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Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results

Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to proce...

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Autores principales: Cumpanas, Alin Adrian, Bratu, Ovidiu Gabriel, Bardan, Razvan Tiberiu, Ferician, Ovidiu Catalin, Cumpanas, Andrei Dragos, Horhat, Florin George, Licker, Monica, Pricop, Catalin, Cretu, Octavian Marius
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7345871/
https://www.ncbi.nlm.nih.gov/pubmed/32471022
http://dx.doi.org/10.3390/diagnostics10060343
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author Cumpanas, Alin Adrian
Bratu, Ovidiu Gabriel
Bardan, Razvan Tiberiu
Ferician, Ovidiu Catalin
Cumpanas, Andrei Dragos
Horhat, Florin George
Licker, Monica
Pricop, Catalin
Cretu, Octavian Marius
author_facet Cumpanas, Alin Adrian
Bratu, Ovidiu Gabriel
Bardan, Razvan Tiberiu
Ferician, Ovidiu Catalin
Cumpanas, Andrei Dragos
Horhat, Florin George
Licker, Monica
Pricop, Catalin
Cretu, Octavian Marius
author_sort Cumpanas, Alin Adrian
collection PubMed
description Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to processing and analyzing, have been described (e.g., urine collection modality, sample volume size, snap freezing, negative controls usage, laboratory risks for contamination assessment, contamination of negative results reporting, exploration and discussion of the impact of contamination for the final results, etc.) We performed a literature search (Pubmed, Scopus and Embase) and reviewed the published articles related to urinary microbiome, evaluating how the aforementioned critical steps to obtain unbiased, reliable results have been taken or have been reported. We identified different urinary microbiome evaluation protocols, with non-homogenous reporting systems, which can make gathering results into consistent data for similar topics difficult and further burden the already so complex emerging field of urinary microbiome. We concluded that to ease the progress in this field, a joint approach from researchers, authors and publishers would be necessary in order to create mandatory reporting systems which would allow to recognize pitfalls and avoid compromising a promising field of research.
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spelling pubmed-73458712020-07-09 Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results Cumpanas, Alin Adrian Bratu, Ovidiu Gabriel Bardan, Razvan Tiberiu Ferician, Ovidiu Catalin Cumpanas, Andrei Dragos Horhat, Florin George Licker, Monica Pricop, Catalin Cretu, Octavian Marius Diagnostics (Basel) Review Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to processing and analyzing, have been described (e.g., urine collection modality, sample volume size, snap freezing, negative controls usage, laboratory risks for contamination assessment, contamination of negative results reporting, exploration and discussion of the impact of contamination for the final results, etc.) We performed a literature search (Pubmed, Scopus and Embase) and reviewed the published articles related to urinary microbiome, evaluating how the aforementioned critical steps to obtain unbiased, reliable results have been taken or have been reported. We identified different urinary microbiome evaluation protocols, with non-homogenous reporting systems, which can make gathering results into consistent data for similar topics difficult and further burden the already so complex emerging field of urinary microbiome. We concluded that to ease the progress in this field, a joint approach from researchers, authors and publishers would be necessary in order to create mandatory reporting systems which would allow to recognize pitfalls and avoid compromising a promising field of research. MDPI 2020-05-27 /pmc/articles/PMC7345871/ /pubmed/32471022 http://dx.doi.org/10.3390/diagnostics10060343 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Cumpanas, Alin Adrian
Bratu, Ovidiu Gabriel
Bardan, Razvan Tiberiu
Ferician, Ovidiu Catalin
Cumpanas, Andrei Dragos
Horhat, Florin George
Licker, Monica
Pricop, Catalin
Cretu, Octavian Marius
Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results
title Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results
title_full Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results
title_fullStr Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results
title_full_unstemmed Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results
title_short Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results
title_sort urinary microbiota—are we ready for prime time? a literature review of study methods’ critical steps in avoiding contamination and minimizing biased results
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7345871/
https://www.ncbi.nlm.nih.gov/pubmed/32471022
http://dx.doi.org/10.3390/diagnostics10060343
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