DOI: 10.5061/dryad.cs4h8
title: Data from: Three-phase succession of autochthonous lactic acid bacteria to reach a stable ecosystem within seven days of natural bamboo shoot fermentation as revealed by different molecular approaches

description: Microbial community structure and population dynamics during spontaneous
 bamboo shoot fermentation for production of ‘soidon’ (indigenous fermented
 food) in North-east India were studied using cultivation-dependent and
 cultivation-independent molecular approaches. Cultivation-dependent
 analyses (PCR-amplified ribosomal DNA restriction analysis and rRNA gene
 sequencing) and cultivation-independent analyses (PCR-DGGE, qPCR and
 Illumina amplicon sequencing) were conducted on the time series samples
 collected from three independent indigenous soidon fermentation batches.
 The current findings revealed three-phase succession of autochthonous
 lactic acid bacteria to attain a stable ecosystem within 7 days natural
 fermentation of bamboo shoots. Weissella spp. (Weissella cibaria,
 uncultured Weissella ghanensis) and Lactococcus lactis subsp. cremoris
 predominated the early phase (1–2 days) which was joined by Leuconostoc
 citreum during the mid-phase (3 days), while Lactobacillus brevis and
 Lactobacillus plantarum emerged and became dominant in the late phase (5–7
 days) with concurrent disappearance of W. cibaria and L. lactis subsp.
 cremoris. Lactococcus lactis subsp. lactis and uncultured Lactobacillus
 acetotolerans were predominantly present throughout the fermentation with
 no visible dynamics. The above identified dominant bacterial species along
 with their dynamics can be effectively utilized for designing a starter
 culture for industrialization of soidon production. Our results showed
 that a more realistic view on the microbial ecology of soidon fermentation
 could be obtained by cultivation-dependent studies complemented with
 cultivation-independent molecular approaches. Moreover, the critical
 issues to be considered for reducing methodological biases while studying
 the microbial ecology of traditional food fermentation were also
 highlighted with this soidon fermentation model.
description: Fig. S2 Neighbor-joining
 phylogenetic tree based on the nucleotide sequence of SSU rRNA gene
 showing the evolutionary relationships of the novel bacterial
 isolatesThe aligned sequences in
 FASTA file format (.fas)Aligned sequences for Fig.
 S2.fas.fasFig. S2 Neighbor-joining
 phylogenetic tree based on the nucleotide sequence of SSU rRNA gene
 showing the evolutionary relationships of the novel bacterial isolates
 -Tree filePhylogenetic tree file
 in NEWICK format (.nwk)Tree File for Fig.
 S2.nwkFig. S3 Neighbor-joining
 phylogenetic tree based on the nucleotide sequence of ITS1-5.8S-ITS2
 showing the evolutionary relationships of the novel yeast
 isolatesThe aligned sequences in
 FASTA file format (.fas)Aligned sequences for Fig.
 S3.fas.fasFig. S3 Neighbor-joining
 phylogenetic tree based on the nucleotide sequence of ITS1-5.8S-ITS2
 showing the evolutionary relationships of the novel yeast isolates -tree
 filephylogenetic tree file
 in NEWICK format (.nwk)Tree File for Fig.
 S3.nwkTable S3 Molecular
 grouping and identification of culturable bacteria isolated from the
 stage-wise collected samples of the indigenous fermentation of S. munroi
 meristem for production of soidon by ARDRA and rRNA
 sequencingThe aligned sequences in
 FASTA file format (.fas)Table S3_Aligned_All 16S
 sequences.fas.fasTable S3 Molecular
 grouping and identification of culturable yeasts from the stage-wise
 collected samples of the indigenous fermentation of S. munroi meristem for
 production of soidon by ARDRA and 26S rRNA D1/D2 region
 sequencingThe aligned sequences in
 FASTA file format (.fas)Table S3_Aligned_All 26S D1D2
 sequences.fas.fasTable S3 Molecular
 grouping and identification ofculturable yeasts isolated from the
 stage-wise collected samples of the indigenous fermentation of S. munroi
 meristem for production of soidon by ARDRA and ITS
 sequencingThe aligned sequences in
 FASTA file format (.fas)Table S3_Aligned_All ITS
 sequences.fas.fas