Ref.

Evaluation method

Host animal

Output

[24]

Comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA)

Rumen fluid treatment (cheesecloth squeezed, centrifuged filtered),

Storage temperature (RT, −80˚C) and

Cryo protectants (PBS-glycerol, ethanol)

cow rumen

Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at −80˚C was found as the optimal method to study ruminal bacterial profile.

[22]

Fifteen different DNA extraction methods

cow and sheep rumen

There is significant differences in microbial community between extraction methods, e.g. Relative abundances some bacteria e.g. phyla Bacteroidetes and Firmicutes

DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable.

[25]

DNA extraction such as:

Repeated bead beating (RBB),

Phenol dependent bead beating (PBB),

Fast spin DNA kit for soil (FDSS), and

PQIAmini.

On observed microbial communities from fibrous and liquid rumen fractions

Dairy cows.

All four extraction procedures yielded DNA suitable for further analysis of bacterial, archaeal and anaerobic fungal communities using quantitative PCR and pyrosequencing of relevant taxonomic markers.

[26]

Ten improved DNA extraction methods

Yak

hexadecyltrimethylammomium bromide-lysozyme using physical lysis by bead beating is recommended for the DNA isolation of the rumen microbial community. It also showed that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria.