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

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.

针对印度东北部本土发酵食品soidon的自发竹笋发酵过程，本研究采用依赖培养法（cultivation-dependent）与非依赖培养法（cultivation-independent）的分子生物学手段，对其微生物群落结构及种群动态展开了探究。本研究对3个独立的本土soidon发酵批次采集的时序样本，开展了两类分子分析：依赖培养分析包括PCR扩增核糖体DNA限制性酶切分析（PCR-amplified ribosomal DNA restriction analysis）与核糖体RNA（rRNA）基因测序；非依赖培养分析则包括PCR-变性梯度凝胶电泳（PCR-DGGE）、实时定量PCR（qPCR）以及Illumina扩增子测序（Illumina amplicon sequencing）。研究结果显示，在竹笋7天自然发酵过程中，本土乳酸菌（autochthonous lactic acid bacteria）经历了三阶段演替，最终形成稳定的微生态系统：发酵早期（1~2天）以魏斯菌属（Weissella spp.）（包含食窦魏斯菌（Weissella cibaria）、未培养加纳魏斯菌（uncultured Weissella ghanensis））及乳酸乳球菌乳脂亚种（Lactococcus lactis subsp. cremoris）为优势类群；发酵中期（第3天）柠檬明串珠菌（Leuconostoc citreum）加入该群落；发酵后期（5~7天）短乳杆菌（Lactobacillus brevis）与植物乳杆菌（Lactobacillus plantarum）成为优势类群，同时食窦魏斯菌与乳酸乳球菌乳脂亚种逐渐消失。乳酸乳球菌乳酸亚种（Lactococcus lactis subsp. lactis）与未培养乙酸耐受乳杆菌（uncultured Lactobacillus acetotolerans）则在整个发酵过程中持续存在，未表现出明显的种群动态变化。上述已鉴定的优势细菌类群及其种群动态特征，可有效用于设计soidon工业化生产的发酵剂（starter culture）。本研究结果表明，结合依赖培养与非依赖培养的分子生物学方法，能够更真实地揭示soidon发酵的微生物生态学特征。此外，本研究以soidon发酵为模型，还强调了在传统食品发酵微生物生态学研究中，需关注的降低方法学偏倚的关键问题。