E-Posters-Comparison of DNA Extraction kits in Compositional Analyses of Urinary Microbiome

Comparison of DNA Extraction kits in Compositional Analyses of Urinary Microbiome - Tatyana A Sysoeva, PhD

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In this study, researchers tested the efficiency of five different commercially available microbial DNA extraction kits on urine samples collected from 11 women. The DNA amount was measured using Qubit, and the V4 region of the 16S rRNA gene was sequenced with Illumina. The sequences were processed with DADA2 and the SILVA reference database before being analyzed with phyloseq and vegan in R. The overall microbial composition was assessed using beta diversity with the Bray Curtis distance.<br /><br />The researchers compared the DNA quantities and beta diversity values across the five extraction kits using ANOVA and PERMANOVA, respectively. They found that the DNA yields varied significantly depending on the extraction kit used. However, the overall microbial composition showed little variability due to the DNA extraction kit for most samples. The relative abundances of some bacteria differed in a subset of the urine samples.<br /><br />The study highlights the importance of considering the effect of the DNA extraction kit in cross-study analyses. The storage and DNA extraction protocols can strongly affect microbial composition analyses, especially in low biomass niches like the urinary tract.<br /><br />The researchers observed significant differences in the amount of DNA recovered by different extraction kits, but this did not translate into a significant difference in the total number of reads acquired after sequencing. The recovered microbes differed between the urine samples, but not based on the DNA isolation protocol.<br /><br />Overall, the study provides insight into the variability in DNA extraction kits and their impact on microbial composition analyses of the urinary microbiome. It recommends further investigation to understand the reasons for the differences observed in certain samples.

Keywords

microbial DNA extraction kits

urine samples

16S rRNA gene

phyloseq

beta diversity

DNA quantities

microbial composition

sequencing

recovered microbes

urinary microbiome