Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection

Study information

Reviewed Marked as Reviewed by Svetlana up on 2023-10-16

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

35722326

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2022.888681

URI

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200618/

Authors

Huang L, Li X, Zheng B, Li P, Wei D, Huang C, Sun L, Li H

Journal

Frontiers in microbiology

Year

2022

Keywords:

16S rRNA, next generation sequencing (NGS), recurrent urinary tract infection (RUTI), standard urine culture, urinary microbiota

BACKGROUND: Recurrent urinary tract infection (RUTI) is common and burdensome in women. Due to the low concentration or slow-growing of uropathogens in RUTI, standard urine cultures (SUCs) are often negative. Next-generation sequencing (NGS) of bacterial 16S rRNA gene is more sensitive and could be used to reveal the differential microbiota between patients with RUTI and asymptomatic controls. METHODS: Women (aged ≥ 18 years) with clinically diagnosed RUTI with negative SUC and age-matched women asymptomatic controls with normal urinalysis were enrolled. Their midstream voided urine specimens were collected and processed for NGS (Illumina MiSeq) targeting the bacterial 16S rRNA gene V3-V4 region. The dataset was clustered into operational taxonomic units (OTUs) using QIIME. Taxonomic analysis, alpha diversity, beta diversity, multivariate statistical analysis, and linear discriminant analysis effect size (LEfSe) for differential analysis were performed and compared between patients with RUTI and asymptomatic controls. RESULTS: A total of 90 patients with RUTI and 62 asymptomatic controls were enrolled in this study. Among them, 74.4% (67/90) and 71.0% (44/62) were successfully amplified and sequenced their bacterial 16S rRNA gene. In the alpha diversity analysis, the chao1 index and observed species index were significantly lower in the RUTI group than in the control group (P = 0.015 and 0.028, respectively). In the beta diversity analysis, there was a significant difference between the 2 groups [Analysis of similarities (ANOSIM), R = 0.209, P = 0.001]. The relative abundance of 36 bacterial taxa was significantly higher, and another 24 kinds of bacteria were significantly lower in the RUTI group compared with the control group [LEfSe analysis, P < 0.05, linear discriminative analysis (LDA) score > 3], suggesting that Ralstonia, Prevotella, Dialister, and Corynebacterium may play an important role in RUTI. CONCLUSION: The urinary microbiota of women with clinically diagnosed RUTI were significantly different from age-matched asymptomatic controls.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2023-10-17

Curated date: 2023/10/07

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Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Urine Urine,urine

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Bacterial urinary tract infection

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Asymptomatic controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: Recurrent Urinary Tract Infection (RUTI) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Women with clinically diagnosed RUTI with negative Standard Urine Cultures (SUCs)

Group 0 sample size Number of subjects in the control (unexposed) group: 44

Group 1 sample size Number of subjects in the case (exposed) group: 67

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Patients with antibiotic treatment in the previous 48 hours (2 days) and their symptoms relieved.

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3

Matched on Factors on which subjects have been matched on in a case-control study: age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: decreased

Richness Number of species: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

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Curated date: 2023/10/07

Curator: Aleru002

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Source: Figure 5

Description: Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.

Abundance in Group 1: increased abundance in

NCBI	Quality Control	Links
Anaerococcus
Betaproteobacteria
Burkholderiaceae
Burkholderiales
Corynebacterium
Dialister
Megasphaera
Mycobacteriales
Porphyromonas
Prevotella
Prevotella bivia DSM 20514
Prevotellaceae
Pseudomonadota
Ralstonia
Actinotignum
Peptoniphilus
Actinomycetales
Actinomycetaceae
Epsilonproteobacteria
Campylobacterales
Campylobacteraceae
Campylobacter
Fusobacterium
Fusobacteriaceae
Enhydrobacter
Corynebacteriaceae

Revision editor(s): Aleru002, WikiWorks

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Source: Figure 5

Description: Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.

Abundance in Group 1: decreased abundance in

NCBI	Quality Control	Links
Acinetobacter
Alistipes
Bacilli
Ezakiella
Gardnerella
Lachnospiraceae bacterium NK4A136
Lactobacillaceae
Lactobacillales
Lactobacillus
Lactobacillus gasseri
Leptotrichiaceae
Phaseolus acutifolius
Sneathia
Streptococcaceae
Streptococcus
Streptococcus pneumoniae
Bacillota

Revision editor(s): Aleru002, WikiWorks