Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass

A major challenge for microbiome studies is maintaining an even and accurate DNA extraction in the presence of samples with a wide range of bacterial content. Here we compare five DNA extraction methods using replicate stool samples that were diluted to create high and low biomass samples. Our resul...
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Gespeichert in:

Autor*in:	Amy Davis [verfasserIn] Christina Kohler [verfasserIn] Ramzi Alsallaq [verfasserIn] Randall Hayden [verfasserIn] Gabriela Maron [verfasserIn] Elisa Margolis [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	bacterial load DNA extraction high throughput low bacterial load metagenomics microbiome

Übergeordnetes Werk:	In: BioTechniques - Future Science Ltd, 2019, 66(2019), 6, Seite 285-289
Übergeordnetes Werk:	volume:66 ; year:2019 ; number:6 ; pages:285-289

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.2144/btn-2019-0016

Katalog-ID:	DOAJ01619425X

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language	English
source	In BioTechniques 66(2019), 6, Seite 285-289 volume:66 year:2019 number:6 pages:285-289
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topic_facet	bacterial load DNA extraction high throughput low bacterial load metagenomics microbiome Biology (General)
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container_title	BioTechniques
authorswithroles_txt_mv	Amy Davis @@aut@@ Christina Kohler @@aut@@ Ramzi Alsallaq @@aut@@ Randall Hayden @@aut@@ Gabriela Maron @@aut@@ Elisa Margolis @@aut@@
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callnumber-first	Q - Science
author	Amy Davis
spellingShingle	Amy Davis misc QH301-705.5 misc bacterial load misc DNA extraction misc high throughput misc low bacterial load misc metagenomics misc microbiome misc Biology (General) Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass
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topic_title	QH301-705.5 Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass bacterial load DNA extraction high throughput low bacterial load metagenomics microbiome
topic	misc QH301-705.5 misc bacterial load misc DNA extraction misc high throughput misc low bacterial load misc metagenomics misc microbiome misc Biology (General)
topic_unstemmed	misc QH301-705.5 misc bacterial load misc DNA extraction misc high throughput misc low bacterial load misc metagenomics misc microbiome misc Biology (General)
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title	Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass
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title_full	Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass
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title_sort	improved yield and accuracy for dna extraction in microbiome studies with variation in microbial biomass
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title_auth	Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass
abstract	A major challenge for microbiome studies is maintaining an even and accurate DNA extraction in the presence of samples with a wide range of bacterial content. Here we compare five DNA extraction methods using replicate stool samples that were diluted to create high and low biomass samples. Our results indicate greater variation in microbiome composition between high and low biomass samples than variation between methods. Many of the extraction methods had reduced yield from low biomass samples; however, our adapted plate column-based extraction method was evenly efficient and captured the largest number of high-quality reads. Based on these results, we have identified a DNA extraction method that ensures adequate yield in metagenomic microbiome studies that have samples with a broad range of bacterial content.
abstractGer	A major challenge for microbiome studies is maintaining an even and accurate DNA extraction in the presence of samples with a wide range of bacterial content. Here we compare five DNA extraction methods using replicate stool samples that were diluted to create high and low biomass samples. Our results indicate greater variation in microbiome composition between high and low biomass samples than variation between methods. Many of the extraction methods had reduced yield from low biomass samples; however, our adapted plate column-based extraction method was evenly efficient and captured the largest number of high-quality reads. Based on these results, we have identified a DNA extraction method that ensures adequate yield in metagenomic microbiome studies that have samples with a broad range of bacterial content.
abstract_unstemmed	A major challenge for microbiome studies is maintaining an even and accurate DNA extraction in the presence of samples with a wide range of bacterial content. Here we compare five DNA extraction methods using replicate stool samples that were diluted to create high and low biomass samples. Our results indicate greater variation in microbiome composition between high and low biomass samples than variation between methods. Many of the extraction methods had reduced yield from low biomass samples; however, our adapted plate column-based extraction method was evenly efficient and captured the largest number of high-quality reads. Based on these results, we have identified a DNA extraction method that ensures adequate yield in metagenomic microbiome studies that have samples with a broad range of bacterial content.
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title_short	Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass
url	https://doi.org/10.2144/btn-2019-0016 https://doaj.org/article/d4c1f33ea4c445d681d7da4cabd109da https://www.future-science.com/doi/10.2144/btn-2019-0016 https://doaj.org/toc/0736-6205 https://doaj.org/toc/1940-9818
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Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass

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