The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Ibarbalz, Federico Matías, Figuerola, Eva Lucía Margarita, Erijman, Leonardo
Publicado:	2014
Materias:	RNA 16S sewage activated sludge amplicon article community dynamics fluorescence in situ hybridization gene sequence genetic variability high throughput sequencing microbial community nonhuman population abundance quantitative analysis taxon temperature Thiothrix analysis bacterial gene bacterium biodiversity classification DNA sequence duplicate gene gene amplification genetics growth, development and aging microbial consortium microbiology procedures RNA gene statistical bias statistics and numerical data Bacteria Bias (Epidemiology) Biodiversity Gene Amplification Genes, Bacterial Genes, Duplicate Genes, rRNA High-Throughput Nucleotide Sequencing Microbial Consortia RNA, Ribosomal, 16S Sequence Analysis, DNA Sewage
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v9_n6_p_Ibarbalz http://hdl.handle.net/20.500.12110/paper_19326203_v9_n6_p_Ibarbalz
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_19326203_v9_n6_p_Ibarbalz
record_format	dspace
spelling	paper:paper_19326203_v9_n6_p_Ibarbalz2023-06-08T16:31:24Z The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics Ibarbalz, Federico Matías Figuerola, Eva Lucía Margarita Erijman, Leonardo RNA 16S RNA 16S sewage activated sludge amplicon article community dynamics fluorescence in situ hybridization gene sequence genetic variability high throughput sequencing microbial community nonhuman population abundance quantitative analysis taxon temperature Thiothrix analysis bacterial gene bacterium biodiversity classification DNA sequence duplicate gene gene amplification genetics growth, development and aging high throughput sequencing microbial consortium microbiology procedures RNA gene sewage statistical bias statistics and numerical data Bacteria Bias (Epidemiology) Biodiversity Gene Amplification Genes, Bacterial Genes, Duplicate Genes, rRNA High-Throughput Nucleotide Sequencing Microbial Consortia RNA, Ribosomal, 16S Sequence Analysis, DNA Sewage The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. © 2014 Ibarbalz et al. Fil:Ibarbalz, F.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Figuerola, E.L.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Erijman, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2014 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v9_n6_p_Ibarbalz http://hdl.handle.net/20.500.12110/paper_19326203_v9_n6_p_Ibarbalz
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	RNA 16S RNA 16S sewage activated sludge amplicon article community dynamics fluorescence in situ hybridization gene sequence genetic variability high throughput sequencing microbial community nonhuman population abundance quantitative analysis taxon temperature Thiothrix analysis bacterial gene bacterium biodiversity classification DNA sequence duplicate gene gene amplification genetics growth, development and aging high throughput sequencing microbial consortium microbiology procedures RNA gene sewage statistical bias statistics and numerical data Bacteria Bias (Epidemiology) Biodiversity Gene Amplification Genes, Bacterial Genes, Duplicate Genes, rRNA High-Throughput Nucleotide Sequencing Microbial Consortia RNA, Ribosomal, 16S Sequence Analysis, DNA Sewage
spellingShingle	RNA 16S RNA 16S sewage activated sludge amplicon article community dynamics fluorescence in situ hybridization gene sequence genetic variability high throughput sequencing microbial community nonhuman population abundance quantitative analysis taxon temperature Thiothrix analysis bacterial gene bacterium biodiversity classification DNA sequence duplicate gene gene amplification genetics growth, development and aging high throughput sequencing microbial consortium microbiology procedures RNA gene sewage statistical bias statistics and numerical data Bacteria Bias (Epidemiology) Biodiversity Gene Amplification Genes, Bacterial Genes, Duplicate Genes, rRNA High-Throughput Nucleotide Sequencing Microbial Consortia RNA, Ribosomal, 16S Sequence Analysis, DNA Sewage Ibarbalz, Federico Matías Figuerola, Eva Lucía Margarita Erijman, Leonardo The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics
topic_facet	RNA 16S RNA 16S sewage activated sludge amplicon article community dynamics fluorescence in situ hybridization gene sequence genetic variability high throughput sequencing microbial community nonhuman population abundance quantitative analysis taxon temperature Thiothrix analysis bacterial gene bacterium biodiversity classification DNA sequence duplicate gene gene amplification genetics growth, development and aging high throughput sequencing microbial consortium microbiology procedures RNA gene sewage statistical bias statistics and numerical data Bacteria Bias (Epidemiology) Biodiversity Gene Amplification Genes, Bacterial Genes, Duplicate Genes, rRNA High-Throughput Nucleotide Sequencing Microbial Consortia RNA, Ribosomal, 16S Sequence Analysis, DNA Sewage
description	The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. © 2014 Ibarbalz et al.
author	Ibarbalz, Federico Matías Figuerola, Eva Lucía Margarita Erijman, Leonardo
author_facet	Ibarbalz, Federico Matías Figuerola, Eva Lucía Margarita Erijman, Leonardo
author_sort	Ibarbalz, Federico Matías
title	The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics
title_short	The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics
title_full	The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics
title_fullStr	The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics
title_full_unstemmed	The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics
title_sort	bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics
publishDate	2014
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19326203_v9_n6_p_Ibarbalz http://hdl.handle.net/20.500.12110/paper_19326203_v9_n6_p_Ibarbalz
work_keys_str_mv	AT ibarbalzfedericomatias thebiasassociatedwithampliconsequencingdoesnotaffectthequantitativeassessmentofbacterialcommunitydynamics AT figuerolaevaluciamargarita thebiasassociatedwithampliconsequencingdoesnotaffectthequantitativeassessmentofbacterialcommunitydynamics AT erijmanleonardo thebiasassociatedwithampliconsequencingdoesnotaffectthequantitativeassessmentofbacterialcommunitydynamics AT ibarbalzfedericomatias biasassociatedwithampliconsequencingdoesnotaffectthequantitativeassessmentofbacterialcommunitydynamics AT figuerolaevaluciamargarita biasassociatedwithampliconsequencingdoesnotaffectthequantitativeassessmentofbacterialcommunitydynamics AT erijmanleonardo biasassociatedwithampliconsequencingdoesnotaffectthequantitativeassessmentofbacterialcommunitydynamics
_version_	1768542712386027520

The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics

Ejemplares similares