Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples

ABSTRACT The role of the gut microbiome in critical illness is being actively investigated, but the optimal sampling methods for sequencing studies of gut microbiota remain unknown. Stool samples are generally considered the reference standard but are not practical to obtain in the intensive care un...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Katherine Fair, Daniel G. Dunlap, Adam Fitch, Tatiana Bogdanovich, Barbara Methé, Alison Morris, Bryan J. McVerry, Georgios D. Kitsios
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	gut dysbiosis gut microbiome microbiome rectal swab stool Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/84a0c4212df34b719b95bb6b33cefa4f
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:84a0c4212df34b719b95bb6b33cefa4f
record_format	dspace
spelling	oai:doaj.org-article:84a0c4212df34b719b95bb6b33cefa4f2021-11-15T15:22:27ZRectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples10.1128/mSphere.00358-192379-5042https://doaj.org/article/84a0c4212df34b719b95bb6b33cefa4f2019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00358-19https://doaj.org/toc/2379-5042ABSTRACT The role of the gut microbiome in critical illness is being actively investigated, but the optimal sampling methods for sequencing studies of gut microbiota remain unknown. Stool samples are generally considered the reference standard but are not practical to obtain in the intensive care unit (ICU), and thus, rectal swabs are often used. However, the reliability of rectal swabs for gut microbiome profiling has not been established in the ICU setting. In this study, we compared 16S rRNA gene sequencing results between rectal swab and stool samples collected at three time points from mechanically ventilated critically ill adults. Rectal swabs comprised 89% of the samples collected at the baseline time point, but stool samples became more extensively available at later time points. Significant differences in alpha-diversity and beta-diversity between rectal swabs and stool samples were observed, but these differences were primarily due to baseline samples. Higher relative abundances of members of the Actinobacteria phylum (typically skin microbes) were present in rectal swabs than in stool samples (P = 0.05), a difference that was attenuated over time. The progressively increasing similarity of rectal swabs and stool samples likely resulted from increasing levels of stool coating of the rectal vault and direct soiling of the rectal swabs taken at later time points. Therefore, inferences about the role of the gut microbiome in critical illness should be drawn cautiously and should take into account the type and timing of samples analyzed. IMPORTANCE Rectal swabs have been proposed as potential alternatives to stool samples for gut microbiome profiling in outpatients or healthy adults, but their reliability in assessment of critically ill patients has not been defined. Because stool sampling is not practical and often not feasible in the intensive care unit, we performed a detailed comparison of gut microbial sequencing profiles between rectal swabs and stool samples in a longitudinal cohort of critically ill patients. We identified systematic differences in gut microbial profiles between rectal swabs and stool samples and demonstrated that the timing of the rectal swab sampling had a significant impact on sequencing results. Our methodological findings should provide valuable information for the design and interpretation of future investigations of the role of the gut microbiome in critical illness.Katherine FairDaniel G. DunlapAdam FitchTatiana BogdanovichBarbara MethéAlison MorrisBryan J. McVerryGeorgios D. KitsiosAmerican Society for Microbiologyarticlegut dysbiosisgut microbiomemicrobiomerectal swabstoolMicrobiologyQR1-502ENmSphere, Vol 4, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	gut dysbiosis gut microbiome microbiome rectal swab stool Microbiology QR1-502
spellingShingle	gut dysbiosis gut microbiome microbiome rectal swab stool Microbiology QR1-502 Katherine Fair Daniel G. Dunlap Adam Fitch Tatiana Bogdanovich Barbara Methé Alison Morris Bryan J. McVerry Georgios D. Kitsios Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples
description	ABSTRACT The role of the gut microbiome in critical illness is being actively investigated, but the optimal sampling methods for sequencing studies of gut microbiota remain unknown. Stool samples are generally considered the reference standard but are not practical to obtain in the intensive care unit (ICU), and thus, rectal swabs are often used. However, the reliability of rectal swabs for gut microbiome profiling has not been established in the ICU setting. In this study, we compared 16S rRNA gene sequencing results between rectal swab and stool samples collected at three time points from mechanically ventilated critically ill adults. Rectal swabs comprised 89% of the samples collected at the baseline time point, but stool samples became more extensively available at later time points. Significant differences in alpha-diversity and beta-diversity between rectal swabs and stool samples were observed, but these differences were primarily due to baseline samples. Higher relative abundances of members of the Actinobacteria phylum (typically skin microbes) were present in rectal swabs than in stool samples (P = 0.05), a difference that was attenuated over time. The progressively increasing similarity of rectal swabs and stool samples likely resulted from increasing levels of stool coating of the rectal vault and direct soiling of the rectal swabs taken at later time points. Therefore, inferences about the role of the gut microbiome in critical illness should be drawn cautiously and should take into account the type and timing of samples analyzed. IMPORTANCE Rectal swabs have been proposed as potential alternatives to stool samples for gut microbiome profiling in outpatients or healthy adults, but their reliability in assessment of critically ill patients has not been defined. Because stool sampling is not practical and often not feasible in the intensive care unit, we performed a detailed comparison of gut microbial sequencing profiles between rectal swabs and stool samples in a longitudinal cohort of critically ill patients. We identified systematic differences in gut microbial profiles between rectal swabs and stool samples and demonstrated that the timing of the rectal swab sampling had a significant impact on sequencing results. Our methodological findings should provide valuable information for the design and interpretation of future investigations of the role of the gut microbiome in critical illness.
format	article
author	Katherine Fair Daniel G. Dunlap Adam Fitch Tatiana Bogdanovich Barbara Methé Alison Morris Bryan J. McVerry Georgios D. Kitsios
author_facet	Katherine Fair Daniel G. Dunlap Adam Fitch Tatiana Bogdanovich Barbara Methé Alison Morris Bryan J. McVerry Georgios D. Kitsios
author_sort	Katherine Fair
title	Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples
title_short	Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples
title_full	Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples
title_fullStr	Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples
title_full_unstemmed	Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples
title_sort	rectal swabs from critically ill patients provide discordant representations of the gut microbiome compared to stool samples
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/84a0c4212df34b719b95bb6b33cefa4f
work_keys_str_mv	AT katherinefair rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples AT danielgdunlap rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples AT adamfitch rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples AT tatianabogdanovich rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples AT barbaramethe rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples AT alisonmorris rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples AT bryanjmcverry rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples AT georgiosdkitsios rectalswabsfromcriticallyillpatientsprovidediscordantrepresentationsofthegutmicrobiomecomparedtostoolsamples
_version_	1718427961054461952

Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut Microbiome Compared to Stool Samples

Ejemplares similares