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Supporting information - Results
Development and optimization of DNA extraction from fermented bamboo shoot
The cultivation-independent study of microbial diversity and community structure
greatly depends on the nucleic acid extraction method. Moreover, no established method for
extraction of metagenomic DNA from bamboo-based fermented products is available. In the
present study, a modified enzymatic and chemical lysis-based DNA extraction protocol
(designated MII) for fermented bamboo shoot was developed and optimized for maximum
DNA recovery, purity, high microbial DNA content and maximum microbial diversity in
comparison with the commercial PowerFood (MO BIO) metagenomic DNA extraction kit.
The yields of metagenomic DNA from fresh and fermented bamboo shoot samples were
significantly higher (p < 0.005) for the method MII than the kit, reflecting an approximate 3
fold increase in DNA recovery (Fig. S4A). During optimization of method MII, an increase
(58  78 %) in metagenomic DNA recovery after CTAB treatment was noticed. Although the
DNA yield was higher in both the methods for the fermented samples than the fresh raw
material, no significant difference (p > 0.05) in DNA recovery ratio of the two methods was
observed between the sample types. This indicated that the efficiency of the extraction
methods was not affected by the type of samples used for the extraction. The quality of the
extracted DNA was equally high (A260/280(MII) = 1.90 ± 0.02, A260/280(Kit) = 1.91 ± 0.02) for
both the methods. In order to confirm the difference between the two methods in terms of
their ability to recover microbial DNA, qPCR analysis was performed using Eubacteria and
Lactobacillales specific primers targeting SSU rRNA gene. Both the methods recovered
considerably high microbial DNA (Fig.S4B  E) comparable with the culturable population
load suggesting that these methods efficiently extracted microbial DNA. The yields
(expressed as SSU rRNA gene copies per g sample) of Eubacteria and Lactobacillales
specific DNA were significantly higher (p < 0.001) for the method MII than the kit.
Interestingly, the Eubacteria and Lactobacillales specific DNA contents (expressed as SSU
rRNA gene copies per ng DNA) were also significantly higher (p < 0.001) for the method
MII than the kit indicating that the method MII recovered more of bacterial DNA than plant
DNA compared to the kit. Further analysis of DGGE fingerprints of total bacterial
community showed that the method MII brought out more microbial diversity than the kit
(Table S6). In short, an enzymatic and chemical lysis-based DNA extraction method was
developed for bamboo-based fermented products which can efficiently extract microbial
DNA with high yield, purity, content and diversity.
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