Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome

[1]  Rahel Nardos,et al.  The Impact of Local Estrogen on the Urogenital Microbiome in Genitourinary Syndrome of Menopause: A Randomized-Controlled Trial , 2022, Female pelvic medicine & reconstructive surgery.

[2]  R. Pickard,et al.  Alternative to prophylactic antibiotics for the treatment of recurrent urinary tract infections in women: multicentre, open label, randomised, non-inferiority trial , 2022, BMJ.

[3]  Dhwani K. Desai,et al.  Microbiome differential abundance methods produce different results across 38 datasets , 2022, Nature Communications.

[4]  E. Lukacz,et al.  Forming Consensus To Advance Urobiome Research , 2021, mSystems.

[5]  A. Wolfe,et al.  Phenyl-Lactic Acid Is an Active Ingredient in Bactericidal Supernatants of Lactobacillus crispatus , 2021, Journal of bacteriology.

[6]  A. Wolfe,et al.  Recurrent urinary tract infection: Association of clinical profiles with urobiome composition in women , 2021, Neurourology and urodynamics.

[7]  O. Shynlova,et al.  The effect of local estrogen therapy on the urinary microbiome composition of postmenopausal women with and without recurrent urinary tract infections , 2021, International Urogynecology Journal.

[8]  A. Wolfe,et al.  Genome Investigation of Urinary Gardnerella Strains and Their Relationship to Isolates of the Vaginal Microbiota , 2021, mSphere.

[9]  L. Brubaker,et al.  Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods , 2021, International Urogynecology Journal.

[10]  K. Glavind,et al.  Pre- and postmenopausal women have different core urinary microbiota , 2021, Scientific Reports.

[11]  K. Schmader,et al.  The Urinary Microbiome in Postmenopausal Women with Recurrent Urinary Tract Infections , 2020, bioRxiv.

[12]  L. Brubaker,et al.  Vaginal Estrogen Therapy Is Associated with Increased Lactobacillus in the Urine of Post-Menopausal Women with Overactive Bladder Symptoms. , 2020, American journal of obstetrics and gynecology.

[13]  R. Knight,et al.  The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences. , 2020, Cell host & microbe.

[14]  S. Peddada,et al.  Analysis of compositions of microbiomes with bias correction , 2020, Nature Communications.

[15]  P. Zimmern,et al.  Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection , 2020, mBio.

[16]  F. H. van der Westhuizen,et al.  Data on the optimisation of a solid phase extraction method for fractionating estrogen metabolites from small urine volumes , 2020, Data in brief.

[17]  K. Thomas-White,et al.  The urobiome of continent adult women: a cross‐sectional study , 2020, BJOG : an international journal of obstetrics and gynaecology.

[18]  K. Orth,et al.  Direct Detection of Tissue-Resident Bacteria and Chronic Inflammation in the Bladder Wall of Postmenopausal Women with Recurrent Urinary Tract Infection. , 2019, Journal of molecular biology.

[19]  C. Consolandi,et al.  Diversity of vaginal microbiome and metabolome during genital infections , 2019, Scientific Reports.

[20]  P. Gajer,et al.  The Cervicovaginal Microbiota-Host Interaction Modulates Chlamydia trachomatis Infection , 2019, mBio.

[21]  A. Simor,et al.  Association of Increased Colony-Count Threshold for Urinary Pathogens in Hospitalized Patients With Antimicrobial Treatment. , 2019, JAMA internal medicine.

[22]  E. Lukacz,et al.  Vaginal Estrogen for the Prevention of Recurrent Urinary Tract Infection in Postmenopausal Women: A Randomized Clinical Trial. , 2019, Female pelvic medicine & reconstructive surgery.

[23]  R. Chou,et al.  Recurrent Uncomplicated Urinary Tract Infections in Women: AUA/CUA/SUFU Guideline. , 2019, The Journal of urology.

[24]  Shuang Jiang,et al.  Bayesian Modeling of Microbiome Data for Differential Abundance Analysis. , 2019, 1902.08741.

[25]  T. Fait.  Menopause hormone therapy: latest developments and clinical practice , 2019, Drugs in context.

[26]  L. Brubaker,et al.  Urobiome updates: advances in urinary microbiome research , 2018, Nature Reviews Urology.

[27]  D. Fair,et al.  Community profiling of the urinary microbiota: considerations for low-biomass samples , 2018, Nature Reviews Urology.

[28]  Luke R. Thompson,et al.  Species-level functional profiling of metagenomes and metatranscriptomes , 2018, Nature Methods.

[29]  G. Pujalte,et al.  Urinary Tract Infection Antibiotic Resistance in the United States. , 2018, Primary care.

[30]  S. Wingett,et al.  FastQ Screen: A tool for multi-genome mapping and quality control , 2018, F1000Research.

[31]  P. Fournier,et al.  Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. , 2018, MicrobiologyOpen.

[32]  Nitin Kumar,et al.  Culturing of female bladder bacteria reveals an interconnected urogenital microbiota , 2018, Nature Communications.

[33]  P. Zimmern,et al.  Financial Burden of Recurrent Urinary Tract Infections in Women: A Time-driven Activity-based Cost Analysis. , 2018, Urology.

[34]  Will P. M. Rowe,et al.  Indexed variation graphs for efficient and accurate resistome profiling , 2018, bioRxiv.

[35]  A. Christie,et al.  Impact of Allergy and Resistance on Antibiotic Selection for Recurrent Urinary Tract Infections in Older Women. , 2017, Urology.

[36]  J. Terzic,et al.  The urinary microbiome associated with bladder cancer , 2017, bioRxiv.

[37]  P. Zimmern,et al.  Definition of Recurrent Urinary Tract Infections in Women: Which One to Adopt? , 2017, Female pelvic medicine & reconstructive surgery.

[38]  L. Brubaker,et al.  The female urinary microbiota, urinary health and common urinary disorders. , 2017, Annals of translational medicine.

[39]  Markus Krummenacker,et al.  The MetaCyc database of metabolic pathways and enzymes , 2017, Nucleic acids research.

[40]  N. Segata,et al.  Shotgun metagenomics, from sampling to analysis , 2017, Nature Biotechnology.

[41]  H. Kuo,et al.  Recent advances in recurrent urinary tract infection from pathogenesis and biomarkers to prevention , 2017, Ci ji yi xue za zhi = Tzu-chi medical journal.

[42]  Marina Vannucci,et al.  A Bayesian mixture model for clustering and selection of feature occurrence rates under mean constraints , 2017, Stat. Anal. Data Min..

[43]  Ana-Marija Cikoš,et al.  16-membered macrolide antibiotics: a review. , 2017, International journal of antimicrobial agents.

[44]  J. Venter,et al.  Microbial metagenome of urinary tract infection , 2017, bioRxiv.

[45]  J. Capelo,et al.  Mechanisms of quinolone action and resistance: where do we stand? , 2017, Journal of medical microbiology.

[46]  Jesse R. Zaneveld,et al.  Normalization and microbial differential abundance strategies depend upon data characteristics , 2017, Microbiome.

[47]  Rohan B. H. Williams,et al.  Enterococcal Metabolite Cues Facilitate Interspecies Niche Modulation and Polymicrobial Infection. , 2016, Cell host & microbe.

[48]  D. Fair,et al.  Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity? , 2016, Front. Cell. Infect. Microbiol..

[49]  A. Althouse.  Adjust for Multiple Comparisons? It's Not That Simple. , 2016, The Annals of thoracic surgery.

[50]  L. Forney,et al.  Effects of low dose estrogen therapy on the vaginal microbiomes of women with atrophic vaginitis , 2016, Scientific Reports.

[51]  J. Ravel,et al.  Translating the vaginal microbiome: gaps and challenges , 2016, Genome Medicine.

[52]  J. H. van de Wijgert,et al.  A fruitful alliance: the synergy between Atopobium vaginae and Gardnerella vaginalis in bacterial vaginosis-associated biofilm , 2016, Sexually Transmitted Infections.

[53]  L. Brubaker,et al.  The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms , 2016, Journal of Clinical Microbiology.

[54]  R. Fichorova,et al.  The Human Microbiome during Bacterial Vaginosis , 2016, Clinical Microbiology Reviews.

[55]  M. Vaneechoutte,et al.  Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes , 2015, PloS one.

[56]  S. Hultgren,et al.  Urinary tract infections: epidemiology, mechanisms of infection and treatment options , 2015, Nature Reviews Microbiology.

[57]  W. Wade,et al.  Actinomyces and Related Organisms in Human Infections , 2015, Clinical Microbiology Reviews.

[58]  R. Santen.  Vaginal administration of estradiol: effects of dose, preparation and timing on plasma estradiol levels , 2015, Climacteric : the journal of the International Menopause Society.

[59]  C. Alteri,et al.  Preferential Use of Central Metabolism In Vivo Reveals a Nutritional Basis for Polymicrobial Infection , 2015, PLoS pathogens.

[60]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[61]  Peter B. McGarvey,et al.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches , 2014, Bioinform..

[62]  Paul Turner,et al.  Reagent and laboratory contamination can critically impact sequence-based microbiome analyses , 2014, BMC Biology.

[63]  Michael J. Zilliox,et al.  The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence , 2014, mBio.

[64]  T. Hooton,et al.  Antimicrobial Stewardship and Urinary Tract Infections , 2014, Antibiotics.

[65]  D. Papeš,et al.  d-mannose powder for prophylaxis of recurrent urinary tract infections in women: a randomized clinical trial , 2014, World Journal of Urology.

[66]  Michael J. Zilliox,et al.  Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder , 2013, Journal of Clinical Microbiology.

[67]  J. Marchesi,et al.  The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults , 2013, Front. Cell. Infect. Microbiol..

[68]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[69]  J. Rohn,et al.  Spectrum of Bacterial Colonization Associated with Urothelial Cells from Patients with Chronic Lower Urinary Tract Symptoms , 2013, Journal of Clinical Microbiology.

[70]  M. Unemo,et al.  Composition of the Vaginal Microbiota in Women of Reproductive Age – Sensitive and Specific Molecular Diagnosis of Bacterial Vaginosis Is Possible? , 2013, PloS one.

[71]  Inger Ljungberg,et al.  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 , 2012, Journal of Translational Medicine.

[72]  Curtis Huttenhower,et al.  Microbial Co-occurrence Relationships in the Human Microbiome , 2012, PLoS Comput. Biol..

[73]  C. Huttenhower,et al.  Metagenomic microbial community profiling using unique clade-specific marker genes , 2012, Nature Methods.

[74]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[75]  L. Brubaker,et al.  Evidence of Uncultivated Bacteria in the Adult Female Bladder , 2012, Journal of Clinical Microbiology.

[76]  A. Nederbragt,et al.  Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons , 2011, BMC Microbiology.

[77]  R. Ley,et al.  The Antibacterial Lectin RegIIIγ Promotes the Spatial Segregation of Microbiota and Host in the Intestine , 2011, Science.

[78]  C. Huttenhower,et al.  Metagenomic biomarker discovery and explanation , 2011, Genome Biology.

[79]  A. Stapleton,et al.  Randomized, placebo-controlled phase 2 trial of a Lactobacillus crispatus probiotic given intravaginally for prevention of recurrent urinary tract infection. , 2011, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[80]  R. Preston,et al.  Plasma estrogen concentrations after oral and vaginal estrogen administration in women with atrophic vaginitis. , 2010, Fertility and sterility.

[81]  Y. Gustafson,et al.  Do urinary tract infections affect morale among very old women? , 2010, Health and quality of life outcomes.

[82]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[83]  P. Gajer,et al.  Vaginal microbiome of reproductive-age women , 2010, Proceedings of the National Academy of Sciences.

[84]  Jan Hudzicki,et al.  Kirby-Bauer Disk Diffusion Susceptibility Test Protocol , 2009 .

[85]  Peter D. Hoff,et al.  A First Course in Bayesian Statistical Methods , 2009 .

[86]  C. Labrie,et al.  Effect of one-week treatment with vaginal estrogen preparations on serum estrogen levels in postmenopausal women , 2009, Menopause.

[87]  J. Marrazzo,et al.  Relationship of Specific Vaginal Bacteria and Bacterial Vaginosis Treatment Failure in Women Who Have Sex with Women , 2008, Annals of Internal Medicine.

[88]  W. Stamm.  Estrogens and urinary-tract infection. , 2007, The Journal of infectious diseases.

[89]  S. Garland,et al.  The association of Atopobium vaginae and Gardnerella vaginalis with bacterial vaginosis and recurrence after oral metronidazole therapy. , 2006, The Journal of infectious diseases.

[90]  D. Chessel,et al.  From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. , 2004, Journal of theoretical biology.

[91]  Michael L Wilson,et al.  Laboratory diagnosis of urinary tract infections in adult patients. , 2004, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[92]  Deepayan Sarkar,et al.  Detecting differential gene expression with a semiparametric hierarchical mixture method. , 2004, Biostatistics.

[93]  M. Nader-Macías,et al.  Growth and lactic acid production by vaginal Lactobacillus acidophilus CRL 1259, and inhibition of uropathogenic Escherichia coli. , 2003, Journal of medical microbiology.

[94]  H. Okamura,et al.  Short term oral estriol treatment restores normal premenopausal vaginal flora to elderly women. , 2001, Maturitas.

[95]  W. Stamm,et al.  Urinary tract infections: disease panorama and challenges. , 2001, The Journal of infectious diseases.

[96]  A. Andreu,et al.  Assessment of the capacity of Lactobacillus to inhibit the growth of uropathogens and block their adhesion to vaginal epithelial cells. , 2001, The Journal of infectious diseases.

[97]  M. O’Connell.  Pharmacokinetic and Pharmacologic Variation Between Different Estrogen Products , 1995, Journal of clinical pharmacology.

[98]  W. Stamm,et al.  A controlled trial of intravaginal estriol in postmenopausal women with recurrent urinary tract infections. , 1993, The New England journal of medicine.

[99]  H. Jeffreys.  An invariant form for the prior probability in estimation problems , 1946, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[100]  A. Suskind,et al.  Recurrent Urinary Tract Infections are Associated With Frailty in Older Adults. , 2019, Urology.

[101]  E. Lukacz,et al.  Evaluation of the urinary microbiota of women with uncomplicated stress urinary incontinence , 2017, American journal of obstetrics and gynecology.

[102]  Stephen Tu,et al.  The Dirichlet-Multinomial and Dirichlet-Categorical models for Bayesian inference , 2014 .