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

BioTechniques

Amy Davis¹  Gabriela Maron¹  Elisa Margolis¹  Ramzi Alsallaq¹  Christina Kohler¹  Randall Hayden² 

[1] 1Department of Infectious Disease, St Jude Children's Research Hospital, Memphis, Tennessee, USA;2Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA;

关键词: bacterial load;    DNA extraction;    high throughput;    low bacterial load;    metagenomics;    microbiome;   

DOI  :  10.2144/btn-2019-0016

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown