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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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/10/6/343 |
| _version_ | 1797566985923461120 |
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| author | Alin Adrian Cumpanas Ovidiu Gabriel Bratu Razvan Tiberiu Bardan Ovidiu Catalin Ferician Andrei Dragos Cumpanas Florin George Horhat Monica Licker Catalin Pricop Octavian Marius Cretu |
| author_facet | Alin Adrian Cumpanas Ovidiu Gabriel Bratu Razvan Tiberiu Bardan Ovidiu Catalin Ferician Andrei Dragos Cumpanas Florin George Horhat Monica Licker Catalin Pricop Octavian Marius Cretu |
| author_sort | Alin Adrian Cumpanas |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T19:35:14Z |
| format | Article |
| id | doaj.art-f6a28e481570468d83b5e172700d78c4 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-10T19:35:14Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-f6a28e481570468d83b5e172700d78c42023-11-20T01:51:07ZengMDPI AGDiagnostics2075-44182020-05-0110634310.3390/diagnostics10060343Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased ResultsAlin Adrian Cumpanas0Ovidiu Gabriel Bratu1Razvan Tiberiu Bardan2Ovidiu Catalin Ferician3Andrei Dragos Cumpanas4Florin George Horhat5Monica Licker6Catalin Pricop7Octavian Marius Cretu8Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, RomaniaDepartment of Urology, Emergency Military Central Hospital, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, RomaniaDepartment of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, RomaniaDepartment of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, RomaniaFaculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, RomaniaDepartment of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, RomaniaDepartment of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, RomaniaDepartment of Urology, Gr.Tr.Popa University of Medicine and Pharmacy, 700115 Iasi, RomaniaDepartment of Surgery, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, RomaniaWithin 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.https://www.mdpi.com/2075-4418/10/6/343urinary microbiota16S mRNA gene sequencingcontamination |
| spellingShingle | Alin Adrian Cumpanas Ovidiu Gabriel Bratu Razvan Tiberiu Bardan Ovidiu Catalin Ferician Andrei Dragos Cumpanas Florin George Horhat Monica Licker Catalin Pricop Octavian Marius Cretu Urinary Microbiota—Are We Ready for Prime Time? A Literature Review of Study Methods’ Critical Steps in Avoiding Contamination and Minimizing Biased Results Diagnostics urinary microbiota 16S mRNA gene sequencing contamination |
| 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 | urinary microbiota 16S mRNA gene sequencing contamination |
| url | https://www.mdpi.com/2075-4418/10/6/343 |
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