lactobacillus species, which are considered to be one of the simplest yet most important microbial communities. However, this relationship between macro- and micro-organisms seems to have a number of physiological functions, e.g., the vaginal and cervical microbiota have unique impact on reproductive health. The aim of this review was to provide current view on female genital tract microbiota and its role in reproductive health. We describe in detail the association of vaginal or tubal epithelium with microbiota or the role of microbiota in normal placental function.

Microbiota of female genital tract - functional overview of microbial flora from vagina to uterine tubes and placenta

Microorganisms and eukaryotic human cells coexist in synergistic relationships in nearly every niche of the human body. The female genital tract consisting of the vagina, uterus with its cervix and endometrium, uterine tubes and ovaries - harbors its own typical microbiota, which accounts for 9 % of the total bacterial population in females. To this organ system, we also assigned the microbiome of the placenta, which has not been studied much until now. Among the spectrum of microbial species, the female genital tract is mainly dominated by Lactobacillus species, which are considered to be one of the simplest yet most important microbial communities. However, this relationship between macro- and micro-organisms seems to have a number of physiological functions, e.g., the vaginal and cervical microbiota have unique impact on reproductive health. The aim of this review was to provide current view on female genital tract microbiota and its role in reproductive health. We describe in detail the association of vaginal or tubal epithelium with microbiota or the role of microbiota in normal placental function.

Microbiome in Male Genital Mucosa (Prepuce, Glans, and Coronal Sulcus): A Systematic Review

The human body represents a complex and diverse reservoir of microorganisms. Although the human microbiome remains poorly characterized and understood, it should not be underestimated, since recent studies have highlighted its importance in health. This is especially evident when considering microbiota in the male reproductive system, responsible for men’s fertility and sexual behavior. Therefore, the aim of this systematic review is to provide an overview of the microbial communities of the healthy male genital mucosa and its role in disease. This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was limited to the English language and studies published until August 2022 that included culture-independent techniques for microbiome characterization in male genital mucosa. Ten articles were included. The bacterial composition of the male genital mucosa consists of several genera including Prevotella, Finegoldia, Peptoniphilus, Staphylococcus, Corynebacterium, and Anaerococcus, suggesting that the male genital microbiome composition shows similarities with the adjacent anatomical sites and is related with sexual intercourse. Moreover, male circumcision appears to influence the penile microbiome. Despite the lack of knowledge on the male genital mucosa microbiome in disease, it was reported that Staphylococcus warneri and Prevotella bivia were associated with balanoposthitis, whereas Enterobacteriaceae, Prevotella, and Fusobacterium were more abundant in male genital lichen sclerosus. The limited data and paucity of prospective controlled studies highlight the need for additional studies and established criteria for sampling methods and the microbiome assay procedure. Such a consensus would foster the knowledge about the composition of the genital microbiome of healthy males and its role in disease.

The Oncobiome in Gastroenteric and Genitourinary Cancers

Early evidence suggests a strong association of microorganisms with several human cancers, and great efforts have been made to understand the pathophysiology underlying microbial carcinogenesis. Bacterial dysbiosis causes epithelial barrier failure, immune dysregulation and/or genotoxicity and, consequently, creates a tumor-permissive microenvironment. The majority of the bacteria in our body reside in the gastrointestinal tract, known as gut microbiota, which represents a complex and delicate ecosystem. Gut microbes can reach the pancreas, stomach and colon via the bloodstream. Oral bacterial translocations can also occur. In the stomach, pancreas and colon, low microbial diversity is associated with cancer, in particular with a bad prognosis. The urogenital tract also harbors unique microbiota, distinct from the gut microbiota, which might have a role in the urinary and female/male reproductive cancers’ pathogenesis. In healthy women, the majority of bacteria reside in the vagina and cervix and unlike other mucosal sites, the vaginal microbiota exhibits low microbial diversity. Genital dysbiosis might have an active role in the development and/or progression of gynecological malignancies through mechanisms including modulation of oestrogen metabolism. Urinary dysbiosis may influence the pathogenesis of bladder cancer and prostate cancer in males. Modulation of the microbiome via pre, pro and postbiotics, fecal or vaginal microbiota transplantation and engineering bacteria might prove useful in improving cancer treatment response and quality of life. Elucidating the complex host-microbiome interactions will result in prevention and therapeutic efficacy interventions.

The Potential Role of Urinary Microbiome in Benign Prostate Hyperplasia/Lower Urinary Tract Symptoms

Historically, urine in the urinary tract was considered “sterile” based primarily on culture-dependent methods of bacterial detection. Rapidly developing sequencing methods and analytical techniques have detected bacterial deoxyribonucleic acid and live bacteria in urine, improving our ability to understand the urinary tract microbiome. Recently, many studies have revealed evidence of a microbial presence in human urine in the absence of clinical infections. In women, fascinating evidence associates urinary tract microbiota with lower urinary tract symptoms (LUTS). However, the association between urinary tract microbiota and men with LUTS, particularly those with benign prostate hyperplasia (BPH), has not been established. In addition, the identification of the proinflammatory cytokines and pathogens responsible for the clinical progression of BPH is still underway. This review article aimed to address microbiome-related evidence for BPH. Further studies are required for a comprehensive understanding of the relationship between the urogenital microbiome and BPH pathogenesis to facilitate the development of preventive and therapeutic approaches for male LUTS.

Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer

Apart from other risk factors, chronic inflammation is also associated with the onset of Prostate Cancer (PCa), wherein pathogen infection and tissue microbiome dysbiosis are known to play a major role in both inflammatory response and cancer development. However, except for a few studies, the link between microbes and PCa remained poorly understood. To explore the potential microbiome signature associated with PCa in Indian patients, we investigated differential compositions of commensal bacteria among patients with benign prostatic hyperplasia (BPH) and PCa using 16S rRNA amplicon sequencing followed by qPCR analyses using two distinct primer sets. Using two independent cohorts, we show that Prevotella copri, Cupriavidus campinensis, and Propionibacterium acnes represent the three most abundant bacteria in diseased prostate lesions. LEfSe analyses identified that while Cupriavidus taiwanensis and Methylobacterium organophilum are distinctly elevated in PCa samples, Kocuria palustris and Cellvibrio mixtus are significantly enriched in BPH samples. Furthermore, we identify that a number of human tumor viruses, including Epstein-Barr virus (EBV) and hepatitis B virus (HBV), along with two high-risk human papillomaviruses - HPV-16 and HPV-18, are significantly associated with the PCa development and strongly correlated with PCa bacterial signature. The study may thus offer to develop a framework for exploiting this microbial signature for early diagnosis and prognosis of PCa development.

The pediatric urobiome in genitourinary conditions: a narrative review

The microbial ecosystem within the bladder that can be measured within the urine, or urobiome, is an emerging field of study with little published data regarding children. However, investigations into urobiome research have the potential to significantly impact the understanding of the pathophysiology of genitourinary conditions, as well as potentially identify novel therapeutics. Therefore, both researchers and clinicians should be aware of pediatric urobiome research. The purpose of this review is to highlight the literature around urobiome research in urinary tract infections, nephrolithiasis, and neurogenic bladder; comment on pediatric-specific considerations when reading and interpreting the urobiome literature; and to identify new potential areas of research.

Improving the Diagnostic Potential of Extracellular miRNAs Coupled to Multiomics Data by Exploiting the Power of Artificial Intelligence

In recent years, the clinical use of extracellular miRNAs as potential biomarkers of disease has increasingly emerged as a new and powerful tool. Serum, urine, saliva and stool contain miRNAs that can exert regulatory effects not only in surrounding epithelial cells but can also modulate bacterial gene expression, thus acting as a “master regulator” of many biological processes. We think that in order to have a holistic picture of the health status of an individual, we have to consider comprehensively many “omics” data, such as miRNAs profiling form different parts of the body and their interactions with cells and bacteria. Moreover, Artificial Intelligence (AI) and Machine Learning (ML) algorithms coupled to other multiomics data (i.e., big data) could help researchers to classify better the patient’s molecular characteristics and drive clinicians to identify personalized therapeutic strategies. Here, we highlight how the integration of “multiomic” data (i.e., miRNAs profiling and microbiota signature) with other omics (i.e., metabolomics, exposomics) analyzed by AI algorithms could improve the diagnostic and prognostic potential of specific biomarkers of disease.

A Child's urine is not sterile: A pilot study evaluating the Pediatric Urinary Microbiome

INTRODUCTION

A bladder microbiome (urobiome) exists in adults. Data supports the effects of the adult urobiome on urinary tract health with associations between dysbiotic urobiomes and lower urinary tract disorders. Understanding urobiome origin is important since other microbiomes establish around birth and microbiome alterations are linked to disease development. However, the pediatric urobiome has not been well studied.

OBJECTIVES

We sought to determine the age when the urobiome develops, compare the pediatric urobiome to microbiomes of adjacent urogenital niches, and compare the urobiomes between boys and girls and across age groups.

STUDY DESIGN

Seventy-four children less than 18 years of age without recent antibiotic exposure were recruited, including 48 males and 26 females, aged 2 weeks to 209 months of age. Transurethral catheterized urine samples and samples from the perineum, urethra, vagina, and foreskin were collected. Specimens were assessed using the expanded quantitative urine culture protocol and by 16S rRNA gene sequencing. Dada2 was used to profile microbial compositions, and BLCA was used to identify microbial taxa.

RESULTS

Bacteria were detected in 90.5% of urine samples and identified in children as young as 2 weeks of age. Microbial communities and compositions of the female bladder and other urogenital niches (urethra, perineum, and vagina) differed significantly by age. Lactobacillus predominated the bladder, urethral, and vaginal microbiomes in post-pubertal girls. Compared to female urinary microbiomes, those of males differed less substantially. Only perineal microbiomes differed significantly by age, whereas male urethral and foreskin microbiomes did not differ significantly.

DISCUSSION

We identified that a urinary microbiome is established as early as infancy. In addition, the female urobiome changes throughout childhood, until the post-pubertal bacterial taxa becomes consistent with that seen in adult females. Whereas in boys, the urinary microbiome changed very little over time. In addition, the surrounding urogenital microbiomes differed less in boys as compared to females. Microbiomes established at a young age may have long-term influences on immune, metabolic, and neurobehavioral traits. The same may be true for the urobiome. Our study provides a foundation for future research to determine the influence of the pediatric urobiome on the development of urinary and even non-urinary disorders.

CONCLUSIONS

A pediatric urobiome exists, with differences between males and females and can be detected at a young age with changes occurring throughout childhood. Similarities and differences are also seen between the pediatric urobiome and adjacent niches.

Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection

Background

Recurrent urinary tract infection (RUTI) is common and burdensome in women. Due to the low concentration or slow-growing of uropathogens in RUTI, standard urine cultures (SUCs) are often negative. Next-generation sequencing (NGS) of bacterial 16S rRNA gene is more sensitive and could be used to reveal the differential microbiota between patients with RUTI and asymptomatic controls.

Methods

Women (aged ≥ 18 years) with clinically diagnosed RUTI with negative SUC and age-matched women asymptomatic controls with normal urinalysis were enrolled. Their midstream voided urine specimens were collected and processed for NGS (Illumina MiSeq) targeting the bacterial 16S rRNA gene V3-V4 region. The dataset was clustered into operational taxonomic units (OTUs) using QIIME. Taxonomic analysis, alpha diversity, beta diversity, multivariate statistical analysis, and linear discriminant analysis effect size (LEfSe) for differential analysis were performed and compared between patients with RUTI and asymptomatic controls.

Results

A total of 90 patients with RUTI and 62 asymptomatic controls were enrolled in this study. Among them, 74.4% (67/90) and 71.0% (44/62) were successfully amplified and sequenced their bacterial 16S rRNA gene. In the alpha diversity analysis, the chao1 index and observed species index were significantly lower in the RUTI group than in the control group (P = 0.015 and 0.028, respectively). In the beta diversity analysis, there was a significant difference between the 2 groups [Analysis of similarities (ANOSIM), R = 0.209, P = 0.001]. The relative abundance of 36 bacterial taxa was significantly higher, and another 24 kinds of bacteria were significantly lower in the RUTI group compared with the control group [LEfSe analysis, P < 0.05, linear discriminative analysis (LDA) score > 3], suggesting that Ralstonia, Prevotella, Dialister, and Corynebacterium may play an important role in RUTI.

Conclusion

The urinary microbiota of women with clinically diagnosed RUTI were significantly different from age-matched asymptomatic controls.

Molecular Regulatory Mechanisms Drive Emergent Pathogenetic Properties of Neisseria gonorrhoeae

Neisseria gonorrhoeae is the causative agent of the sexually transmitted infection (STI) gonorrhea, with an estimated 87 million annual cases worldwide. N. gonorrhoeae predominantly colonizes the male and female genital tract (FGT). In the FGT, N. gonorrhoeae confronts fluctuating levels of nutrients and oxidative and non-oxidative antimicrobial defenses of the immune system, as well as the resident microbiome. One mechanism utilized by N. gonorrhoeae to adapt to this dynamic FGT niche is to modulate gene expression primarily through DNA-binding transcriptional regulators. Here, we describe the major N. gonorrhoeae transcriptional regulators, genes under their control, and how these regulatory processes lead to pathogenic properties of N. gonorrhoeae during natural infection. We also discuss the current knowledge of the structure, function, and diversity of the FGT microbiome and its influence on gonococcal survival and transcriptional responses orchestrated by its DNA-binding regulators. We conclude with recent multi-omics data and modeling tools and their application to FGT microbiome dynamics. Understanding the strategies utilized by N. gonorrhoeae to regulate gene expression and their impact on the emergent characteristics of this pathogen during infection has the potential to identify new effective strategies to both treat and prevent gonorrhea.

Microbial community signatures for estimation of postmortem time intervals

The human body provides a complex ecosystem for symbiotic habitation of a huge number of microorganisms. These commensal microorganisms provide a huge benefit to the living host by acting against many deadly infections. Once the host dies, many changes in the complex ecosystem of the human body take place. The personalized microbes of a human body undergo successional change as many exogenous microbes attack the nutrient-rich cadaver after death. The succession pattern change of microbes in human cadaver allows postulating different models for estimation of Postmortem time interval (PMI). Estimation of PMI has a broad prospect from the criminal investigation point of view. Though many techniques are being used nowadays to estimate PMI, all of them have their pros and cons. With the advent of advanced molecular biological techniques, studies on the thanatomicrobiome of a human cadaver have gained pace and provide a superior alternative for conventional methods of PMI estimation. This chapter summarizes the recent advancements in the changes in signature microflora postmortem with change in human microenvironment to postulate a consensus model for estimation of PMI.

Prospective observational study of the role of the microbiome in BCG responsiveness prediction (SILENT-EMPIRE): a study protocol

INTRODUCTION

The human microbiota, the community of micro-organisms in different cavities, has been increasingly linked with inflammatory and neoplastic diseases. While investigation into the gut microbiome has been robust, the urinary microbiome has only recently been described. Investigation into the relationship between bladder cancer (BC) and the bladder and the intestinal microbiome may elucidate a pathophysiological relationship between the two. The bladder or the intestinal microbiome or the interplay between both may also act as a non-invasive biomarker for tumour behaviour. While these associations have not yet been fully investigated, urologists have been manipulating the bladder microbiome for treatment of BC for more than 40 years, treating high grade non-muscle invasive BC (NMIBC) with intravesical BCG immunotherapy. Neither the association between the microbiome sampled directly from bladder tissue and the response to BCG-therapy nor the association between response to BCG-therapy with the faecal microbiome has been studied until now. A prognostic tool prior to initiation of BCG-therapy is still needed.

METHODS AND ANALYSIS

In patients with NMIBC bladder samples will be collected during surgery (bladder microbiome assessment), faecal samples (microbiome assessment), instrumented urine and blood samples (biobank) will also be taken. We will analyse the microbial community by 16S rDNA gene amplicon sequencing. The difference in alpha diversity (diversity of species within each sample) and beta diversity (change in species diversity) between BCG-candidates will be assessed. Subgroup analysis will be performed which will lead to the development of a clinical prediction model estimating risk of BCG-response.

ETHICS AND DISSEMINATION

The study has been approved by the Cantonal Ethics Committee Zurich (2021-01783) and it is being conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Study results will be disseminated through peer-reviewed journals and national and international scientific conferences.

TRIAL REGISTRATION NUMBER

NCT05204199.

Human microbial dysbiosis as driver of gynecological malignancies

Gynecological cancers that affect female reproductive tract, remain at the top of the global cancer burden list with high relapse rate and mortality. Notwithstanding development of several novel therapeutic interventions including poly-ADP-ribose polymerase inhibitors, this family of malignancies remain deadly. The human microbiome project demonstrated that dysbiosis of health resident microflora is associated with several pathologies including malignancies of the female reproductive tract and detailed characterization of species variation and host-microbe interaction could provide clues for identification of early diagnostic biomarker, preventive and therapeutic interventions. Emerging evidence suggests that several microbial signatures are significantly associated with gynecological cancers. An increased population of Proteobacteria and Firmicutes followed by significantly reduced Lactobacilli are associated with lethal epithelial ovarian cancer. Similarly, a constant association of elevated level of Atopobium vaginae, Porphyromonas somerae, Micrococci and Gardnerella vaginalis are observed in endometrial and cervical cancers. Moreover, human papilloma virus infection significantly augments colonization of pathogenic microbes including Sneathia sanguinegens, Anaerococcus tetradius, and Peptostreptococcus anaerobius and drives carcinoma of the cervix. Interestingly, microbial dysbiosis in female reproductive tract modulates expression of several microbial and immune-responsive genes such as TLR-4, TLR-5, TLR-6 and NOD-1. Therefore, stringent investigation into the microbial dysbiosis and its underlying mechanism could provide valuable cues for identification of early diagnostic biomarker, preventive and therapeutic interventions against rogue gynecological malignancies.

Assessment of the Urinary Microbiota of MSM Using Urine Culturomics Reveals a Diverse Microbial Environment

BACKGROUND

The urinary tract is not sterile and is populated by microbial communities that influence urinary health. Men who have sex with men (MSM) are understudied yet have increased risk factors for genitourinary infections. Our objective was to interrogate the composition of MSM urinary microbiota.

METHODS

Midstream urine specimens (n = 129) were collected from MSM (n = 63) and men seen for routine care (clinical cohort, n = 30). Demographics and sexual/medical history were documented. Specimens underwent culture using standard-of-care and enhanced methods designed to isolate fastidious and anaerobic microorganisms. Isolates were identified by MALDI-TOF mass spectrometry or 16S rRNA gene sequencing.

RESULTS

The MSM cohort was younger (mean (SD), 35.4 (11.26) years) compared to the clinical cohort (62.7 (15.95) years). Organism recovery was significantly increased using enhanced vs standard culture for the MSM (mean of 9.1 vs 0.6 species/sample [P < 0.001]) and clinical (7.8 vs 0.9 species/sample [P < 0.001]) cohorts. The microbial composition of MSM urine specimens was dominated by Gram-positive and anaerobic microbes and clustered distinctly from that of clinical urine specimens. Composition of microbial species recovered within the same subject was dynamic between urine specimens but more similar relative to inter-individual comparisons. Principal coordinate analysis showed no correlation between urinary microbiota composition and age, recent antibiotic use, sexually transmitted infection/HIV status, or sexual practices.

CONCLUSIONS

Enhanced culture recovered a large diversity of microbial species from MSM urine specimens, especially taxa typically associated with mucosal surfaces. These findings may increase understanding of urologic disease in MSM and improve diagnostic methods for detection of genitourinary infections.

Sneathia amnii bacteraemia and chorioamnionitis leading to second trimester abortion: a case report

Background

Sneathia amnii (formerly designated as Leptotrichia amnionii) was first described in 2002 in the USA. Members of the genus Sneathia can be part of the normal flora of the genitourinary tract, but have been implicated in invasive (mostly gynaecological) infections.

Case presentation

To the best of our knowledge, here we present the first case of S. amnii infection in Belgium, in a young woman presenting with fever leading to second trimester septic abortion.

Conclusion

Despite its pathogenicity, S. amnii remains an underrated cause of infections due to inherent difficulties with conventional laboratory methods. By extracting the bacterial DNA directly from the blood culture broth and performing a 16S ribosomal RNA gene sequence analysis we succeeded in identifying S. amnii as the most probable cause of the septic abortion in our patient.

Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method

Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.