Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing

Hoffman, Carter; Siddiqui, Nazema Y.; Fields, Ian; Gregory, W. Thomas; Simon, Holly M.; Mooney, Michael A.; Wolfe, Alan J.; Karstens, Lisa

doi:10.1128/msystems.00518-21

Cited by 23 publications

(28 citation statements)

References 77 publications

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“…These studies consistently demonstrated that the choice of the 16S rRNA primer set can significantly influence the analysis of microbiota diversity and composition. Apart from a recent study evaluating the female urobiome ( Hoffman et al., 2021 ), similar studies for urinary microbiota profiling are lacking. As reviewed by Cumpanas et al.…”

Section: Discussionmentioning

confidence: 99%

“…Focusing on species cultured from the female urobiome and using an in silico approach with 16S rRNA sequences retrieved from the SILVA database, Hoffman et al. (2021) showed that taxonomic assignment algorithms, 16S rRNA databases, and the choice of 16S rRNA hypervariable regions influence the taxonomic profiles of female urine.…”

Section: Discussionmentioning

confidence: 99%

“…Despite evidence showing that the choice of 16S hypervariable regions in microbiota profiling studies is critical ( Cabral et al., 2017 ; Fadeev et al., 2021 ; Hoffman et al., 2021 ; Kameoka et al., 2021 ; Sirichoat et al., 2021 ), no study has systematically compared the performance of sequencing different 16S rRNA hypervariable regions for microbial characterization of urine samples. In this work, we compared the performance of different sets of 16S rRNA primers for male urinary microbiota profiling.…”

Section: Introductionmentioning

confidence: 99%

“…Bladder urine often contains <10 5 colony forming units per milliliter, a number at least a million times lower than that found in feces per gram ( Karstens et al., 2018 ). As a consequence, while gut microbiota DNA-based studies are shifting from 16S ribosomal RNA (rRNA) amplicon sequencing towards shotgun metagenomic sequencing - which is problematic with low amounts of input bacterial DNA ( Pereira-Marques et al., 2019 ) -, urinary microbiota profiling still relies on 16S rRNA amplicon sequencing ( Cumpanas et al., 2020 ; Hoffman et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…(2021) found that V1V2 is more precise than V3V4 for gut microbiota profiling of Japanese individuals. Furthermore, Hoffman et al. (2021) concluded based on a computational analysis that V1V3 and V2V3 allow a more complete assessment of the female urobiome, but validation by sequencing these regions was not performed.…”

Section: Introductionmentioning

confidence: 99%

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Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling

Heidrich

Inoue

Asprino

et al. 2022

Front. Cell. Infect. Microbiol.

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Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, sequencing the full-length 16S rRNA gene is impractical. Therefore, choosing which 16S rRNA hypervariable region to sequence is critical in microbiota profiling studies. All nine 16S rRNA hypervariable regions are taxonomically informative, but due to variability in profiling performance for specific clades, choosing the ideal 16S rRNA hypervariable region will depend on the bacterial composition of the habitat under study. Recently, NGS allowed the identification of microbes in the urinary tract, and urinary microbiota has become an active research area. However, there is no current study evaluating the performance of different 16S rRNA hypervariable regions for male urinary microbiota profiling. We collected urine samples from male volunteers and profiled their urinary microbiota by sequencing a panel of six amplicons encompassing all nine 16S rRNA hypervariable regions. Systematic comparisons of their performance indicate V1V2 hypervariable regions better assess the taxa commonly present in male urine samples, suggesting V1V2 amplicon sequencing is more suitable for male urinary microbiota profiling. We believe our results will be helpful to guide this crucial methodological choice in future male urinary microbiota studies.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling

Heidrich

Inoue

Asprino

et al. 2022

Front. Cell. Infect. Microbiol.

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The urinary and prostatic microbiome in non‐neurogenic male LUTS/BPH: A systematic review

Pina‐Vaz,

Silva,

Silva

et al. 2024

Neurourology and Urodynamics

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IntroductionDespite advancements in the treatment of benign prostatic hyperplasia (BPH), the mechanisms underlying BPH development and progression remain elusive and lacks a one‐size‐fits‐all therapeutic solution. Prostatic inflammation contributes to BPH and lower urinary tract symptoms (LUTS), but the initial trigger remains unknown. Current research suggests dysbiosis of the urinary microbiome as a potential culprit. This systematic review explores the emerging field of the male urinary and prostatic microbiome and its relationship with BPH/LUTS.MethodsThe Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines were followed. A systematic search in the Pubmed and Scopus databases was performed using specific terms. Inclusion criteria considered male non‐neurogenic patients with LUTS due to BPH with analyses of urinary microbiome, concerning evaluation of English‐language publications with relevance.ResultsAmong seven articles involving 542 patients, there was an association between male LUTS/BPH and the urinary microbiome. Findings indicate a correlation between urinary microbiome dysbiosis and LUTS severity, with specific bacterial genera such as Streptococcus and Haemophilus linked to higher International Prostate Symptom Score (IPSS) scores and PSA levels. The fecal microbiome may be associated with LUTS, although contradictory findings are reported. The review also highlights methodological inconsistencies, small sample sizes, few negative controls and a lack of comprehensive clinical data as major limitations.ConclusionsWhile there is an undeniable correlation between the microbiome and LUTS/BPH, future research should aim to standardize sampling techniques and expand the score to include functional microbiome characterization, potentially leading to novel, microbiome‐targeted therapeutic strategies for BPH.

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