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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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2019-06-01
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| Series: | BioTechniques |
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| Online Access: | https://www.future-science.com/doi/10.2144/btn-2019-0016 |
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| _version_ | 1850152836026859520 |
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| author | Amy Davis Christina Kohler Ramzi Alsallaq Randall Hayden Gabriela Maron Elisa Margolis |
| author_facet | Amy Davis Christina Kohler Ramzi Alsallaq Randall Hayden Gabriela Maron Elisa Margolis |
| author_sort | Amy Davis |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-d4c1f33ea4c445d681d7da4cabd109da |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2019-06-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-d4c1f33ea4c445d681d7da4cabd109da2025-08-20T02:25:51ZengTaylor & Francis GroupBioTechniques0736-62051940-98182019-06-0166628528910.2144/btn-2019-0016Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomassAmy Davis0Christina Kohler1Ramzi Alsallaq2Randall Hayden3Gabriela Maron4Elisa Margolis51Department of Infectious Disease, St Jude Children's Research Hospital, Memphis, Tennessee, USA1Department of Infectious Disease, St Jude Children's Research Hospital, Memphis, Tennessee, USA1Department of Infectious Disease, St Jude Children's Research Hospital, Memphis, Tennessee, USA2Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA1Department of Infectious Disease, St Jude Children's Research Hospital, Memphis, Tennessee, USA1Department of Infectious Disease, St Jude Children's Research Hospital, Memphis, Tennessee, USAA 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.https://www.future-science.com/doi/10.2144/btn-2019-0016bacterial loadDNA extractionhigh throughputlow bacterial loadmetagenomicsmicrobiome |
| spellingShingle | Amy Davis Christina Kohler Ramzi Alsallaq Randall Hayden Gabriela Maron Elisa Margolis Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass BioTechniques bacterial load DNA extraction high throughput low bacterial load metagenomics microbiome |
| title | Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass |
| title_full | Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass |
| title_fullStr | Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass |
| title_full_unstemmed | Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass |
| title_short | Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass |
| title_sort | improved yield and accuracy for dna extraction in microbiome studies with variation in microbial biomass |
| topic | bacterial load DNA extraction high throughput low bacterial load metagenomics microbiome |
| url | https://www.future-science.com/doi/10.2144/btn-2019-0016 |
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