Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

Worby, Colin J.; Schreiber, Henry L.; Straub, Timothy J.; van Dijk, Lucas R.; Bronson, Ryan A.; Olson, Benjamin S.; Pinkner, Jerome S.; Obernuefemann, Chloe L. P.; Muñoz, Vanessa L.; Paharik, Alexandra E.; Azimzadeh, Philippe N.; Walker, Bruce J.; Desjardins, Christopher A.; Chou, Wen-Chi; Bergeron, Karla; Chapman, Sinéad B.; Klim, Aleksandra; Manson, Abigail L.; Hannan, Thomas J.; Hooton, Thomas M.; Kau, Andrew L.; Lai, H. Henry; Dodson, Karen W.; Hultgren, Scott J.; Earl, Ashlee M.

doi:10.1038/s41564-022-01107-x

Cited by 188Gut microbiota and healthUrinary Tract Infections ManagementReproductive tract infections research

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

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Worby, Colin J., Schreiber, Henry L., Straub, Timothy J., van Dijk, Lucas R., Bronson, Ryan A., Olson, Benjamin S., Pinkner, Jerome S., Obernuefemann, Chloe L. P. +17 more·2022·Nature Microbiology

DOI 10.1038/s41564-022-01107-xPMC PMC9136705

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Abstract

Recurrent urinary tract infections (rUTIs) are a major health burden worldwide, with history of infection being a significant risk factor. While the gut is a known reservoir for uropathogenic bacteria, the role of the microbiota in rUTI remains unclear. We conducted a year-long study of women with (n = 15) and without (n = 16) history of rUTI, from whom we collected urine, blood and monthly faecal samples for metagenomic and transcriptomic interrogation. During the study 24 UTIs were reported, with additional samples collected during and after infection. The gut microbiome of individuals with a history of rUTI was significantly depleted in microbial richness and butyrate-producing bacteria compared with controls, reminiscent of other inflammatory conditions. However, Escherichia coli gut and bladder populations were comparable between cohorts in both relative abundance and phylogroup. Transcriptional analysis of peripheral blood mononuclear cells revealed expression profiles indicative of differential systemic immunity between cohorts. Altogether, these results suggest that rUTI susceptibility is in part mediated through the gut-bladder axis, comprising gut dysbiosis and differential immune response to bacterial bladder colonization, manifesting in symptoms.

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A strain of E. coli may be relatively harmless in the colon, but cause a urinary tract infection if it invades the urethra.
“a strain of E. coli may be relatively harmless in the colon, but cause a urinary tract infection if it invades the urethra 20 .”
From Human microbiome myths and misconceptions (2023) · cites this paper as [20]
It is not evidence-based to conclude that a characteristic 'pathobiome' has a role in most diseases.
“It is, therefore, a leap that is not yet evidence-based to conclude that a characteristic 'pathobiome' has a role in most diseases.”
From Human microbiome myths and misconceptions (2023) · cites this paper as [20]
The Discussion (page unavailable) says the study was not designed to establish causal links between gut dysbiosis and recurrent urinary tract infections. A search for ‘pathobiome’ and disease-wide microbial signatures found no passage assessing whether a characteristic pathobiome has a role in most diseases; the paper’s narrower caution does not establish that claim. (LLM, conf=0.76)
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Human microbiome myths and misconceptions
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Dysbiosis of a microbiota–immune metasystem in critical illness is associated with nosocomial infections
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The impact of biological sex on diseases of the urinary tract
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An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections
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The global burden of antimicrobial resistance – urinary tract infections
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Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae
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Current and emerging strategies to curb antibiotic-resistant urinary tract infections
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Gut-bladder axis enters the stage: Implication for recurrent urinary tract infections
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Effects of aging on urinary tract epithelial homeostasis and immunity
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Ecology of the respiratory tract microbiome
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Multi-omics time-series analysis in microbiome research: a systematic review
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From hype to hope: Considerations in conducting robust microbiome science
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Bioinspired Nanozymes as Nanodecoys for Urinary Tract Infection Treatment
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Gut Microbiota in Nutrition and Health with a Special Focus on Specific Bacterial Clusters
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Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study
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D-Mannose reduces cellular senescence and NLRP3/GasderminD/IL-1β-driven pyroptotic uroepithelial cell shedding in the murine bladder
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Bacterial live therapeutics for human diseases
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Urinary Tract Infections in Children
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Rise of the guardians: Gut microbial maneuvers in bacterial infections
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Risk Factors for Recurrent Urinary Tract Infections Among Women in a Large Integrated Health Care Organization in the United States
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Rapid and accurate testing for urinary tract infection: new clothes for the emperor
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Gut–bladder axis in recurrent UTI
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The clinical implications of bacterial pathogenesis and mucosal immunity in chronic urinary tract infection
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Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics
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Gut microbiome in men with chronic prostatitis/chronic pelvic pain syndrome: profiling and its predictive significance
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Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract
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Environmental Change, Changing Biodiversity, and Infections–Lessons for Kidney Health Community
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Etiology of recurrent cystitis in postmenopausal women based on vaginal microbiota and the role of Lactobacillus vaginal suppository
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Diagnostic accuracy of urine biomarkers for urinary tract infection in older women: a case-control study
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Interconnected microbiomes—insights and innovations in female urogenital health
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Consequences of host-microbiome interactions in preterm infants
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The human microbiome links to prostate cancer risk and treatment (Review)
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The microbiota in patients with interstitial cystitis/bladder pain syndrome: a systematic review
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Mechanisms of uropathogenic E. coli mucosal association in the gastrointestinal tract
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Longitudinal omics data analysis: approaches and applications
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Integrative Multi-Omics Analysis for the Determination of Non-Muscle Invasive vs. Muscle Invasive Bladder Cancer: A Pilot Study
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The Role of the Gut Microbiome in Urinary Tract Infections: A Narrative Review
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Pediatric urinary tract infections caused by poultry-associated Escherichia coli
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Gut Microbiome Implication and Modulation in the Management of Recurrent Urinary Tract Infection
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Current Viewpoint on Female Urogenital Microbiome—The Cause or the Consequence?
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Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection
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Aging Gut Microbiome in Healthy and Unhealthy Aging
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Gut microbiota and interstitial cystitis: exploring the gut-bladder axis through mendelian randomization, biological annotation and bulk RNA sequencing
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Transmission of Antibiotic-Susceptible Escherichia coli Causing Urinary Tract Infections in a Fecal Microbiota Transplantation Recipient: Consequences for Donor Screening?
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The Role of Metabolomics and Microbiology in Urinary Tract Infection
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Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection
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A systematic and comprehensive review of the role of microbiota in urinary chronic pelvic pain syndrome
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Intestinal microbiology and urinary tract infection associated risk in long-term aged care residents
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Leveraging the microbiome in the treatment of sepsis: potential pitfalls and new perspectives
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Nitrofurantoin: what is the evidence for current UK guidance?
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Pathogen-specific alterations in intestinal microbiota precede urinary tract infections in preterm infants: a longitudinal case-control study
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Emergence of recurrent urinary tract infection: Dissecting the mechanism of antimicrobial resistance, host-pathogen interaction, and hormonal imbalance
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Fabrication of levofloxacin-loaded porcine acellular dermal matrix hydrogel and functional assessment in urinary tract infection
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Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection
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Exploring urinary microbiome: insights into neurogenic bladder and improving management of urinary tract infections
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Gut microbiota and Parkinson’s disease: exploring pathogenesis and potential therapeutic strategies from a gut-brain axis perspective
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Intravesical aminoglycoside instillations as prophylaxis for recurrent urinary tract infection: patient satisfaction, long-term safety and efficacy
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Tumor-colonizing Lachnoclostridium-mediated chemokine expression enhances the immune infiltration of bladder urothelial carcinoma
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Associations of overactive bladder (OAB) with suicidal ideation incidence and all-cause mortality among the U.S. population
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Case report: A successfully treated case of community-acquired urinary tract infection due to Klebsiella aerogenes in Bangladesh
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Unnecessary Antibiotics in Older Female Patients with Recurrent Urinary Tract Infections
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Advances in Autophagy–Lysosomal Pathway and Neurodegeneration via Brain–Gut Axis
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Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome
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Underexplored maternal microbiomes: immune, metabolic, and microbial pathways shaping pregnancy outcomes
Michita, R. T., Jimenez, N. R., Herbst‐Kralovetz, M. M., & Mysorekar, I. U. (2026) · Infection and Immunity · doi:10.1128/iai.00608-25 · Cited by 8 · see citing works
Functional hypothalamic amenorrhea: gut microbiota composition and the effects of exogenous estrogen administration
Notaristefano, G., Ponziani, F. R., Ranalli, M., Diterlizzi, A., Policriti, M. A., Stella, L., Zompo, F. D., Fianchi, F., Picca, A., Petito, V., et al. (2023) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00281.2023 · Cited by 8 · see citing works
Enlisting Probiotics to Combat Recurrent Urinary Tract Infections in Women—A Military Strategy for Meeting the Challenge
Watson, R. A. (2023) · Antibiotics · doi:10.3390/antibiotics12010167 · Cited by 8 · see citing works
Case Commentary: Unlocking the Potential of Bacteriophage to Prevent Recurrent Urinary Tract Infections after Kidney Transplantation
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Research progress of hydrogels in the prevention of pelvic inflammatory disease
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Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain
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Fecal microbiota transplantation alleviates immunosuppressant-associated diarrhea and recurrent urinary tract infection in kidney transplant recipients: a retrospective analysis
Hu, J., Liu, D., Liao, G., Guo, Y., Liu, Y., Liao, J., Chen, H., Zhou, S., Yang, S., Li, S., et al. (2025) · Gut Pathogens · doi:10.1186/s13099-025-00705-4 · Cited by 7 · see citing works
Uropathogenic Escherichia coli niche occupancy determines the effects of mucosal vaccine against FimH
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The female urogenital microbiome: Ecological insights, therapeutic strategies, and molecular mechanisms
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Fecal Microbiota Transplant Is Associated With Resolution of Recurrent Urinary Tract Infection
Jeong, S. H., Vasavada, S. P., Lashner, B. A., & Werneburg, G. T. (2025) · Urology · doi:10.1016/j.urology.2025.05.052 · Cited by 7 · see citing works
Blood Microbiota and Its Products: Mechanisms of Interference with Host Cells and Clinical Outcomes
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Diagnosing and engineering gut microbiomes
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Non-coding RNAs in bladder cancer, a bridge between gut microbiota and host?
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The role of the microbiota-gut-brain axis and artificial intelligence in cognitive health of pediatric obstructive sleep apnea: A narrative review
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Effects of the Curcuminoid and Non-Curcuminoid Compounds of Turmeric on the Gut Microbiome and Inflammation: Potential Use in the Treatment and Prevention of Disease
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Distinct ecological fitness factors coordinated by a conserved Escherichia coli regulator during systemic bloodstream infection
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Gut-bladder axis syndrome associated with recurrent UTIs in humansPreprint
Worby, C. J., Schreiber, H. L., Straub, T. J., van Dijk, L. R., Bronson, R. A., Olson, B. S., Pinkner, J. S., Obernuefemann, C. L. P., Muñoz, V. L., Paharik, A. E., et al. (2021) · medRxiv · doi:10.1101/2021.11.15.21266268 · Cited by 4 · see citing works
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THE URINARY MICROBIOME AND RECURRENT URINARY TRACT INFECTIONS
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Authors: Worby, C. J., Schreiber, H. L., Straub, T. J., van Dijk, L. R., Bronson, R. A., Olson, B. S., Pinkner, J. S., Obernuefemann, C. L. P., Muñoz, V. L., Paharik, A. E., Azimzadeh, P. N., Walker, B. J., Desjardins, C. A., Chou, W.-C., Bergeron, K., Chapman, S. B., Klim, A., Manson, A. L., Hannan, T. J., Hooton, T. M., Kau, A. L., Lai, H. H., Dodson, K. W., Hultgren, S. J., & Earl, A. M.
Affiliations: Broad Institute (US)
California Institute of Technology (US)
Washington University in St. Louis (US)
University of Miami (US)
Corresponding author: Hultgren, Scott J.
Earl, Ashlee M.
ORCID: Worby, Colin J.
Schreiber, Henry L.
Straub, Timothy J.
van Dijk, Lucas R.
Olson, Benjamin S.
Pinkner, Jerome S.
Paharik, Alexandra E.
Azimzadeh, Philippe N.
Desjardins, Christopher A.
Chapman, Sinéad B.
Manson, Abigail L.
Hannan, Thomas J.
Hooton, Thomas M.
Kau, Andrew L.
Lai, H. Henry
Dodson, Karen W.
Hultgren, Scott J.
Earl, Ashlee M.
Venue: Nature Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2022-05-02
Volume: 7
Issue: 5
Pages: 630-639
ISSN: 2058-5276 (ISSN-L)
DOI: 10.1038/s41564-022-01107-x
PMC: PMC9136705
OpenAlex: W4225388682
Cited by: 188
References: 64
Citations by year: 2026: 48 · 2025: 46 · 2024: 48 · 2023: 34 · 2022: 11 · 2012: 1
FWCI: 11.35
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Microbiology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
CaltechAUTHORS (California Institute of Technology) (submittedVersion)
Funders: U.S. Department of Health & Human Services | National Institutes of Health (U01AI095542)
U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (U19AI110818)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Medicine › Epidemiology › Urinary Tract Infections Management
Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
Keywords: recurrent urinary tract infection, gut dysbiosis, women, butyrate-producing bacteria, Escherichia coli, uropathogenic bacteria, peripheral blood mononuclear cells, systemic immunity, microbial richness, bladder colonization, multi-omics
MeSH terms: Gastrointestinal Microbiome, Escherichia coli, Escherichia coli Infections, Female, Humans, Leukocytes, Mononuclear, Male, Urinary Tract Infections, Dysbiosis

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Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

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