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Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation

OBJECTIVE: An approach for assessing the urinary microbiome is 16S rRNA gene sequencing, where analysis methods are rapidly evolving. This re-analysis of an existing dataset aimed to determine whether updated bioinformatic and statistical techniques affect clinical inferences. METHODS: A prior study...

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Autores principales: Siddiqui, Nazema Y., Ma, Li, Brubaker, Linda, Mao, Jialiang, Hoffman, Carter, Dahl, Erin M., Wang, Zhuoqun, Karstens, Lisa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9309214/
https://www.ncbi.nlm.nih.gov/pubmed/35899056
http://dx.doi.org/10.3389/fcimb.2022.789439
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author Siddiqui, Nazema Y.
Ma, Li
Brubaker, Linda
Mao, Jialiang
Hoffman, Carter
Dahl, Erin M.
Wang, Zhuoqun
Karstens, Lisa
author_facet Siddiqui, Nazema Y.
Ma, Li
Brubaker, Linda
Mao, Jialiang
Hoffman, Carter
Dahl, Erin M.
Wang, Zhuoqun
Karstens, Lisa
author_sort Siddiqui, Nazema Y.
collection PubMed
description OBJECTIVE: An approach for assessing the urinary microbiome is 16S rRNA gene sequencing, where analysis methods are rapidly evolving. This re-analysis of an existing dataset aimed to determine whether updated bioinformatic and statistical techniques affect clinical inferences. METHODS: A prior study compared the urinary microbiome in 123 women with mixed urinary incontinence (MUI) and 84 controls. We obtained unprocessed sequencing data from multiple variable regions, processed operational taxonomic unit (OTU) tables from the original analysis, and de-identified clinical data. We re-processed sequencing data with DADA2 to generate amplicon sequence variant (ASV) tables. Taxa from ASV tables were compared to the original OTU tables; taxa from different variable regions after updated processing were also compared. Bayesian graphical compositional regression (BGCR) was used to test for associations between microbial compositions and clinical phenotypes (e.g., MUI versus control) while adjusting for clinical covariates. Several techniques were used to cluster samples into microbial communities. Multivariable regression was used to test for associations between microbial communities and MUI, again while adjusting for potentially confounding variables. RESULTS: Of taxa identified through updated bioinformatic processing, only 40% were identified originally, though taxa identified through both methods represented >99% of the sequencing data in terms of relative abundance. Different 16S rRNA gene regions resulted in different recovered taxa. With BGCR analysis, there was a low (33.7%) probability of an association between overall microbial compositions and clinical phenotype. However, when microbial data are clustered into bacterial communities, we confirmed that bacterial communities are associated with MUI. Contrary to the originally published analysis, we did not identify different associations by age group, which may be due to the incorporation of different covariates in statistical models. CONCLUSIONS: Updated bioinformatic processing techniques recover different taxa compared to earlier techniques, though most of these differences exist in low abundance taxa that occupy a small proportion of the overall microbiome. While overall microbial compositions are not associated with MUI, we confirmed associations between certain communities of bacteria and MUI. Incorporation of several covariates that are associated with the urinary microbiome improved inferences when assessing for associations between bacterial communities and MUI in multivariable models.
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spelling pubmed-93092142022-07-26 Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation Siddiqui, Nazema Y. Ma, Li Brubaker, Linda Mao, Jialiang Hoffman, Carter Dahl, Erin M. Wang, Zhuoqun Karstens, Lisa Front Cell Infect Microbiol Cellular and Infection Microbiology OBJECTIVE: An approach for assessing the urinary microbiome is 16S rRNA gene sequencing, where analysis methods are rapidly evolving. This re-analysis of an existing dataset aimed to determine whether updated bioinformatic and statistical techniques affect clinical inferences. METHODS: A prior study compared the urinary microbiome in 123 women with mixed urinary incontinence (MUI) and 84 controls. We obtained unprocessed sequencing data from multiple variable regions, processed operational taxonomic unit (OTU) tables from the original analysis, and de-identified clinical data. We re-processed sequencing data with DADA2 to generate amplicon sequence variant (ASV) tables. Taxa from ASV tables were compared to the original OTU tables; taxa from different variable regions after updated processing were also compared. Bayesian graphical compositional regression (BGCR) was used to test for associations between microbial compositions and clinical phenotypes (e.g., MUI versus control) while adjusting for clinical covariates. Several techniques were used to cluster samples into microbial communities. Multivariable regression was used to test for associations between microbial communities and MUI, again while adjusting for potentially confounding variables. RESULTS: Of taxa identified through updated bioinformatic processing, only 40% were identified originally, though taxa identified through both methods represented >99% of the sequencing data in terms of relative abundance. Different 16S rRNA gene regions resulted in different recovered taxa. With BGCR analysis, there was a low (33.7%) probability of an association between overall microbial compositions and clinical phenotype. However, when microbial data are clustered into bacterial communities, we confirmed that bacterial communities are associated with MUI. Contrary to the originally published analysis, we did not identify different associations by age group, which may be due to the incorporation of different covariates in statistical models. CONCLUSIONS: Updated bioinformatic processing techniques recover different taxa compared to earlier techniques, though most of these differences exist in low abundance taxa that occupy a small proportion of the overall microbiome. While overall microbial compositions are not associated with MUI, we confirmed associations between certain communities of bacteria and MUI. Incorporation of several covariates that are associated with the urinary microbiome improved inferences when assessing for associations between bacterial communities and MUI in multivariable models. Frontiers Media S.A. 2022-07-08 /pmc/articles/PMC9309214/ /pubmed/35899056 http://dx.doi.org/10.3389/fcimb.2022.789439 Text en Copyright © 2022 Siddiqui, Ma, Brubaker, Mao, Hoffman, Dahl, Wang and Karstens https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Siddiqui, Nazema Y.
Ma, Li
Brubaker, Linda
Mao, Jialiang
Hoffman, Carter
Dahl, Erin M.
Wang, Zhuoqun
Karstens, Lisa
Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
title Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
title_full Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
title_fullStr Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
title_full_unstemmed Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
title_short Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
title_sort updating urinary microbiome analyses to enhance biologic interpretation
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9309214/
https://www.ncbi.nlm.nih.gov/pubmed/35899056
http://dx.doi.org/10.3389/fcimb.2022.789439
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