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Supporting Information Figures
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Fig. S1 DGGE profile of LAB DGGE marker (DMI) ( A ) and yeasts DGGE marker (DMIII) ( B ) obtained from the optimized conditions. The markers were developed by mixing 100
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150 ng of
SSU rRNA gene V3 region (for LAB) and LSU rRNA gene D1/D2 domain (for yeasts) obtained after PCR amplification using eubacteria and yeasts specific primers, respectively, as described in the Materials and Method section. Type strains or fermented food isolate DNA or identified
V3 region and D1/D2 domain from fermented food metagenomic DNA were used as amplification template. ( A ) M1: Weissella beninensis (GenBank ID: JF427731), M2:
Lactobacillus plantarum (ATCC 8014), M3: Lactobacillus fermentum (ATCC 9338), M4:

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Lactobacillus brevis strain A1S3L5 (GenBank ID: JF427708), M5: Lactobacillus acetotolerans
(GenBank ID: JF427746), M6: Lactobacillus versmoldensis (GenBank ID: JF427747), M7:
Carnobacterium sp. strain A2S10L14 (GenBank ID: JF427719), M8: Vagococcus fluvialis
(GenBank ID: JF427769), M9: Lactobacillus farciminis (GenBank ID: JF427750), M10:
Lactococcus lactis (ATCC 19257), M11: Lactobacillus zymae (GenBank ID: JF427756), M12:
Lactobacillus frumenti (GenBank ID: JF427758) and M13: Lactobacillus rhamnosus (ATCC
7469). ( B ) Y1: Uncultured yeast A3SY1 (GenBank ID: JF439338), Y2: Uncultured yeast
A1SY2 (GenBank ID: JF439313), Y3: Uncultured yeast A2S3Y1 (GenBank ID: JF439362), Y4:
Uncultured yeast A1SY4 (GenBank ID: JF439315), Y5: Uncultured yeast A1SY8 (GenBank ID:
JF439318), Y6: Debaryomyces hansenii A1S2Y1 (GenBank ID: JF439364), Y7: Uncultured yeast Kw2SY7 (GenBank ID: JF439358), Y8: Meyerozyma guilliermondii ATCC 6260, Y9:
Meyerozyma caribbica Kw3S2Y1 (GenBank ID: JF439367), Y10: Uncultured yeast A1SY10
(GenBank ID: JF439320), Y11: Uncultured yeast Kw1SY11 (GenBank ID: JF439353), Y12:
Uncultured yeast A1SY13 (GenBank ID: JF439322), Y13: Uncultured yeast A1SY15 (GenBank
ID: JF439323) and Y14: Uncultured yeast A1SY16 (GenBank ID: JF439324).

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Fig. S2 Neighbor-joining phylogenetic tree based on the nucleotide sequence of SSU rRNA gene showing the evolutionary relationships of the novel bacterial isolates obtained in the present study with their nearest known taxa. The tree was constructed based on the evolutionary distance calculated using Kimura-2-parameter substitution model. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches for values > 50 %. The bar represents
0.05 substitutions per nucleotide position (5 % sequence divergence). Phylotype groups and
GenBank accession numbers are mentioned within the parentheses. Bacteroides fragilis w as the outgroup in the analysis. T = Type strain.

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Fig. S3 Neighbor-joining phylogenetic tree based on the nucleotide sequence of ITS1-5.8S-
ITS2 showing the evolutionary relationships of the novel yeast isolates obtained in the present study with their nearest known taxa. The tree was constructed based on the evolutionary distance calculated using Kimura-2-parameter substitution model. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches for values > 50 %. The bar represents 0.01 substitutions per nucleotide position (1 % sequence divergence). GenBank accession numbers are mentioned within the parentheses along with the phylotype groups. T = Type strain.

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Fig. S4 Developed metagenomic DNA extraction method efficiently extract microbial DNA with high yield, purity and content.
(A) Recovery of metagenomic DNA extracted using the developed method (MII) and commercial MO BIO PowerFood kit (Kit) from the raw material (fresh bamboo apical shoot meristem, n =
3) and fermented samples (collected at 1, 2, 3, 5 and 7 days of fermentation, n = 15) of soidon . Data are expressed as the arithmetic means ± standard error of the means. Significant difference between the two methods is indicated by asterisk (
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: p < 0.005 in case of raw material, p < 0.001 in case of fermented samples; one-tailed, paired Student's t -test). Value within the parenthesis represents ratio of the amount of
DNA recovered using the method MII to that using the kit. (B
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E) Comparison of the developed method with the commercial kit in terms of yield and content of Eubacteria (B, D respectively) and Lactobacillales
(C, E respectively) specific DNA. The population loads are estimated by qPCR assay and are expressed as
SSU rRNA gene copies per g sample (B, C) and per ng metagenomic DNA (D, E). Each data represents values from three assay replicates for six different samples. Significant difference between the two methods is indicated by asterisk (

: p < 0.001; one-tailed, paired Student’s t -test; n = 6).

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Fig. S5 PCA biplot based on the densitometric values of DGGE banding patterns of the predominant bacterial species in different stages of the indigenous soidon fermentation. Solid shapes with the same color indicate a particular period of three independent fermentations
(black: fresh shoot; magenta: 1 day; green: 2 days; orange: 3 days; red: 5 days; brown: 7 days).
Solid blue arrows and their lengths indicate the species directions towards the stages and their abundances. Dotted arrow indicates the direction of microbiota changes during the fermentation.