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Honors & Awards

  • Stanford Postdoctoral Deans' Fellow, Stanford University (2020-2021)
  • Microbiology and Immunology Departmental T32 Fellowship, Stanford University (2020)
  • Oscar Ortiz Contreras Award for IUJ impact factor 2018, International Urogynecological Association (IUGA). (Sept 27th, 2019)
  • Dissertation of the Year, Biomedical and Sciences Category, Loyola University Chicago (2018)
  • Arthur J. Schmitt Dissertation Fellowship, Loyola University (2016-2017)

Boards, Advisory Committees, Professional Organizations

  • Scientific Advisor, LiveUTIFree (2019 - Present)

Professional Education

  • Bachelor of Science, Calif Polytechnic State Univ, S.L.O. (2008)
  • Doctor of Philosophy, Loyola University Of Chicago (2017)

Stanford Advisors

Community and International Work

  • LiveUTIFree


    Urinary Tract Infections -



    Ongoing Project


    Opportunities for Student Involvement


Research & Scholarship

Current Research and Scholarly Interests

I study the intersection between the microbiome and women's health


All Publications

  • Forming Consensus To Advance Urobiome Research. mSystems Brubaker, L., Gourdine, J. F., Siddiqui, N. Y., Holland, A., Halverson, T., Limeria, R., Pride, D., Ackerman, L., Forster, C. S., Jacobs, K. M., Thomas-White, K. J., Putonti, C., Dong, Q., Weinstein, M., Lukacz, E. S., Karstens, L., Wolfe, A. J. 2021: e0137120


    Urobiome research has the potential to advance the understanding of a wide range of diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early research method consensus to facilitate the greater, common good. This consensus document, developed by a group of expert investigators currently engaged in urobiome research (UROBIOME 2020 conference participants), aims to promote standardization and advances in this field by the adoption of common core research practices. We propose a standardized nomenclature as well as considerations for specimen collection, preservation, storage, and processing. Best practices for urobiome study design include our proposal for standard metadata elements as part of core metadata collection. Although it is impractical to follow fixed analytical procedures when analyzing urobiome data, we propose guidelines to document and report data originating from urobiome studies. We offer this first consensus document with every expectation of subsequent revision as our field progresses.

    View details for DOI 10.1128/mSystems.01371-20

    View details for PubMedID 34282932

  • Genome Investigation of Urinary Gardnerella Strains and Their Relationship to Isolates of the Vaginal Microbiota. mSphere Putonti, C., Thomas-White, K., Crum, E., Hilt, E. E., Price, T. K., Wolfe, A. J. 2021; 6 (3)


    Gardnerella is a frequent member of the urogenital microbiota. Given the association between Gardnerella vaginalis and bacterial vaginosis (BV), significant efforts have been focused on characterizing this species in the vaginal microbiota. However, Gardnerella also is a frequent member of the urinary microbiota. In an effort to characterize the bacterial species of the urinary microbiota, we present here 10 genomes of urinary Gardnerella isolates from women with and without lower urinary tract symptoms. These genomes complement those of 22 urinary Gardnerella strains previously isolated and sequenced by our team. We included these genomes in a comparative genome analysis of all publicly available Gardnerella genomes, which include 33 urinary isolates, 78 vaginal isolates, and 2 other isolates. While once this genus was thought to consist of a single species, recent comparative genome analyses have revealed 3 new species and an additional 9 groups within Gardnerella Based upon our analysis, we suggest a new group for the species. We also find that distinction between these Gardnerella species/groups is possible only when considering the core or whole-genome sequence, as neither the sialidase nor vaginolysin genes are sufficient for distinguishing between species/groups despite their clinical importance. In contrast to the vaginal microbiota, we found that only five Gardnerella species/groups have been detected within the lower urinary tract. Although we found no association between a particular Gardnerella species/group(s) and urinary symptoms, further sequencing of urinary Gardnerella isolates is needed for both comprehensive taxonomic characterization and etiological classification of Gardnerella in the urinary tract.IMPORTANCE Prior research into the bacterium Gardnerella vaginalis has largely focused on its association with bacterial vaginosis (BV). However, G. vaginalis is also frequently found within the urinary microbiota of women with and without lower urinary tract symptoms as well as individuals with chronic kidney disease, interstitial cystitis, and BV. This prompted our investigation into Gardnerella from the urinary microbiota and all publicly available Gardnerella genomes from the urogenital tract. Our work suggests that while some Gardnerella species can survive in both the urinary tract and vagina, others likely cannot. This study provides the foundation for future studies of Gardnerella within the urinary tract and its possible contribution to lower urinary tract symptoms.

    View details for DOI 10.1128/mSphere.00154-21

    View details for PubMedID 33980674

  • Vaginal Estrogen Therapy Is Associated with Increased Lactobacillus in the Urine of Post-Menopausal Women with Overactive Bladder Symptoms. American journal of obstetrics and gynecology Thomas-White, K., Taege, S., Limeira, R., Brincat, C., Joyce, C., Hilt, E. E., Mac-Daniel, L., Radek, K. A., Brubaker, L., Mueller, E. R., Wolfe, A. J. 2020


    INTRODUCTION: Previous work has shown that the vaginal microbiome decreases in Lactobacillus predominance and becomes more diverse following menopause. It has also been shown that estrogen therapy restores Lactobacillus-dominance in the vagina, and that topical estrogen is associated with OAB symptom improvement. We now know that the bladder contains a unique microbiome, and increased bladder microbiome diversity is associated with OAB. However, there is no understanding of how quickly each pelvic floor microbiome responds to estrogen or if those changes are associated with symptom improvement.STUDY DESIGN: Analysis of data from post-menopausal participants in two trials (NCT02524769 and NCT02835846) who chose vaginal estrogen as their primary OAB treatment and used 0.5 grams of conjugated estrogen (Premarin Cream, (Pfizer, New York City, NY)) twice weekly for 12 weeks. Baseline and 12-week follow-up data included the OAB-q questionnaire and participants provided catheterized urine, vaginal swabs, perineal swabs, and voided urine. Microbes were detected by an enhanced culture protocol. Linear mixed models were used to estimate microbiome changes over time. Urinary AMP activity was assessed by a bacterial growth inhibition assay and correlated with relative abundance of members of the urobiome.RESULTS: Twelve weeks of estrogen treatment resulted in decreased microbial diversity within the vagina (Shannon, p=0.047; Richness, p=0.043), but not in the other niches. A significant increase in Lactobacillus was detected in the bladder (p=0.037), but not the vagina (p=0.33), perineum (p=0.56), or voided urine (p=0.28). The change in Lactobacillus levels in the bladder was associated with modest changes in urgency incontinence symptoms (p=0.02). The relative abundance of the genus Corynebacterium correlated positively with urinary AMP activity after estrogen treatment.CONCLUSION: Estrogen therapy may change the microbiome of different pelvic floor niches. The vagina begins to decrease in diversity and the bladder experiences a significant increase in Lactobacillus levels; the latter is correlated with a modest improvement in the symptom severity sub-scale of the OAB-q.

    View details for DOI 10.1016/j.ajog.2020.08.006

    View details for PubMedID 32791124

  • Aerococcus urinae Isolated from Women with Lower Urinary Tract Symptoms: In Vitro Aggregation and Genome Analysis JOURNAL OF BACTERIOLOGY Hilt, E. E., Putonti, C., Thomas-White, K., Lewis, A. L., Visick, K. L., Gilbert, N. M., Wolfe, A. J. 2020; 202 (13)


    Aerococcus urinae is increasingly recognized as a potentially significant urinary tract bacterium. A. urinae has been isolated from urine collected from both males and females with a wide range of clinical conditions, including urinary tract infection (UTI), urgency urinary incontinence (UUI), and overactive bladder (OAB). A. urinae is of particular clinical concern because it is highly resistant to many antibiotics and, when undiagnosed, can cause invasive and life-threatening bacteremia, sepsis, or soft tissue infections. Previous genomic characterization studies have examined A. urinae strains isolated from patients experiencing UTI episodes. Here, we analyzed the genomes of A. urinae strains isolated as part of the urinary microbiome from patients with UUI or OAB. Furthermore, we report that certain A. urinae strains exhibit aggregative in vitro phenotypes, including flocking, which can be modified by various growth medium conditions. Finally, we performed in-depth genomic comparisons to identify pathways that distinguish flocking and nonflocking strains.IMPORTANCEAerococcus urinae is a urinary bacterium of emerging clinical interest. Here, we explored the ability of 24 strains of A. urinae isolated from women with lower urinary tract symptoms to display aggregation phenotypes in vitro We sequenced and analyzed the genomes of these A. urinae strains. We performed functional genomic analyses to determine whether the in vitro hyperflocking aggregation phenotype displayed by certain A. urinae strains was related to the presence or absence of certain pathways. Our findings demonstrate that A. urinae strains have different propensities to display aggregative properties in vitro and suggest a potential association between phylogeny and flocking.

    View details for DOI 10.1128/JB.00170-20

    View details for Web of Science ID 000540454600005

    View details for PubMedID 32284319

    View details for PubMedCentralID PMC7283593

  • Bladder Bacterial Diversity Differs In Continent and Incontinent Women: A Cross-Sectional Study. American journal of obstetrics and gynecology Price, T. K., Lin, H. n., Gao, X. n., Thomas-White, K. J., Hilt, E. E., Mueller, E. R., Wolfe, A. J., Dong, Q. n., Brubaker, L. n. 2020


    Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and/or provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence (UI).To test our hypothesis that the bladder urobiome differs between continent women and women affected by UI by assessing associations between UI status and the cultured urobiome.With IRB oversight, transurethral catheterized urine specimens were collected from 309 adult women, who were categorized into three groups using response to the validated Pelvic Floor Distress Inventory (PFDI): Continent Controls (N=150) and 2 Urinary Incontinence (UI cohorts) - Stress Urinary Incontinence (SUI) (N=50) and Urgency Urinary Incontinence (UUI) (N=109). Symptom severity was assessed with the Urinary Distress Inventory (UDI) subscale score of the PFDI. Microbes were assessed by the Expanded Quantitative Urine Culture protocol, which detects the most common bladder microbes (bacteria and yeast). Microbes were identified to the species level by MALDI-TOF mass spectrometry. Alpha diversity indices were calculated for culture-positive samples and compared across the three groups. The association between UDI scores versus alpha diversity indices and species abundance were estimated.Participants had a mean age of 53 years (range 22-90); most were Caucasian (65%). Women with UI were slightly older (Control=47, SUI=54, UUI=61). By design, UDI symptom scores differed (Control = 8.43 (10.1), SUI = 97.95 (55.36), UUI = 93.71 (49.12), p<0.001). While most participants (216, 70%) had Expanded Quantitative Urine Culture-detected bacteria, the UI cohorts had a higher detection frequency than did the Control cohort (Control=57%, SUI 86%, UUI 81%, p<0.001). The most frequently detected species were as follows: Controls, Lactobacillus iners (12.7%), Streptococcus anginosus (12.7%), L. crispatus (10.7%), and L. gasseri (10%); SUI, S. anginosus (26%), L. iners (18%), Staphylococcus epidermidis (18%), and L. jensenii (16%); UUI, S. anginosus (30.3%), L. gasseri (22%), Aerococcus urinae (18.3%), and Gardnerella vaginalis (17.4%). However, only Actinotignum (formerly Actinobaculum) schaalii, A. urinae, A. sanguinicola, and Corynebacterium lipophile group were found at significantly higher mean abundances in at least one of the UI cohorts when compared to the Control cohort (Wilcoxon p<0.02), and no individual genus differed significantly between the two UI cohorts. Both UI cohorts had increased alpha diversity relative to continent controls with indices of species richness, but not evenness, strongly associated with UI.In adult women, the composition of the culturable bladder urobiome is associated with UI, regardless of common incontinence subtype. Detection of more unique living microbes was associated with worse incontinence severity. Culturable species richness is significantly greater in the UI cohorts than continent controls.

    View details for DOI 10.1016/j.ajog.2020.04.033

    View details for PubMedID 32380174

  • Characteristics of the microbiota in the urine of women with type 2 diabetes. Journal of diabetes and its complications Penckofer, S. n., Limeira, R. n., Joyce, C. n., Grzesiak, M. n., Thomas-White, K. n., Wolfe, A. J. 2020: 107561


    The urinary microbiota in women with type 2 diabetes (T2DM) can have bacterial uropathogens which are more virulent. The primary objective was to describe and compare the characteristics of the microbiota in voided urine of women with and without T2DM.Two cohorts of women: those with T2DM (n?=?87) and those without T2DM (n?=?49) were studied. Demographic data, hemoglobin A1c (HbA1c), fasting serum glucose, and voided urine were collected. To determine the characteristics of the microbiota in the urine, 16S rRNA gene sequencing was used.The genus Lactobacillus was more often present in women with T2DM (75.9%, n?=?66) than in the controls (59.2%, n?=?30) (p?=?0.042), as was the family Enterobacteriaceae (12.6% T2DM versus 2.0% control, p?=?0.055). There was evidence of an association between HbA1c and the relative abundance of the various bacteria in the total cohort. The relative abundance of Lactobacillus was positively associated (??=?0.19, 95% CI: 0.02, 0.34), while Corynebacterium (??=?-0.26, 95% CI: -0.41, -0.10) and Prevotella (??=?-0.23, 95% CI: -0.38, -0.06) were inversely associated with HbA1c.Enterobacteriaceae (e.g. E. coli) predispose women to urinary tract infections and since T2DM increases this risk, further study is needed. The species of Lactobacillus and its impact needs exploration.

    View details for DOI 10.1016/j.jdiacomp.2020.107561

    View details for PubMedID 32184058

  • Cultivable Bacteria in Urine of Women With Interstitial Cystitis: (Not) What We Expected. Female pelvic medicine & reconstructive surgery Jacobs, K. M., Price, T. K., Thomas-White, K. n., Halverson, T. n., Davies, A. n., Myers, D. L., Wolfe, A. J. 2020


    Multiple studies show cultivatable bacteria in urine of most women. The existence of these bacteria challenges interstitial cystitis (IC)/painful bladder syndrome (PBS) diagnosis, which presumes a sterile bladder. The aims of this study were (1) to compare the female bladder microbiomes in women with IC/PBS and unaffected controls and (2) to correlate baseline bladder microbiome composition with symptoms.This cross-sectional study enrolled 49 IC/PBS and 40 controls. All provided catheterized urine samples and completed validated questionnaires. A subset of the IC/PBS cohort provided voided and catheterized urine samples. All samples from both cohorts were assessed by the expanded quantitative urine culture (EQUC) protocol; a subset was assessed by 16S rRNA gene sequencing.Of the IC/PBS cohort, 49.0% (24/49) were EQUC positive; in these EQUC-positive samples, the most common urotypes were Lactobacillus (45.8%) and Streptococcus (33.3%). Of the controls, 40.0% were EQUC positive; of these EQUC-positive samples, the most common urotype was Lactobacillus (50.0%). The urotype distribution was significantly different (P < 0.05), as 16% of the IC/PBS cohort, but 0% of controls, were Streptococcus urotype (P < 0.01). Symptom-free IC/PBS participants were less likely to be EQUC positive (12.5%) than IC/PBS participants with moderate or severe symptoms (68.8% and 46.2%) and the control cohort (60%; P < 0.05).Lactobacillus was the most common urotype. However, the presence of Lactobacillus did not differ between cohorts, and it did not impact IC/PBS symptom severity. Bacteria were not isolated from most participants with active IC/PBS symptoms. These findings suggest that bacteria may not be an etiology for IC/PBS.

    View details for DOI 10.1097/SPV.0000000000000854

    View details for PubMedID 32265402

  • The urobiome of continent adult women: a cross-sectional study. BJOG : an international journal of obstetrics and gynaecology Price, T. K., Hilt, E. E., Thomas-White, K. n., Mueller, E. R., Wolfe, A. J., Brubaker, L. n. 2019


    To characterize the bladder microbiota of continent adult women.Cross-sectional study of adult women who contributed catheterized urine samples, completed validated symptom questionnaires and provided demographic data.US academic medical center.Well-characterized continent adult women.Participants contributed symptoms questionnaires, demographic data and catheterized urine samples that were analyzed by enhanced urine culture methodology and 16S rRNA gene sequencing.Associations between demographics and microbial community state structures (urotypes, defined by a specimen's dominant taxon).The bladder microbiota (urobiome) of 224 continent control women were characterized, showing variability in terms of urotype. The most common urotype was Lactobacillus (19%), which did not differ with any demographic. In contrast, the Gardnerella (p<0.001) and Escherichia (p=0.005) urotypes were more common in younger and older women, respectively.For urobiome research, enhanced culture methods and/or DNA sequencing are preferred techniques for bacterial detection. Clinical interpretation of clinical tests, such as the standard urine culture, should incorporate knowledge that some women have Gardnerella or Escherichia urotypes without evidence of clinical disorder. Clinical care strategies should preserve or restore the beneficial effects of the native urobiome, as disruption of that microbial community could result in unintended vulnerability to uropathogen invasion or opportunistic pathogen overgrowth. Longitudinal studies of urobiome responses to therapies should be encouraged. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1111/1471-0528.15920

    View details for PubMedID 31469215

  • Urinary microbes and postoperative urinary tract infection risk in urogynecologic surgical patients. International urogynecology journal Thomas-White, K. J., Gao, X., Lin, H., Fok, C. S., Ghanayem, K., Mueller, E. R., Dong, Q., Brubaker, L., Wolfe, A. J. 2018


    INTRODUCTION AND HYPOTHESIS: Women have a 20% risk of developing a urinary tract infection (UTI) following urogynecologic surgery. This study assessed the association of postoperative UTI with bacteria in preoperative samples of catheterized urine.METHODS: Immediately before surgery, vaginal swabs, perineal swabs, and catheterized urine samples were collected, and the V4 region of the 16S ribosomal RNA (rRNA) gene was sequenced. The cohort was dichotomized in two ways: (1) standard day-of-surgery urine culture result (positive/negative), and (2) occurrence of postoperative UTI (positive/negative). Characteristics of bladder, vaginal, and perineal microbiomes were assessed to identify factors associated with postoperative UTI.RESULTS: Eighty-seven percent of the 104 surgical patients with pelvic organ prolapse/urinary incontinence (POP/UI) were white; mean age was 57years. The most common genus was Lactobacillus, with a mean relative abundance of 39.91% in catheterized urine, 53.88% in vaginal swabs, and 30.28% in perineal swabs. Two distinct clusters, based on dispersion of catheterized urine (i.e., bladder) microbiomes, had highly significant (p<2.2-16) differences in age, microbes, and postoperative UTI risk. Postoperative UTI was most frequently associated with the bladder microbiome; microbes in adjacent pelvic floor niches also contributed to UTI risk. UTI risk was associated with depletion of Lactobacillus iners and enrichment of a diverse mixture of uropathogens.CONCLUSIONS: Postoperative UTI risk appears to be associated with preoperative bladder microbiome composition, where an abundance of L. iners appears to protect against postoperative UTI.

    View details for PubMedID 30267143

  • Detecting viral genomes in the female urinary microbiome JOURNAL OF GENERAL VIROLOGY Garretto, A., Thomas-White, K., Wolfe, A. J., Putonti, C. 2018; 99 (8): 1141?46


    Viruses are the most abundant component of the human microbiota. Recent evidence has uncovered a rich diversity of viruses within the female bladder, including both bacteriophages and eukaryotic viruses. We conducted whole-genome sequencing of the bladder microbiome of 30 women: 10 asymptomatic 'healthy' women and 20 women with an overactive bladder. These metagenomes include sequences representative of human, bacterial and viral DNA. This analysis, however, focused specifically on viral sequences. Using the bioinformatic tool virMine, we discovered sequence fragments, as well as complete genomes, of bacteriophages and the eukaryotic virus JC polyomavirus. The method employed here is a critical proof of concept: the genomes of viral populations within the low-biomass bladder microbiota can be reconstructed through whole-genome sequencing of the entire microbial community.

    View details for DOI 10.1099/jgv.0.001097

    View details for Web of Science ID 000440461400019

    View details for PubMedID 29889019

  • Diversity of the midstream urine microbiome in adults with chronic kidney disease INTERNATIONAL UROLOGY AND NEPHROLOGY Kramer, H., Kuffel, G., Thomas-White, K., Wolfe, A. J., Vellanki, K., Leehey, D. J., Bansal, V. K., Brubaker, L., Flanigan, R., Koval, J., Wadhwa, A., Zilliox, M. J. 2018; 50 (6): 1123?30


    To examine the characteristics of the midstream urine microbiome in adults with stage 3-5 non-dialysis-dependent chronic kidney disease (CKD).Patients with non-dialysis-dependent CKD (estimated glomerular filtration rate [eGFR]??50% reads) by the genera Corynebacterium (n?=?11), Staphylococcus (n?=?9), Streptococcus (n?=?7), Lactobacillus (n?=?7), Gardnerella (n?=?7), Prevotella (n?=?4), Escherichia_Shigella (n?=?3), and Enterobacteriaceae (n?=?2); the rest lacked a dominant genus. The samples had high levels of diversity, as measured by the inverse Simpson [7.24 (95% CI 6.76, 7.81)], Chao [558.24 (95% CI 381.70, 879.35)], and Shannon indices [2.60 (95% CI 2.51, 2.69)]. Diversity measures were generally higher in participants with urgency urinary incontinence and higher estimated glomerular filtration rate (eGFR). After controlling for demographics and diabetes status, microbiome diversity was significantly associated with estimated eGFR (P?

    View details for DOI 10.1007/s11255-018-1860-7

    View details for Web of Science ID 000434276700017

    View details for PubMedID 29651696

    View details for PubMedCentralID PMC5986845

  • Culturing of female bladder bacteria reveals an interconnected urogenital microbiota NATURE COMMUNICATIONS Thomas-White, K., Forster, S. C., Kumar, N., Van Kuiken, M., Putonti, C., Stares, M. D., Hilt, E. E., Price, T. K., Wolfe, A. J., Lawley, T. D. 2018; 9: 1557


    Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder in the same women identifies highly similar Escherichia coli, Streptococcus anginosus, Lactobacillus iners, and Lactobacillus crispatus, suggesting an interlinked female urogenital microbiota that is not only limited to pathogens but is also characteristic of health-associated commensals.

    View details for DOI 10.1038/s41467-018-03968-5

    View details for Web of Science ID 000430389100009

    View details for PubMedID 29674608

    View details for PubMedCentralID PMC5908796

  • Bacteriophages of the Urinary Microbiome JOURNAL OF BACTERIOLOGY Miller-Ensminger, T., Garretto, A., Brenner, J., Thomas-White, K., Zambom, A., Wolfe, A. J., Putonti, C. 2018; 200 (7)


    Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain Escherichia coli C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions.IMPORTANCE Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic "healthy" individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.

    View details for DOI 10.1128/JB.00738-17

    View details for Web of Science ID 000427113600012

    View details for PubMedID 29378882

    View details for PubMedCentralID PMC5847656

  • Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients. International urogynecology journal Fok, C. S., Gao, X. n., Lin, H. n., Thomas-White, K. J., Mueller, E. R., Wolfe, A. J., Dong, Q. n., Brubaker, L. n. 2018; 29 (12): 1765?71


    Persistent and de novo symptoms decrease satisfaction after urogynecologic surgery. We investigated whether the preoperative bladder microbiome is associated with urinary symptoms prior to and after urogynecologic surgery.One hundred twenty-six participants contributed responses to the validated OABq symptom questionnaire. Catheterized (bladder) urine samples and vaginal and perineal swabs were collected immediately preoperatively. Bacterial DNA in the urine samples and swabs was sequenced and classified.Preoperative symptom severity was significantly worse in sequence-positive patients. Higher OABq Symptom Severity (OABqSS) scores (more symptomatic) were associated with higher abundance in bladder urine of two bacterial species: Atopobium vaginae and Finegoldia magna. The presence of Atopobium vaginae in bladder urine also was correlated with its presence in either the vagina or perineum.Two specific bacterial species detected in bladder urine, Atopobium vaginae and Finegoldia magna, are associated with preoperative urinary symptom severity in women undergoing POP/SUI surgery. The reservoir for Atopobium vaginae may be adjacent pelvic floor niches. This observation should be validated in a larger cohort to determine whether there is a microbiologic etiology for certain preoperative urinary symptoms.

    View details for DOI 10.1007/s00192-018-3732-1

    View details for PubMedID 30116843

  • Urinary Symptoms and Their Associations With Urinary Tract Infections in Urogynecologic Patients Dune, T. J., Price, T. K., Hilt, E. E., Thomas-White, K. J., Kliethermes, S., Brincat, C., Brubaker, L., Schreckenberger, P., Wolfe, A. J., Mueller, E. R. LIPPINCOTT WILLIAMS & WILKINS. 2017: 718?25


    To assess urinary symptoms associated with urinary tract infection (UTI) in a urogynecologic population of women.In this cohort study, we enrolled 150 urogynecologic patients who completed the validated UTI Symptom Assessment questionnaire and contributed transurethral catheterized urine samples. The primary measure (UTI diagnosis) was defined in three ways. Self-report (a nonculture-based UTI diagnosis) was defined by a yes or no response to the query "Do you think you have a UTI?" Two culture-based UTI diagnoses also were analyzed: standard urine culture (10 colony-forming units [CFU]/mL or greater) and enhanced quantitative urine culture (10 CFU/mL or greater) of any uropathogen. Statistical analyses were performed on patient demographics and urinary symptom prevalence among patient groups.Although the presence of the urinary symptoms of frequency and urgency (respectively) differ somewhat between UTI-positive and UTI-negative women (self-report [P=.005 and P<.001], standard urine culture [P=.038 and P=.044], or enhanced quantitative urine culture [P=.059 and P=.098]), the presence of dysuria (pain or burning) during urination was significantly more prevalent in UTI-positive women for all UTI definitions (self-report P<.001, standard urine culture P<.001, and enhanced quantitative urine culture P=.010). Furthermore, women reporting dysuria had higher severity and bother scores for all other urinary symptoms assessed by the UTI Symptom Assessment questionnaire compared with women not reporting dysuria (frequency P=.001, urgency P=.006, dysuria P<.001).Our findings show that, in women seeking urogynecologic care, the presence of frequency and urgency of urination does not confirm a culture-based UTI diagnosis. Instead, clinicians can more readily detect UTI using the presence of dysuria, which more effectively discriminates UTI-positive and UTI-negative individuals, regardless of the culture-based method used to diagnose UTI.

    View details for DOI 10.1097/AOG.0000000000002239

    View details for Web of Science ID 000411453500014

    View details for PubMedID 28885414

    View details for PubMedCentralID PMC5679107

  • Microorganisms Identified in the Maternal Bladder: Discovery of the Maternal Bladder Microbiota AJP REPORTS Jacobs, K. M., Thomas-White, K. J., Hilt, E. E., Wolfe, A. J., Waters, T. P. 2017; 7 (3): e188?e196


    Objective ?The objective of this study was to characterize the bladder microbiota in pregnancy. Methods ?A prospective observational study of 51 pregnant women, admitted to a tertiary care hospital, who underwent straight catheterization urine collection or transurethral Foley catheter placement. 16S rRNA gene sequencing and enhanced quantitative urine culture assessed the maternal bladder microbiota with comparisons made to standard urine culture results. Results ?Enhanced quantitative urine culture and 16S rRNA gene sequencing detected bacteria in the majority of participants. Lactobacillus and Gardnerella were the most commonly detected microbes. In contrast, standard urine culture had a 100% false-negative rate and failed to detect several known or emerging urinary pathogens. Conclusion ?There are live bacteria in the bladders of most pregnant women. This challenges the definition of asymptomatic bacteriuria.

    View details for DOI 10.1055/s-0037-1606860

    View details for Web of Science ID 000411970200001

    View details for PubMedID 28970961

    View details for PubMedCentralID PMC5621969

  • Evaluation of the urinary microbiota of women with uncomplicated stress urinary incontinence AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY Thomas-White, K. J., Kliethermes, S., Rickey, L., Lukacz, E. S., Richter, H. E., Moalli, P., Zimmem, P., Norton, P., Kusek, J. W., Wolfe, A. J., Brubaker, L., Natl Inst Diabet Digestive Kidney 2017; 216 (1): 55.e1?55.e16


    Female urinary microbiota are associated with urgency urinary incontinence and response to medication. The urinary microbiota of women with stress urinary incontinence has not been described.We sought to study the cross-sectional relationships between urinary microbiota features and demographic and clinical characteristics of women undergoing stress urinary incontinence surgery.Preoperative urine specimens were collected from women without urinary tract infection and were available from 197 women (174 voided, 23 catheterized) enrolled in a multicenter prospective randomized trial, the Value of Urodynamic Evaluation study. Demographic and clinical variables were obtained including stress and urgency urinary incontinence symptoms, menopausal status, and hormone use. The bacterial composition of the urine was qualitatively assessed by sequencing the bacterial 16S ribosomal RNA gene. Phylogenetic relatedness and microbial alpha diversity were compared to demographics and symptoms using generalized estimating equation models.The majority of 197 urine samples (86%) had detectable bacterial DNA. Bacterial diversity was significantly associated with higher body mass index (P = .02); increased Medical, Epidemiologic, and Social Aspects of Aging urge index score (P = .04); and hormonal status (P < .001). No associations were detected with stress urinary incontinence symptoms. Increased diversity was also associated with a concomitant lower frequency of Lactobacillus in hormone-negative women.Women undergoing stress urinary incontinence surgery have detectable urinary microbiota. This cross-sectional analysis revealed that increased diversity of the microbiota was associated with urgency urinary incontinence symptoms, hormonal status, and body mass index. In contrast, the female urinary microbiota were not associated with stress urinary incontinence symptoms.

    View details for PubMedID 27498309

    View details for PubMedCentralID PMC5182144

  • Incontinence medication response relates to the female urinary microbiota INTERNATIONAL UROGYNECOLOGY JOURNAL Thomas-White, K. J., Hilt, E. E., Fok, C., Pearce, M. M., Mueller, E. R., Kliethermes, S., Jacobs, K., Zilliox, M. J., Brincat, C., Price, T. K., Kuffel, G., Schreckenberger, P., Gai, X., Brubaker, L., Wolfe, A. J. 2016; 27 (5): 723?33


    Many adult women have resident urinary bacteria (urinary microbiome/microbiota). In adult women affected by urinary urgency incontinence (UUI), the etiologic and/or therapeutic role of the urinary microbiome/microbiota remains unknown. We hypothesized that microbiome/microbiota characteristics would relate to clinically relevant treatment response to UUI medication per os.Adult women initiating medication treatment orally for UUI and a comparator group of unaffected women were recruited in a tertiary care health-care system. All participants provided baseline clinical data and urine samples. Women with UUI were given 5 mg solifenacin, with potential dose escalation to 10 mg for inadequate UUI symptom control at 4 weeks. Additional data and urine samples were collected from women with UUI at 4 and 12 weeks. The samples were assessed using 16S ribosomal RNA (rRNA) gene sequencing and enhanced quantitative urine culturing. The primary outcome was treatment response as measured by the validated Patient Global Symptom Control (PGSC) questionnaire. Clinically relevant UUI symptom control was defined as a 4 or 5 score on the PGSC.Diversity and composition of the urinary microbiome/microbiota of women with and without UUI differed at baseline. Women with UUI had more bacteria and a more diverse microbiome/microbiota. The clinical response to solifenacin in UUI participants was related to baseline microbiome/microbiota, with responders more likely to have fewer bacteria and a less diverse community at baseline. Nonresponders had a more diverse community that often included bacteria not typically found in responders.Knowledge of an individual's urinary microbiome/microbiota may help refine UUI treatment. Complementary tools, DNA sequencing, and expanded urine culture provide information about bacteria that appear to be related to UUI incontinence status and treatment response in this population of adult women.

    View details for DOI 10.1007/s00192-015-2847-x

    View details for Web of Science ID 000374572900005

    View details for PubMedID 26423260

    View details for PubMedCentralID PMC5119460

  • The Bladder Is Not Sterile: History and Current Discoveries on the Urinary Microbiome CURRENT BLADDER DYSFUNCTION REPORTS Thomas-White, K., Brady, M., Wolfe, A. J., Mueller, E. R. 2016; 11 (1): 18?24


    In the human body, there are 10 bacterial cells for every one human cell. This fact highlights the importance of the National institutes of Health's initiative to map the human microbiome. The Human Microbiome Project was the first large-scale mapping of the human microbiome of 5 body sites: GI tract, mouth, vagina, skin and nasal cavity using culture-independent methods. The bladder was not originally tested because it was considered to be sterile and there were complexities regarding sample collection. Over the last couple years our team along with other investigators have shown that a urinary microbiome exists and for most individuals it plays a protective role.

    View details for DOI 10.1007/s11884-016-0345-8

    View details for Web of Science ID 000385630200004

    View details for PubMedID 27182288

    View details for PubMedCentralID PMC4864995

  • The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms. Journal of clinical microbiology Price, T. K., Dune, T. n., Hilt, E. E., Thomas-White, K. J., Kliethermes, S. n., Brincat, C. n., Brubaker, L. n., Wolfe, A. J., Mueller, E. R., Schreckenberger, P. C. 2016; 54 (5): 1216?22


    Enhanced quantitative urine culture (EQUC) detects live microorganisms in the vast majority of urine specimens reported as "no growth" by the standard urine culture protocol. Here, we evaluated an expanded set of EQUC conditions (expanded-spectrum EQUC) to identify an optimal version that provides a more complete description of uropathogens in women experiencing urinary tract infection (UTI)-like symptoms. One hundred fifty adult urogynecology patient-participants were characterized using a self-completed validated UTI symptom assessment (UTISA) questionnaire and asked "Do you feel you have a UTI?" Women responding negatively were recruited into the no-UTI cohort, while women responding affirmatively were recruited into the UTI cohort; the latter cohort was reassessed with the UTISA questionnaire 3 to 7 days later. Baseline catheterized urine samples were plated using both standard urine culture and expanded-spectrum EQUC protocols: standard urine culture inoculated at 1 ?l onto 2 agars incubated aerobically; expanded-spectrum EQUC inoculated at three different volumes of urine onto 7 combinations of agars and environments. Compared to expanded-spectrum EQUC, standard urine culture missed 67% of uropathogens overall and 50% in participants with severe urinary symptoms. Thirty-six percent of participants with missed uropathogens reported no symptom resolution after treatment by standard urine culture results. Optimal detection of uropathogens could be achieved using the following: 100 ?l of urine plated onto blood (blood agar plate [BAP]), colistin-nalidixic acid (CNA), and MacConkey agars in 5% CO2 for 48 h. This streamlined EQUC protocol achieved 84% uropathogen detection relative to 33% detection by standard urine culture. The streamlined EQUC protocol improves detection of uropathogens that are likely relevant for symptomatic women, giving clinicians the opportunity to receive additional information not currently reported using standard urine culture techniques.

    View details for DOI 10.1128/JCM.00044-16

    View details for PubMedID 26962083

    View details for PubMedCentralID PMC4844725

  • Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome. PloS one Malki, K. n., Shapiro, J. W., Price, T. K., Hilt, E. E., Thomas-White, K. n., Sircar, T. n., Rosenfeld, A. B., Kuffel, G. n., Zilliox, M. J., Wolfe, A. J., Putonti, C. n. 2016; 11 (11): e0166757


    Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species' evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts.

    View details for DOI 10.1371/journal.pone.0166757

    View details for PubMedID 27861551

    View details for PubMedCentralID PMC5115800

  • The Interaction between Enterobacteriaceae and Calcium Oxalate Deposits PLOS ONE Barr-Beare, E., Saxena, V., Hilt, E. E., Thomas-White, K., Schober, M., Li, B., Becknell, B., Hains, D. S., Wolfe, A. J., Schwaderer, A. L. 2015; 10 (10): e0139575


    The role of calcium oxalate crystals and deposits in UTI pathogenesis has not been established. The objectives of this study were to identify bacteria present in pediatric urolithiasis and, using in vitro and in vivo models, to determine the relevance of calcium oxalate deposits during experimental pyelonephritis.Pediatric kidney stones and urine were collected and both cultured and sequenced for bacteria. Bacterial adhesion to calcium oxalate was compared. Murine kidney calcium oxalate deposits were induced by intraperitoneal glyoxalate injection and kidneys were transurethrally inoculated with uropathogenic Escherichia coli to induce pyelonephritis.E. coli of the family Enterobacteriaceae was identified in patients by calcium oxalate stone culture. Additionally Enterobacteriaceae DNA was sequenced from multiple calcium oxalate kidney stones. E. coli selectively aggregated on and around calcium oxalate monohydrate crystals. Mice inoculated with glyoxalate and uropathogenic E. coli had higher bacterial burdens, increased kidney calcium oxalate deposits and an increased kidney innate immune response compared to mice with only calcium oxalate deposits or only pyelonephritis.In a murine model, the presence of calcium oxalate deposits increases pyelonephritis risk, likely due to preferential aggregation of bacteria on and around calcium oxalate crystals. When both calcium oxalate deposits and uropathogenic bacteria were present, calcium oxalate deposit number increased along with renal gene transcription of inner stone core matrix proteins increased. Therefore renal calcium oxalate deposits may be a modifiable risk factor for infections of the kidney and urinary tract. Furthermore, bacteria may be present in calcium oxalate deposits and potentially contribute to calcium oxalate renal disease.

    View details for DOI 10.1371/journal.pone.0139575

    View details for Web of Science ID 000362511000035

    View details for PubMedID 26448465

    View details for PubMedCentralID PMC4598009

  • The female urinary microbiome in urgency urinary incontinence AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY Pearce, M. M., Zilliox, M. J., Rosenfeld, A. B., Thomas-White, K. J., Richter, H. E., Nager, C. W., Visco, A. G., Nygaard, I. E., Barber, M. D., Schaffer, J., Moalli, P., Sung, V. W., Smith, A. L., Rogers, R., Nolen, T. L., Wallace, D., Meikle, S. F., Gai, X., Wolfe, A. J., Brubaker, L., Pelvic Floor Disorders Network 2015; 213 (3): 347.e1?11


    The purpose of this study was to characterize the urinary microbiota in women who are planning treatment for urgency urinary incontinence and to describe clinical associations with urinary symptoms, urinary tract infection, and treatment outcomes.Catheterized urine samples were collected from multisite randomized trial participants who had no clinical evidence of urinary tract infection; 16S ribosomal RNA gene sequencing was used to dichotomize participants as either DNA sequence-positive or sequence-negative. Associations with demographics, urinary symptoms, urinary tract infection risk, and treatment outcomes were determined. In sequence-positive samples, microbiotas were characterized on the basis of their dominant microorganisms.More than one-half (51.1%; 93/182) of the participants' urine samples were sequence-positive. Sequence-positive participants were younger (55.8 vs 61.3 years old; P = .0007), had a higher body mass index (33.7 vs 30.1 kg/m(2); P = .0009), had a higher mean baseline daily urgency urinary incontinence episodes (5.7 vs 4.2 episodes; P < .0001), responded better to treatment (decrease in urgency urinary incontinence episodes, -4.4 vs -3.3; P = .0013), and were less likely to experience urinary tract infection (9% vs 27%; P = .0011). In sequence-positive samples, 8 major bacterial clusters were identified; 7 clusters were dominated not only by a single genus, most commonly Lactobacillus (45%) or Gardnerella (17%), but also by other taxa (25%). The remaining cluster had no dominant genus (13%).DNA sequencing confirmed urinary bacterial DNA in many women with urgency urinary incontinence who had no signs of infection. Sequence status was associated with baseline urgency urinary incontinence episodes, treatment response, and posttreatment urinary tract infection risk.

    View details for PubMedID 26210757

  • The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence MBIO Pearce, M. M., Hilt, E. E., Rosenfeld, A. B., Zilliox, M. J., Thomas-White, K., Fok, C., Kliethermes, S., Schreckenberger, P. C., Brubaker, L., Gai, X., Wolfe, A. J. 2014; 5 (4): e01283?14


    Bacterial DNA and live bacteria have been detected in human urine in the absence of clinical infection, challenging the prevailing dogma that urine is normally sterile. Urgency urinary incontinence (UUI) is a poorly understood urinary condition characterized by symptoms that overlap urinary infection, including urinary urgency and increased frequency with urinary incontinence. The recent discovery of the urinary microbiome warrants investigation into whether bacteria contribute to UUI. In this study, we used 16S rRNA gene sequencing to classify bacterial DNA and expanded quantitative urine culture (EQUC) techniques to isolate live bacteria in urine collected by using a transurethral catheter from women with UUI and, in comparison, a cohort without UUI. For these cohorts, we demonstrated that the UUI and non-UUI urinary microbiomes differ by group based on both sequence and culture evidences. Compared to the non-UUI microbiome, sequencing experiments revealed that the UUI microbiome was composed of increased Gardnerella and decreased Lactobacillus. Nine genera (Actinobaculum, Actinomyces, Aerococcus, Arthrobacter, Corynebacterium, Gardnerella, Oligella, Staphylococcus, and Streptococcus) were more frequently cultured from the UUI cohort. Although Lactobacillus was isolated from both cohorts, distinctions existed at the species level, with Lactobacillus gasseri detected more frequently in the UUI cohort and Lactobacillus crispatus most frequently detected in controls. Combined, these data suggest that potentially important differences exist in the urinary microbiomes of women with and without UUI, which have strong implications in prevention, diagnosis, or treatment of UUI. Importance: New evidence indicates that the human urinary tract contains microbial communities; however, the role of these communities in urinary health remains to be elucidated. Urgency urinary incontinence (UUI) is a highly prevalent yet poorly understood urinary condition characterized by urgency, frequency, and urinary incontinence. Given the significant overlap of UUI symptoms with those of urinary tract infections, it is possible that UUI may have a microbial component. We compared the urinary microbiomes of women affected by UUI to those of a comparison group without UUI, using both high-throughput sequencing and extended culture techniques. We identified statistically significant differences in the frequency and abundance of bacteria present. These differences suggest a potential role for the urinary microbiome in female urinary health.

    View details for DOI 10.1128/mBio.01283-14

    View details for Web of Science ID 000341588100052

    View details for PubMedID 25006228

    View details for PubMedCentralID PMC4161260

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