Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing

McGaughey, Kara D.; Yilmaz-Swenson, Tulay; Elsayed, Nourhan M.; Cruz, Dianne A.; Rodriguez, Ramona; Kritzer, Michael D.; Peterchev, Angel V.; Gray, Megan; Lewis, Samantha R.; Roach, Jeffrey; Wetsel, William C.; Williamson, Douglas E.

doi:10.1371/journal.pone.0202858

Cited by 18 publications

(9 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…DNA was isolated from 75 mg of fecal pellets according to a fecal sample-based adaptation to a Maxwell® RSC PureFood GMO and Authentication Kit (Catalog No. AS1600; Promega Corporation, Madison, WI), as previously described 39 . Concentrations were determined fluorometrically using the QuantiFluor® ONE dsDNA System (Promega Corporation) on a Quantus TM fluorometer (Promega Corporation), and purity was assessed via 260/280 and 260/230 absorbance ratios as determined by spectrophotometry (Epoch TM , BioTek Instruments, Inc., Winooski, VT).…”

Section: Methodsmentioning

confidence: 99%

Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice

McGaughey

Yilmaz-Swenson

Elsayed

et al. 2019

Sci Rep

Self Cite

View full text Add to dashboard Cite

As discussion of stress and stress-related disorders rapidly extends beyond the brain, gut microbiota have emerged as a promising contributor to individual differences in the risk of illness, disease course, and treatment response. Here, we employed chronic mild social defeat stress and 16S rRNA gene metagenomic sequencing to investigate the role of microbial composition in mediating anxiety- and depressive-like behavior. In socially defeated animals, we found significant reductions in the overall diversity and relative abundances of numerous bacterial genera, including Akkermansia spp., that positively correlated with behavioral metrics of both anxiety and depression. Functional analyses predicted a reduced frequency of signaling molecule pathways, including G-protein-coupled receptors, in defeated animals. Collectively, our data suggest that shifts in microbial composition may play a role in the pathogenesis of anxiety and depression.

show abstract

Section: Methodsmentioning

confidence: 99%

Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice

McGaughey

Yilmaz-Swenson

Elsayed

et al. 2019

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…53 However, there is also evidence of A 260 /A 230 ratios greater than 1.6 for extracted DNA samples using the QIAmp PowerFecal and Maxwell RSC PureFood GMA Authentication kits, but both of these methods use columnbased extraction as opposed to bead-based. 54 Overall, the GTC present in the Binding Solution and Wash 1 buffers had the greatest effect on the sample purity, measured by the A 260 /A 230 ratio, but other contaminants such as ethanol which make up a large percentage of Wash 2 can also influence the absorbance readings if not properly removed from the sample. 52 In addition to the use of EOF significantly improving the purity of the extracted cfDNA, it was noted that using the microfluidic separator also improved the purity even without the electric field.…”

Section: Discussionmentioning

confidence: 94%

“…When comparing the results of this study to others, it appears that the low A 260 / A 230 ratio is seen as a characteristic of other DNA extraction kits as well, including the MagaZorb DNA Mini‐Prep Kit, which showed an average A 260 / A 230 ratio below 1 across the samples presented 53 . However, there is also evidence of A 260 / A 230 ratios greater than 1.6 for extracted DNA samples using the QIAmp PowerFecal and Maxwell RSC PureFood GMA Authentication kits, but both of these methods use column‐based extraction as opposed to bead‐based 54 . Overall, the GTC present in the Binding Solution and Wash 1 buffers had the greatest effect on the sample purity, measured by the A 260 / A 230 ratio, but other contaminants such as ethanol which make up a large percentage of Wash 2 can also influence the absorbance readings if not properly removed from the sample 52…”

Section: Discussionmentioning

confidence: 99%

A microfluidic platform for high‐purity cell free DNA extraction from plasma for non‐invasive prenatal testing

2022

View full text Add to dashboard Cite

Objectives Increase the yield and purity of cell‐free DNA (cfDNA) extracted from plasma for non‐invasive prenatal testing (NIPT) as inefficiencies in this extraction and purification can dramatically affect the sensitivity and specificity of the test. Methods This work integrates cfDNA extraction from plasma with a microfluidic chip platform by combining magnetic bead‐based extraction and electroosmotic flow on the microfluidic chip. Various wash buffers and voltage conditions were simulated using COMSOL Multiphysics Modeling and tested experimentally. Results When performing the first wash step of this assay on the microfluidic chip with 300 V applied across the channel there was a six‐fold increase in the A260/A230 ratio showing a significant improvement (p value 0.0005) in the purity of the extracted sample all while maintaining a yield of 68.19%. These values are critical as a high yield results in more sample to analyze and an increase in A260/A230 ratio corresponds to a decrease in salt contaminants such as guanidinium thiocyanate which can interfere with downstream processes during DNA library preparation and potentially hinder the NIPT screening results. Conclusions This technique has the potential to improve NIPT outcomes and other clinically relevant workflows that use cfDNA as an analyte such as cancer detection.

show abstract

“…The magnetic beads method is the most commonly used technique for DNA extraction for NGS analysis (McGaughey et al 2018). This method greatly simplifies the extraction procedure and improves the size selection process.…”

Section: Genomic Resourcesmentioning

confidence: 99%

Genomic selection in salmonids: new discoveries and future perspectives

et al. 2021

View full text Add to dashboard Cite

Over the past 20 years, the introduction of new molecular techniques has given a new impetus to genetic and genomic studies of fishes. The main traits selected in the aquaculture sector conform to the polygenic model, and, thus far, effective breeding programmes based on genome-wide association studies (GWAS) and marker-assisted selection (MAS) have been applied to simple traits (e.g. disease resistance and sexual maturation of salmonids) and known Quantitative Trait Loci (QTLs). Genomic selection uses the genomic relationships between candidate loci and SNPs distributed over the entire genome and in tight linkage disequilibrium (LD) with genes that encode the traits. SNP (low and high density) arrays are used for genotyping thousands of genetic markers (single nucleotide polymorphisms, SNPs). The genomic expected breeding value (GEBV) of selection candidates is usually calculated by means of the GBLUP or ssGBLUP (single step) methods. In recent years, in several aquaculture breeding programmes, the genomic selection method has been applied to different fish and crustacean species. While routine implementation of genomic selection is now largely carried out in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), it is expected that, in the near future, this method will progressively spread to other fish species. However, genomic selection is an expensive method, so it will be relevant mostly for traits of high economic value. In several studies (using different salmonid species), the accuracy of the GEBVs varied from 0.10 to 0.80 for different traits (e.g. growth rate and disease resistance) compared to traditional breeding methods based on geneology. Genomic selection applied to aquaculture species has the potential to improve selection programmes substantially and to change ongoing fish breeding systems. In the long term, the ability to use low-pass genome sequencing methods, low-cost genotyping and novel phenotyping techniques will allow genomic selection to be applied to thousands of animals directly at the farm level.

show abstract

Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing

Cited by 18 publications

References 17 publications

Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice

Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice

A microfluidic platform for high‐purity cell free DNA extraction from plasma for non‐invasive prenatal testing

Genomic selection in salmonids: new discoveries and future perspectives

Contact Info

Product

Resources

About