Forming Consensus To Advance Urobiome Research

Linda Brubaker¹, Jean-Philippe F Gourdine², Nazema Y Siddiqui³, Amanda Holland⁴, Thomas Halverson⁵, Roberto Limeria⁶, David Pride^{7

8}, Lenore Ackerman⁹, Catherine S Forster¹⁰, Kristin M Jacobs¹¹, Krystal J Thomas-White¹², Catherine Putonti^{5

13}, Qunfeng Dong^{14

15}, Michael Weinstein^{16

17}, Emily S Lukacz¹, Lisa Karstens¹⁸, Alan J Wolfe^{5

6}

Affiliations

¹ Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, California, USA.
² Oregon Clinical & Translational Research Institute (OCTRI), Oregon Health & Science University, Portland, Oregon, USA.
³ Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Duke University, Durham, North Carolina, USA.
⁴ Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA.
⁵ Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicagogrid.164971.c, Maywood, Illinois, USA.
⁶ Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicagogrid.164971.c, Maywood, Illinois, USA.
⁷ Department of Pathology, University of California, San Diego, San Diego, California, USA.
⁸ Department of Medicine, University of California, San Diego, San Diego, California, USA.
⁹ Department of Urology, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, Los Angeles, Los Angeles, California, USA.
¹⁰ Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
¹¹ Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Rush University, Chicago, Illinois, USA.
¹² Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
¹³ Department of Biology, Bioinformatics Program, Loyola University Chicagogrid.164971.c, Chicago, Illinois, USA.
¹⁴ Department of Medicine, Stritch School of Medicine, Loyola University Chicagogrid.164971.c, Maywood, Illinois, USA.
¹⁵ Center for Biomedical Informatics, Loyola University Chicagogrid.164971.c, Chicago, Illinois, USA.
¹⁶ Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA.
¹⁷ Zymo Research, Irvine, California, USA.
¹⁸ Department of Clinical Epidemiology and Medical Informatics, Oregon Health & Science University, Portland, Oregon, USA.

PMID: 34282932
PMCID: PMC8409733
DOI: 10.1128/mSystems.01371-20

Forming Consensus To Advance Urobiome Research

Linda Brubaker et al. mSystems. 2021.

. 2021 Aug 31;6(4):e0137120.

doi: 10.1128/mSystems.01371-20. Epub 2021 Jul 20.

Authors

Affiliations

¹ Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, California, USA.
² Oregon Clinical & Translational Research Institute (OCTRI), Oregon Health & Science University, Portland, Oregon, USA.
³ Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Duke University, Durham, North Carolina, USA.
⁴ Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA.
⁵ Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicagogrid.164971.c, Maywood, Illinois, USA.
⁶ Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicagogrid.164971.c, Maywood, Illinois, USA.
⁷ Department of Pathology, University of California, San Diego, San Diego, California, USA.
⁸ Department of Medicine, University of California, San Diego, San Diego, California, USA.
⁹ Department of Urology, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, Los Angeles, Los Angeles, California, USA.
¹⁰ Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
¹¹ Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Rush University, Chicago, Illinois, USA.
¹² Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
¹³ Department of Biology, Bioinformatics Program, Loyola University Chicagogrid.164971.c, Chicago, Illinois, USA.
¹⁴ Department of Medicine, Stritch School of Medicine, Loyola University Chicagogrid.164971.c, Maywood, Illinois, USA.
¹⁵ Center for Biomedical Informatics, Loyola University Chicagogrid.164971.c, Chicago, Illinois, USA.
¹⁶ Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA.
¹⁷ Zymo Research, Irvine, California, USA.
¹⁸ Department of Clinical Epidemiology and Medical Informatics, Oregon Health & Science University, Portland, Oregon, USA.

PMID: 34282932
PMCID: PMC8409733
DOI: 10.1128/mSystems.01371-20

Abstract

Urobiome research has the potential to advance the understanding of a wide range of diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early research method consensus to facilitate the greater, common good. This consensus document, developed by a group of expert investigators currently engaged in urobiome research (UROBIOME 2020 conference participants), aims to promote standardization and advances in this field by the adoption of common core research practices. We propose a standardized nomenclature as well as considerations for specimen collection, preservation, storage, and processing. Best practices for urobiome study design include our proposal for standard metadata elements as part of core metadata collection. Although it is impractical to follow fixed analytical procedures when analyzing urobiome data, we propose guidelines to document and report data originating from urobiome studies. We offer this first consensus document with every expectation of subsequent revision as our field progresses.

Keywords: consensus; guideline; human microbiome; research; statement; urinary microbiome; urobiome.

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Figures

**FIG 1**
Key recommendations for urobiome research.

**FIG 2**
Recommended terminology for urobiome samples.

See this image and copyright information in PMC

References

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Forming Consensus To Advance Urobiome Research

Affiliations

Forming Consensus To Advance Urobiome Research

Authors

Affiliations

Abstract

Figures

References

Grants and funding

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Full Text Sources