Evaluating extraction methods to study canine urine microbiota.

The urinary microbiota is the collection of microbes present in urine that may play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determi...

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Autores principales:	Ryan Mrofchak, Christopher Madden, Morgan V Evans, Vanessa L Hale
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f17ce78efa8149f6b18bce986934e343
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spelling	oai:doaj.org-article:f17ce78efa8149f6b18bce986934e3432021-12-02T20:09:24ZEvaluating extraction methods to study canine urine microbiota.1932-620310.1371/journal.pone.0253989https://doaj.org/article/f17ce78efa8149f6b18bce986934e3432021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253989https://doaj.org/toc/1932-6203The urinary microbiota is the collection of microbes present in urine that may play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determined that a diverse array of microbes is present in health and disease. To study these microbes and their potential role in diseases like bladder cancer or interstitial cystitis, consistent extraction and detection of bacterial DNA from urine is critical. However, urine is a low biomass substrate, requiring sensitive methods to capture DNA and making the risk of contamination high. To address this challenge, we collected urine samples from ten healthy dogs and extracted DNA from each sample using five different commercially available extraction methods. Extraction methods were compared based on total and bacterial DNA concentrations and bacterial community composition and diversity assessed through 16S rRNA gene sequencing. Significant differences in the urinary microbiota were observed by dog and sex but not extraction method. The Bacteremia Kit yielded the highest total DNA concentrations (Kruskal-Wallis, p = 0.165, not significant) and the highest bacterial DNA concentrations (Kruskal-Wallis, p = 0.044). Bacteremia also extracted bacterial DNA from the greatest number of samples. Taken together, these results suggest that the Bacteremia kit is an effective option for studying the urine microbiota. This work lays the foundation to study the urine microbiome in a wide range of urogenital diseases in dogs and other species.Ryan MrofchakChristopher MaddenMorgan V EvansVanessa L HalePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0253989 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ryan Mrofchak Christopher Madden Morgan V Evans Vanessa L Hale Evaluating extraction methods to study canine urine microbiota.
description	The urinary microbiota is the collection of microbes present in urine that may play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determined that a diverse array of microbes is present in health and disease. To study these microbes and their potential role in diseases like bladder cancer or interstitial cystitis, consistent extraction and detection of bacterial DNA from urine is critical. However, urine is a low biomass substrate, requiring sensitive methods to capture DNA and making the risk of contamination high. To address this challenge, we collected urine samples from ten healthy dogs and extracted DNA from each sample using five different commercially available extraction methods. Extraction methods were compared based on total and bacterial DNA concentrations and bacterial community composition and diversity assessed through 16S rRNA gene sequencing. Significant differences in the urinary microbiota were observed by dog and sex but not extraction method. The Bacteremia Kit yielded the highest total DNA concentrations (Kruskal-Wallis, p = 0.165, not significant) and the highest bacterial DNA concentrations (Kruskal-Wallis, p = 0.044). Bacteremia also extracted bacterial DNA from the greatest number of samples. Taken together, these results suggest that the Bacteremia kit is an effective option for studying the urine microbiota. This work lays the foundation to study the urine microbiome in a wide range of urogenital diseases in dogs and other species.
format	article
author	Ryan Mrofchak Christopher Madden Morgan V Evans Vanessa L Hale
author_facet	Ryan Mrofchak Christopher Madden Morgan V Evans Vanessa L Hale
author_sort	Ryan Mrofchak
title	Evaluating extraction methods to study canine urine microbiota.
title_short	Evaluating extraction methods to study canine urine microbiota.
title_full	Evaluating extraction methods to study canine urine microbiota.
title_fullStr	Evaluating extraction methods to study canine urine microbiota.
title_full_unstemmed	Evaluating extraction methods to study canine urine microbiota.
title_sort	evaluating extraction methods to study canine urine microbiota.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/f17ce78efa8149f6b18bce986934e343
work_keys_str_mv	AT ryanmrofchak evaluatingextractionmethodstostudycanineurinemicrobiota AT christophermadden evaluatingextractionmethodstostudycanineurinemicrobiota AT morganvevans evaluatingextractionmethodstostudycanineurinemicrobiota AT vanessalhale evaluatingextractionmethodstostudycanineurinemicrobiota
_version_	1718375098535116800

Evaluating extraction methods to study canine urine microbiota.

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