The After Antibiotics Study: UTI Omics

Investigating the Implications of Antibiotic Treatment for Urinary Tract Infection on the Urinary Microbiome and Metabolome in Young Women

For my senior honors research thesis in Human Biology and Computing in Visual Arts, I will be conducting an observational clinical study to investigate the collateral impacts of urinary tract infection antibiotic treatment and natural remedies on the female urinary microbiome and metabolome in college aged women. Metagenomics and metabolomics will be used to characterize the microbiome and host metabolome. Thesis work includes study design, wet lab experimentation, bioinformatics analysis, clinical protocol creation, and funding the project. This work is currently supported by the Ledell Science and Engineering Fellowship, Marshall Research Scholarship, and Associated Students Research Grant. This study received IRB approval in December 2017.

Principal Investigator: Anika Ullah, B.S Candidate

Primary thesis advisor: Rob Knight, PhD, Director of Center for Microbiome Innovation UC San Diego, Professor of Pediatrics, Computer Science and Engineering, University of California San Diego School of Medicine

Clinical thesis advisor: Linda Brubaker, MD, FACOG, Professor of Reproductive Medicine at University of California San Diego School of Medicine, Former Dean of Stritch School of Medicine, Loyola University Chicago

Metabolomics thesis advisor: Pieter Dorrestein, PhD, Director of Collaborative Mass Spectrometry Innovation Center,
Co-Director of Institute for Metabolomics Medicine, Professor of Pharmacology and Pediatrics, Skaggs School of Pharmacy 

Computing in Visual Arts thesis advisor: Sheldon Brown, Director of the Arthur C. Clarke Center for Human Imagination, Professor of Visual Arts, University of California San Diego

Urine is not sterile.

Healthy microbial flora live in our bladders & urogenital tract.


Until recently, the urinary tract infection (UTI), a disease affecting nearly 1 in 3 women globally by the age of 24[1], was thought to be caused by the invasion of a single foreign pathogenic bacterial species into a sterile urinary tract[2]. However, contemporary advances have revealed that urine is not sterile: like other environments of the human body, the urogenital tract has its own distinct community of bacteria (microbiota) that collectively play a role in maintaining a healthy urinary tract[3]. The current UTI treatment does not take into account the effect of antibiotics on protective microbes in the bladder[4] and contribute to antibiotic resistance[5]. There is a need to investigate the collateral effects of UTI antibiotics and non-antibiotic means of UTI treatment on the urinary microbiome and metabolome.  These therapies include cranberry products, d-mannose, NSAIDS, and urinary analgesics. Our research project will study the metabolic interactions between common clinical UTI treatments and the resident urinary microbiome during recovery after UTI. Laboratory techniques to characterize the urogenital microbiota during and after UTI will include shotgun sequencing, metabolomics, and multi-omics visualization. This work is designed to advance prevention of UTI in young women, and may provide information to develop alternative UTI therapies.

Discovery of the Urinary Microbiome

Discovery of the Urinary Microbiome

Rising Antibiotic Resistance

Inconclusive Studies on Effectiveness of Natural Remedies  (Cranberry Juice)

Need more information

to develop alternative UTI


Additional Background Information

Urinary tract infection (UTI) poses significant burdens individual patients as well as our healthcare system, considering that UTI is the cause of eight million visits clinic and emergency department visits per year, costing approximately $1.6 billion dollars annually. Antibiotics prescribed to treat UTI account for 15% of all outpatient prescriptions, and antibiotic resistance is rising. Between 2000 and 2010, the proportion of UTI resistant to the commonly prescribed broad-spectrum antibiotic ciprofloxacin (Cipro) rose from 3% to over 17%, mirrored by an increase in recurrent UTI (rUTI) as well[6]. The Antimicrobial Resistance Epidemiological Survey on Cystitis (ARESC), an international survey completed in 2009, reported that over 10% of UTI causing E. coli isolates were resistant to at least three different classes of antimicrobial agents[7]. Here at UCSD, patterns of resistance for common uropathogen are reported to be rising each year. Risks of antibiotic usage and resistance aside from the context of UTI include increased vaginal and gastrointestinal infections due to antibiotic caused selection of resistant uropathogens and commensal bacteria in the gut and vaginal microbiota[8],[9],[10]

Previously, urine and the urogenital tract were considered to be sterile; however, recent advancements in culture-independent testing, expanded urine culture techniques, metagenomics, and metabolomics document the existence of a resident urinary microbiome. Similar to other resident microbiomes in the human body, the urinary microbiome is composed of commensal flora, such as staphylococci and streptococci, and protective flora.[11][12] Studies have demonstrated that numerous indigenous commensal and probiotic bacterial strains demonstrated the ability to attenuate mucosal inflammation in the urogenital tract, highlighting a pathway through which the urinary microbiome mediates UTI[13][14]. Generally, the resident urinary microbiome can mediate UTI through competition with pathogenic and commensal bacteria, metabolite mediated interactions with pathogenic and commensal bacteria, crosstalk with the immune system, interactions with the gut or vaginal microbiome, and alteration of the urinary tract’s mucosal lining. 


Thus, there is a demonstrated need to study the collateral effects of UTI antibiotic treatment, as well as broaden the evidence for non-antibiotic therapies for UTI.


Two sets of urine samples, fecal swabs, and vaginal swabs will be collected from patients enrolled in this study: one set from when the patient comes into the clinic seeking therapy for urinary tract infection, and one set after the same patient's antibiotic treatment course has been completed. Each set of samples will then be analyzed with shotgun sequencing to determine the composition of microbial flora and mass spectrometry and to determine the host's metabolite profile before and after antibiotic treatment. A clinical questionnaire provided to patients during the study will characterize usage of any non antibiotic therapies and other lifestyle factors that may impact UTI recovery. Open source bioinformatic tools developed by the Knight lab and Dorrestein lab will be used to evaluate differences and key features in specimen data and metadata.



(Disease State)

Post Antibiotic


(Healthy State)

bacterial metagenomics


clinical metadata

Post Study Public Art Installation

After the study is completed, I will create a public art installation using data visualizations of multi-omics data collected in this study to to explore the complex interactions of omics data in women's health and provoke thought about representations of medical data in a society where precision medicine is increasingly viable. Read more about the visual arts aspect of my thesis work under the Media Arts section of my website.


[1] Foxman, Betsy. "Epidemiology of urinary tract infections: incidence, morbidity, and economic costs." The American journal of medicine 113.1 (2002): 5-13.

[2] McLellan, Lisa K., and David A. Hunstad. "Urinary tract infection: pathogenesis and outlook." Trends in Molecular Medicine 22.11 (2016): 946-957.

[3] Whiteside, S. A., Razvi, H., Dave, S., Reid, G., & Burton, J. P. (2015). The microbiome of the urinary tract—a role beyond infection. Nature Reviews Urology, 12(2), 81-90. doi:10.1038/nrurol.2014.361

[4]Brubaker, L., & Wolfe, A. (2016). The urinary microbiota: a paradigm shift for bladder disorders? Current Opinion in Obstetrics and Gynecology, 28(5), 407-412. doi:10.1097/gco.0000000000000298

[5] Ventola, C. Lee. “The Antibiotic Resistance Crisis: Part 1: Causes and Threats.” Pharmacy and Therapeutics 40.4 (2015): 277–283. Print.

[6]Brumbaugh, Ariel R., and Harry LT Mobley. "Preventing urinary tract infection: progress toward an effective Escherichia coli vaccine." Expert review of vaccines 11.6 (2012): 663-676.

[7]The ARESC study: an international survey on the antimicrobial resistance of pathogens involved in uncomplicated urinary tract infections.Schito GC, Naber KG, Botto H, Palou J, Mazzei T, Gualco L, Marchese AInt J Antimicrob Agents. 2009 Nov; 34(5):407-13.

[8] The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.

Dethlefsen L, Huse S, Sogin ML, Relman DA PLoS Biol. 2008 Nov 18; 6(11):e280.

[9] The risks of symptomatic vaginal candidiasis after oral antibiotic therapy. MacDonald TM, Beardon PH, McGilchrist MM, Duncan ID, McKendrick AD, McDevitt DGQ J Med. 1993 Jul; 86(7):419-24.

[10] Foxman, Betsy. "The epidemiology of urinary tract infection." Nature Reviews Urology 7.12 (2010): 653-660.

[11] BMJ 2015;351:h6544

[12] Pearce, Meghan M., et al. "The female urinary microbiome: a comparison of women with and without urgency urinary incontinence." MBio 5.4 (2014): e01283-14.

[13] Cosseau, C. et al. The commensal Streptococcus salivarius K12 downregulates the innate immune responses of human epithelial cells and promotes host–microbe homeostasis. Infect. Immun. 76, 4163–4175 (2008).

[14]  Stapleton, A. E. et al. Randomized, placebo-controlled phase 2 trial of a Lactobacillus crispatus probiotic given intravaginally for prevention of recurrent urinary tract infection. Clin. Infect. Dis. 52, 1212–1217 (2011).