Data from: Three-phase evolution of autochthonous lactic acid bacteria to reach a stable ecosystem within seven days of natural bamboo shoot fermentation revealed by polyphasic molecular approach

Culture-independent metagenomic study is indispensable for in-depth description of microbial ecology of traditional fermented foods, but the comprehensiveness of this approach is not thoroughly elucidated while investigating natural food fermentation. Here, we described issues related with culture-dependent and culture-independent molecular approaches while studying the microbial community structure and population dynamics during spontaneous bamboo shoot fermentation (‘soidon’ production in North East India) as a model. Culture-dependent PCR amplified ribosomal DNA restriction analysis and rRNA gene sequencing, and culture-independent PCR-DGGE, qPCR and Illumina amplicon sequencing were conducted on the time series samples from three independent indigenous soidon fermentations. The current findings revealed three-phase evolution 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 evolved 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. Our results showed that more realistic view of microbial ecology of traditional food fermentation, in which species and subspecies level population dynamics play highly significant role, could be obtained by culture-dependent approaches supported with culture-independent strategies, and highlighted issues to be considered for reducing methodological biases.