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References from Role of the urobiome in urinary tract infections: current knowledge and research prospects. Local targets link to admitted publications; unresolved targets remain external evidence.
Global, regional, and national burden of urinary tract infections from 1990 to 2019: an analysis of the global burden of disease study 2019
10.1007/s00345-021-03913-0 · 2022 · External reference
Unresolved reference
External reference
Epidemiology of urinary tract infections: incidence, morbidity, and economic costs
10.1016/s0002-9343(02)01054-9 · 2002 · External reference
Recurring urinary tract infection: incidence and risk factors
10.2105/ajph.80.3.331 · 1990 · External reference
Recurrence of urinary tract infection in a primary care setting: analysis of a 1-year follow-up of 179 women
10.1093/clinids/22.1.91 · 1996 · External reference
Antibiotic prescribing patterns and guideline concordance for uncomplicated urinary tract infections among adult women in the US military health system
10.1001/jamanetworkopen.2022.25730 · 2022 · External reference
Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder
10.1128/jcm.02876-13 · 2014 · External reference
Evidence of uncultivated bacteria in the adult female bladder
10.1128/jcm.05852-11 · 2012 · External reference
Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury
10.1186/1479-5876-10-174 · 2012 · External reference
The microbiome of the urinary tract—a role beyond infection
10.1038/nrurol.2014.361 · 2015 · External reference
Advances in understanding the human urinary microbiome and its potential role in urinary tract infection
10.1128/mbio.00218-20 · 2020 · External reference
Urobiome and inflammation: a systematic review on microbial imbalances and diagnostic tools for urinary disorders
10.1016/j.urology.2025.03.050 · 2025 · External reference
Temporal dynamics of the adult female lower urinary tract microbiota
10.1128/mbio.00475-20 · 2020 · External reference
Global chemical effects of the microbiome include new bile-acid conjugations
10.1038/s41586-020-2047-9 · 2020 · External reference
Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections
10.1073/pnas.1713372114 · 2017 · External reference
The good and the bad: ecological interaction measurements between the urinary microbiota and uropathogens
10.3389/fmicb.2021.659450 · 2021 · External reference
The urinary microbiome and biological therapeutics: novel therapies for urinary tract infections
10.1016/j.micres.2022.127010 · 2022 · External reference
A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals
10.1126/sciadv.adi9834 · 2023 · External reference
Building microbial communities to improve antimicrobial strategies
10.1038/s44259-025-00115-1 · 2025 · External reference
Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection
10.1038/s41522-025-00823-6 · 2025 · External reference
Metabolomics strategy for diagnosing urinary tract infections
10.1038/s41467-025-57765-y · 2025 · External reference
A urine-dependent human urothelial organoid offers a potential alternative to rodent models of infection
10.1038/s41598-018-19690-7 · 2018 · External reference
Urine and vaginal microbiota compositions of postmenopausal and premenopausal women differ regardless of recurrent urinary tract infection and renal transplant status
10.1038/s41598-022-06646-1 · 2022 · External reference
The urobiome of continent adult women: a cross-sectional study
10.1111/1471-0528.15920 · 2020 · External reference
The urinary, vaginal, and perineal microbiome: commonalities and differences
10.1007/s00192-025-06144-8 · 2025 · External reference
Culturing of female bladder bacteria reveals an interconnected urogenital microbiota
10.1038/s41467-018-03968-5 · 2018 · External reference
The etiology and management of recurrent urinary tract infections in postmenopausal women
10.1080/13697137.2018.1551871 · 2019 · External reference
Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome
2022 · External reference
The urobiome in men and women: a clinical review
10.1016/j.cmi.2022.08.010 · 2023 · External reference
Increased human pathogenic potential of Escherichia coli from polymicrobial urinary tract infections in comparison to isolates from monomicrobial culture samples
10.1099/jmm.0.020602-0 · 2011 · External reference
Candida urinary tract infections—epidemiology
10.1093/cid/cir109 · 2011 · External reference
The prevalence and association of different uropathogens detected by M-PCR with infection-associated urine biomarkers in urinary tract infections
2024 · External reference
Interconnected microbiomes-insights and innovations in female urogenital health
10.1111/febs.17235 · 2025 · External reference
The urobiomes of adult women with various lower urinary tract symptoms status differ: a re-analysis
10.3389/fcimb.2022.860408 · 2022 · External reference
Urinary tract infections: epidemiology, mechanisms of infection and treatment options
10.1038/nrmicro3432 · 2015 · External reference
UroPathogenic Escherichia coli (UPEC) infections: virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies
10.3389/fmicb.2017.01566 · 2017 · External reference
Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease
10.1371/journal.ppat.1006238 · 2017 · External reference
The pathogenic potential of a microbe
10.1128/msphere.00015-17 · 2017 · External reference
The urobiome, urinary tract infections, and the need for alternative therapeutics
10.1016/j.micpath.2021.105295 · 2021 · External reference
Urinary tract infection: recent insight into the evolutionary arms race between uropathogenic Escherichia coli and our immune system
10.1093/ndt/gfx022 · 2017 · External reference
Urinary tract infections in postmenopausal women revisited (UTIr): a prospective observational cohort study to explore the urobiomes of postmenopausal women with and without recurrent urinary tract infections
10.1186/s12879-025-11269-8 · 2025 · External reference
The urothelium: a multi-faceted barrier against a harsh environment
10.1038/s41385-022-00565-0 · 2022 · External reference
The urothelium: life in a liquid environment
10.1152/physrev.00041.2019 · 2020 · External reference
The glycobiology of uropathogenic E. coli infection: the sweet and bitter role of sugars in urinary tract immunity
10.1111/imm.13330 · 2021 · External reference
Glycosylation of uroplakins. Implications for bladder physiopathology
10.1007/s10719-014-9564-4 · 2014 · External reference
Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection
10.1053/j.gastro.2006.04.020 · 2006 · External reference
Mucin gene expression in human urothelium and in intestinal segments transposed into the urinary tract
10.1016/s0022-5347(05)67206-0 · 2000 · External reference
Urinary glycosaminoglycans are associated with recurrent UTI and urobiome ecology in postmenopausal women
10.1021/acsinfecdis.3c00027 · 2023 · External reference
Urinary tract infections: microbial pathogenesis, host-pathogen interactions and new treatment strategies
10.1038/s41579-020-0324-0 · 2020 · External reference
Architecture and function of human uromodulin filaments in urinary tract infections
10.1126/science.aaz9866 · 2020 · External reference
Uromodulin and risk of upper urinary tract infections: a Mendelian randomization study
10.1053/j.ajkd.2024.11.007 · 2025 · External reference
Immune defenses in the urinary tract
10.1016/j.it.2023.07.001 · 2023 · External reference
Lipocalin 2 imparts selective pressure on bacterial growth in the bladder and is elevated in women with urinary tract infection
10.4049/jimmunol.1401528 · 2014 · External reference
Recurrent infections drive persistent bladder dysfunction and pain via sensory nerve sprouting and mast cell activity
10.1126/sciimmunol.adi5578 · 2024 · External reference
Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics
10.1038/s41579-024-01092-4 · 2025 · External reference
Virulence factors of uropathogens and their role in host pathogen interactions
10.1016/j.tcsw.2022.100075 · 2022 · External reference
Iron regulates contrasting toxicity of uropathogenic Escherichia coli in macrophages and epithelial cells
2022 · External reference
Gram-positive uropathogens, polymicrobial urinary tract infection, and the emerging microbiota of the urinary tract
10.1128/microbiolspec.uti-0012-2012 · 2016 · External reference
Lactobacillus crispatus limits bladder uropathogenic E. coli infection by triggering a host type I interferon response
10.1073/pnas.2117904119 · 2022 · External reference
Environmental fluctuations and their effects on microbial communities, populations and individuals
10.1093/femsre/fuaa068 · 2021 · External reference
Metabolic complexity drives divergence in microbial communities
10.1038/s41559-024-02440-6 · 2024 · External reference
Heterogeneity in bacterial specialized metabolism
10.1016/j.jmb.2019.04.042 · 2019 · External reference
Abundant urinary amino acids activate glutamine synthetase-encoding glnA by two different mechanisms in Escherichia coli
10.1128/jb.00376-23 · 2024 · External reference
Differential expression of urease genes and ureolytic activity of uropathogenic Escherichia coli and Pseudomonas aeruginosa isolates in different nutritional conditions
10.1007/s00203-023-03722-6 · 2023 · External reference
Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract
10.1128/mbio.02515-23 · 2023 · External reference
The evolution and ecology of bacterial warfare
10.1016/j.cub.2019.04.024 · 2019 · External reference
Exploring microbiome functional dynamics through space and time with trait-based theory
10.1128/msystems.00530-21 · 2021 · External reference
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems
10.1038/s41467-018-07946-9 · 2019 · External reference
Context-dependent dynamics lead to the assembly of functionally distinct microbial communities
10.1038/s41467-020-15169-0 · 2020 · External reference
Effectiveness of prophylactic oral and/or vaginal probiotic supplementation in the prevention of recurrent urinary tract infections: a randomized, double-blind, placebo-controlled trial
10.1093/cid/ciad766 · 2024 · External reference
The role of lactic acid production by probiotic Lactobacillus species in vaginal health
10.1016/j.resmic.2017.04.001 · 2017 · External reference
Phenyl-lactic acid is an active ingredient in bactericidal supernatants of Lactobacillus crispatus
10.1128/jb.00360-21 · 2021 · External reference
Enterococcal metabolite cues facilitate interspecies niche modulation and polymicrobial infection
10.1016/j.chom.2016.09.004 · 2016 · External reference
Metabolite co-variation networks reveal keystone functions and an emergent pathogen state in the human urobiome
2026 · External reference
Loss of social behaviours in populations of Pseudomonas aeruginosa infecting lungs of patients with cystic fibrosis
10.1371/journal.pone.0083124 · 2014 · External reference
Long-term social dynamics drive loss of function in pathogenic bacteria
10.1073/pnas.1508324112 · 2015 · External reference
Microbial interactions affect the tempo and mode of antibiotic resistance evolution
2024 · External reference
Metabolic constraints on the evolution of antibiotic resistance
10.15252/msb.20167028 · 2017 · External reference
Pyocyanin produced by Pseudomonas aeruginosa creates legacy effects that promote antibiotic resistance evolution in enterococci
10.1128/aac.00078-26 · 2026 · External reference
Community context influences the conjugation efficiency of Escherichia coli
10.1093/femsmc/xtae023 · 2024 · External reference
Microbiota-mediated colonization resistance against intestinal pathogens
10.1038/nri3535 · 2013 · External reference
Microbiomes in light of traits: a phylogenetic perspective
10.1126/science.aac9323 · 2015 · External reference
Residence time structures microbial communities through niche partitioning
10.1111/ele.70093 · 2025 · External reference
The human urobiome
10.1007/s00335-021-09862-8 · 2021 · External reference
Ecological modelling approaches for predicting emergent properties in microbial communities
10.1038/s41559-022-01746-7 · 2022 · External reference
Unresolved reference
2015 · External reference
Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii
10.3389/fmicb.2022.1064013 · 2022 · External reference
Metabolic interactions affect the biomass of synthetic bacterial biofilm communities
10.1128/msystems.01045-23 · 2023 · External reference
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
10.1038/s41596-021-00593-3 · 2021 · External reference
BacArena: individual-based metabolic modeling of heterogeneous microbes in complex communities
10.1371/journal.pcbi.1005544 · 2017 · External reference
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data
10.1093/nar/gkad407 · 2023 · External reference
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins
10.1093/nar/gky383 · 2018 · External reference
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation
10.1093/nar/gkad344 · 2023 · External reference
Microbial community dynamics in nutrient-pulsed chemostats
10.1111/j.1574-6941.2006.00095.x · 2006 · External reference
The use of chemostats in microbial systems biology
2013 · External reference
Deep reinforcement learning for the control of microbial co-cultures in bioreactors
10.1371/journal.pcbi.1007783 · 2020 · External reference
Removal of toxic volatile compounds in batch culture prolongs stationary phase and delays death of Escherichia coli
10.1128/aem.01860-21 · 2021 · External reference
Reaching unreachables: obstacles and successes of microbial cultivation and their reasons
10.3389/fmicb.2023.1089630 · 2023 · External reference
Modelling the role of the microbiome in antimicrobial resistance across scales
10.1038/s41564-026-02390-8 · 2026 · External reference
Predicting the first steps of evolution in randomly assembled communities
10.1038/s41467-024-52467-3 · 2024 · External reference
Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization
10.1038/s41467-023-39121-0 · 2023 · External reference
Engineering synthetic spatial patterns in microbial populations and communities
10.1016/j.mib.2022.102149 · 2022 · External reference
Surfactin facilitates establishment of Bacillus subtilis in synthetic communities
10.1093/ismejo/wraf013 · 2025 · External reference
The microbiome-shaping roles of bacteriocins
10.1038/s41579-021-00569-w · 2021 · External reference
Yersiniabactin is a quorum-sensing autoinducer and siderophore in uropathogenic Escherichia coli
10.1128/mbio.00277-23 · 2024 · External reference
An exploratory in silico analysis of bacteriocin gene clusters in the urobiome
10.20517/mrr.2023.78 · 2024 · External reference
A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics
10.1016/j.cell.2014.08.032 · 2014 · External reference
Microbial metabolites: cause or consequence in gastrointestinal disease?
10.1152/ajpgi.00008.2022 · 2022 · External reference
Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates
10.1038/s41467-024-49215-y · 2024 · External reference
Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra
10.1038/s41564-023-01524-6 · 2023 · External reference
Large-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides
10.1038/s41467-025-58280-w · 2025 · External reference
Bacterial analogs of plant tetrahydropyridine alkaloids mediate microbial interactions in a rhizosphere model system
10.1128/aem.03058-18 · 2019 · External reference
Mass spectrometry-based metabolomics in microbiome investigations
10.1038/s41579-021-00621-9 · 2022 · External reference
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
10.1038/s41564-023-01575-9 · 2024 · External reference
Linking genomics and metabolomics to chart specialized metabolic diversity
10.1039/d0cs00162g · 2020 · External reference
Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection
10.1038/s41522-025-00844-1 · 2025 · External reference
Malodorous biogenic amines in Escherichia coli-caused urinary tract infections in women-a metabolomics approach
10.1038/s41598-020-66662-x · 2020 · External reference
Untargeted metabolomics pilot study using UHPLC-qTOF MS profile in sows’ urine reveals metabolites of bladder inflammation
10.3390/metabo12121186 · 2022 · External reference
The first lanthipeptide from Lactobacillus iners, Inecin L, exerts high antimicrobial activity against human vaginal pathogens
10.1128/aem.02123-22 · 2023 · External reference
A natural product chemist’s guide to unlocking silent biosynthetic gene clusters
10.1146/annurev-biochem-081420-102432 · 2021 · External reference
Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules
10.1093/femsre/fuw035 · 2017 · External reference
Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications
2023 · External reference
SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria
10.1128/aem.01559-25 · 2026 · External reference
Synthetic microbial communities
10.1016/j.mib.2014.02.002 · 2014 · External reference
Design of synthetic human gut microbiome assembly and butyrate production
10.1038/s41467-021-22938-y · 2021 · External reference
The role of synthetic microbial communities (SynCom) in sustainable agriculture
10.3389/fagro.2022.896307 · 2022 · External reference
Strategies for tailoring functional microbial synthetic communities
10.1093/ismejo/wrae049 · 2024 · External reference
Directed differentiation of human induced pluripotent stem cells into mature stratified bladder urothelium
10.1038/s41598-019-46848-8 · 2019 · External reference
Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model
10.1016/j.celrep.2021.109351 · 2021 · External reference
A microphysiological human mini-bladder reveals urine-urothelium interplay in tissue resilience and UPEC recurrence in urinary tract infections
10.1038/s41467-026-68573-3 · 2026 · External reference
Development of iPSC-derived urothelial organoids towards investigating the effect of hormones on host-defense to urinary tract infections
2026 · External reference
Mouse and human urothelial cancer organoids: a tool for bladder cancer research
10.1073/pnas.1803595116 · 2019 · External reference
Differentiation of human pluripotent stem cells into urothelial organoids via transient activation of WNT signaling
10.1016/j.isci.2025.112398 · 2025 · External reference
Voided midstream urine culture and acute cystitis in premenopausal women
10.1056/nejmoa1302186 · 2013 · External reference
Unresolved reference
External reference
Metagenomic sequencing as a diagnostic tool for urine culture negative febrile urinary tract infection
10.1016/j.jinf.2026.106783 · 2026 · External reference
Reducing antimicrobial use for asymptomatic bacteriuria
10.1016/j.ajic.2026.02.040 · 2026 · External reference
Metagenomics in the diagnosis and treatment of urinary tract infections: a systematic review and meta-analysis
10.1016/j.diagmicrobio.2025.116995 · 2025 · External reference
Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study
10.1016/s2666-5247(22)00088-x · 2022 · External reference
Intravesical Lactobacillus rhamnosus GG is safe and well tolerated in adults and children with neurogenic lower urinary tract dysfunction: first-in-human trial
10.1177/1756287219875594 · 2019 · External reference
Microbiome research in practice: priorities for clinical translation and impact
10.1016/j.cmi.2026.01.021 · 2026 · External reference
