On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples

Abstract The gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In th...

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Autores principales:	Shan Sun, Xiangzhu Zhu, Xiang Huang, Harvey J. Murff, Reid M. Ness, Douglas L. Seidner, Alicia A. Sorgen, Ivory C. Blakley, Chang Yu, Qi Dai, M. Andrea Azcarate-Peril, Martha J. Shrubsole, Anthony A. Fodor
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/13d61f92d21f4c489d52b87400cedf98
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spelling	oai:doaj.org-article:13d61f92d21f4c489d52b87400cedf982021-12-02T17:03:50ZOn the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples10.1038/s41598-021-94205-52045-2322https://doaj.org/article/13d61f92d21f4c489d52b87400cedf982021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94205-5https://doaj.org/toc/2045-2322Abstract The gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.Shan SunXiangzhu ZhuXiang HuangHarvey J. MurffReid M. NessDouglas L. SeidnerAlicia A. SorgenIvory C. BlakleyChang YuQi DaiM. Andrea Azcarate-PerilMartha J. ShrubsoleAnthony A. FodorNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shan Sun Xiangzhu Zhu Xiang Huang Harvey J. Murff Reid M. Ness Douglas L. Seidner Alicia A. Sorgen Ivory C. Blakley Chang Yu Qi Dai M. Andrea Azcarate-Peril Martha J. Shrubsole Anthony A. Fodor On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
description	Abstract The gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.
format	article
author	Shan Sun Xiangzhu Zhu Xiang Huang Harvey J. Murff Reid M. Ness Douglas L. Seidner Alicia A. Sorgen Ivory C. Blakley Chang Yu Qi Dai M. Andrea Azcarate-Peril Martha J. Shrubsole Anthony A. Fodor
author_facet	Shan Sun Xiangzhu Zhu Xiang Huang Harvey J. Murff Reid M. Ness Douglas L. Seidner Alicia A. Sorgen Ivory C. Blakley Chang Yu Qi Dai M. Andrea Azcarate-Peril Martha J. Shrubsole Anthony A. Fodor
author_sort	Shan Sun
title	On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
title_short	On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
title_full	On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
title_fullStr	On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
title_full_unstemmed	On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
title_sort	on the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/13d61f92d21f4c489d52b87400cedf98
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On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples

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