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Table 1 Summary of findings reported in this study

From: The effect of DNA extraction methodology on gut microbiota research applications

Methods

Pros

Cons

Chaotropic (CHAO)

Highest DNA yield

Most fractional loss of reads after different steps of bioinformatics pipeline

High coverage in sequencing

Takes longest to perform

Lowest loss of read trimming

 

Cheap

 

Phenol Chloroform (PHEC)

Cheap

In the middle in terms of performance compared with the other methods

Highest dsDNA in probiotic sample

Use toxic reagents

Quicker than CHAO

 

QIAamp DNA stool minikit (QIAG)

Highest read yield post OTUs assignment

Lowest DNA yield

Quick

Not cheap

Highest quality DNA

Lowest coverage

Can be automated