Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca

Abstract We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting differe...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Nadia Darwish, Jonathan Shao, Lori L. Schreier, Monika Proszkowiec-Weglarz
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/44fc7a844a5d40c9b188cebcab095753
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:44fc7a844a5d40c9b188cebcab095753
record_format	dspace
spelling	oai:doaj.org-article:44fc7a844a5d40c9b188cebcab0957532021-12-02T15:02:23ZChoice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca10.1038/s41598-021-91387-w2045-2322https://doaj.org/article/44fc7a844a5d40c9b188cebcab0957532021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91387-whttps://doaj.org/toc/2045-2322Abstract We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.Nadia DarwishJonathan ShaoLori L. SchreierMonika Proszkowiec-WeglarzNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nadia Darwish Jonathan Shao Lori L. Schreier Monika Proszkowiec-Weglarz Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca
description	Abstract We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.
format	article
author	Nadia Darwish Jonathan Shao Lori L. Schreier Monika Proszkowiec-Weglarz
author_facet	Nadia Darwish Jonathan Shao Lori L. Schreier Monika Proszkowiec-Weglarz
author_sort	Nadia Darwish
title	Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca
title_short	Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca
title_full	Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca
title_fullStr	Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca
title_full_unstemmed	Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca
title_sort	choice of 16s ribosomal rna primers affects the microbiome analysis in chicken ceca
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/44fc7a844a5d40c9b188cebcab095753
work_keys_str_mv	AT nadiadarwish choiceof16sribosomalrnaprimersaffectsthemicrobiomeanalysisinchickenceca AT jonathanshao choiceof16sribosomalrnaprimersaffectsthemicrobiomeanalysisinchickenceca AT lorilschreier choiceof16sribosomalrnaprimersaffectsthemicrobiomeanalysisinchickenceca AT monikaproszkowiecweglarz choiceof16sribosomalrnaprimersaffectsthemicrobiomeanalysisinchickenceca
_version_	1718389134937030656

Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca

Ejemplares similares