Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations

Abstract Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jacquelyn Jones, Stacey N Reinke, Alishum Ali, Debra J Palmer, Claus T. Christophersen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/689a153b06ff4cfb99821f6616066853
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:689a153b06ff4cfb99821f6616066853
record_format	dspace
spelling	oai:doaj.org-article:689a153b06ff4cfb99821f66160668532021-12-02T18:34:13ZFecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations10.1038/s41598-021-93031-z2045-2322https://doaj.org/article/689a153b06ff4cfb99821f66160668532021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93031-zhttps://doaj.org/toc/2045-2322Abstract Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome data. To compare fecal sample collection methods, amplicons from the bacterial 16S rRNA gene (V4) and fungal (ITS2) region, as well as short chain fatty acid (SCFA) concentrations were determined in fecal material over three timepoints. We demonstrated that spot sampling of stool results in variable detection of some microbial members, and inconsistent levels of SCFA; therefore, sample homogenization prior to subsequent analysis or subsampling is recommended. We also identify a trend in microbial and metabolite composition that shifts over two consecutive stool collections less than 25 h apart. Lastly, we show significant differences in bacterial composition that result from collecting stool samples in OMNIgene·Gut tube (DNA Genotec) or Stool Nucleic Acid Collection and Preservation Tube (NORGEN) compared to immediate freezing. To assist with planning fecal sample collection and storage procedures for microbiome investigations with multiple analyses, we recommend participants to collect the first full bowel movement of the day and freeze the sample immediately after collection.Jacquelyn JonesStacey N ReinkeAlishum AliDebra J PalmerClaus T. ChristophersenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jacquelyn Jones Stacey N Reinke Alishum Ali Debra J Palmer Claus T. Christophersen Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
description	Abstract Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome data. To compare fecal sample collection methods, amplicons from the bacterial 16S rRNA gene (V4) and fungal (ITS2) region, as well as short chain fatty acid (SCFA) concentrations were determined in fecal material over three timepoints. We demonstrated that spot sampling of stool results in variable detection of some microbial members, and inconsistent levels of SCFA; therefore, sample homogenization prior to subsequent analysis or subsampling is recommended. We also identify a trend in microbial and metabolite composition that shifts over two consecutive stool collections less than 25 h apart. Lastly, we show significant differences in bacterial composition that result from collecting stool samples in OMNIgene·Gut tube (DNA Genotec) or Stool Nucleic Acid Collection and Preservation Tube (NORGEN) compared to immediate freezing. To assist with planning fecal sample collection and storage procedures for microbiome investigations with multiple analyses, we recommend participants to collect the first full bowel movement of the day and freeze the sample immediately after collection.
format	article
author	Jacquelyn Jones Stacey N Reinke Alishum Ali Debra J Palmer Claus T. Christophersen
author_facet	Jacquelyn Jones Stacey N Reinke Alishum Ali Debra J Palmer Claus T. Christophersen
author_sort	Jacquelyn Jones
title	Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
title_short	Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
title_full	Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
title_fullStr	Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
title_full_unstemmed	Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
title_sort	fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/689a153b06ff4cfb99821f6616066853
work_keys_str_mv	AT jacquelynjones fecalsamplecollectionmethodsandtimeofdayimpactmicrobiomecompositionandshortchainfattyacidconcentrations AT staceynreinke fecalsamplecollectionmethodsandtimeofdayimpactmicrobiomecompositionandshortchainfattyacidconcentrations AT alishumali fecalsamplecollectionmethodsandtimeofdayimpactmicrobiomecompositionandshortchainfattyacidconcentrations AT debrajpalmer fecalsamplecollectionmethodsandtimeofdayimpactmicrobiomecompositionandshortchainfattyacidconcentrations AT claustchristophersen fecalsamplecollectionmethodsandtimeofdayimpactmicrobiomecompositionandshortchainfattyacidconcentrations
_version_	1718377865607643136

Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations

Ejemplares similares