Pham Vi D, Xu Zhaohui S, Simpson David J, Zhang Justina S, Gänzle Michael G
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
Appl Environ Microbiol. 2024 Dec 18;90(12):e0189224. doi: 10.1128/aem.01892-24. Epub 2024 Nov 6.
Sourdoughs are maintained by back-slopping over long time periods. To determine strain-level persistence of bacteria, we characterized four sourdoughs from bakeries over a period of 3.3, 11.0, 18.0, and 19.0 years. One sourdough included isolates of spp. and spp. that differed by fewer than 10 single-nucleotide polymorphisms (SNPs) from the isolates obtained 3.3 years earlier and thus likely represent the same strain. Isolates of differed by 200-300 SNPs; their genomes were under positive selection, indicating transmission from an external source. In two other sourdoughs, isolates of that were obtained 11 and 18 years apart differed by 19 and 29 SNPs, respectively, again indicating repeated isolation of the same strain. The isolate of from the fourth sourdough differed by 45 SNPs from the isolate obtained 19 years previously. We thus identified strain-level persistence in three out of four long-term back-slopped sourdoughs, making it possible that strains persisted over periods that are long enough to allow bacterial speciation and domestication.IMPORTANCEThe assembly of microbial communities in sourdough is shaped by dispersal and selection. Speciation and domestication of fermentation microbes in back-slopped food fermentations have been documented for food-fermenting fungi including sourdough yeasts but not for bacteria, which evolve at a slower rate. Bacterial speciation in food fermentations requires strain-level persistence of fermentation microbes over hundreds or thousands of years. By documenting strain-level persistence in three out of four sourdoughs over a period of up to 18 years, we demonstrate that persistence over hundreds or thousands of years is possible, if not likely. We thus not only open a new perspective on fermentation control in bakeries but also support the possibility that all humans, despite their cultural diversity, share the same fermentation microbes.
酸面团通过长期回接来维持。为了确定细菌菌株水平的持久性，我们对来自面包店的四种酸面团进行了长达3.3年、11.0年、18.0年和19.0年的特征分析。其中一种酸面团包含的分离株与3.3年前获得的分离株相比，单核苷酸多态性（SNP）差异少于10个，因此可能代表同一菌株。 的分离株差异为200 - 300个SNP；它们的基因组处于正选择状态，表明是从外部来源传播而来。在另外两种酸面团中，相隔11年和18年获得的 的分离株分别有19个和29个SNP差异，再次表明是同一菌株的重复分离。来自第四个酸面团的 的分离株与19年前获得的分离株有45个SNP差异。因此，我们在四个长期回接的酸面团中的三个中鉴定出了菌株水平的持久性，这使得菌株有可能在足够长的时间内持续存在，从而实现细菌的物种形成和驯化。重要性酸面团中微生物群落的组装受到扩散和选择的影响。在回接食品发酵中，包括酸面团酵母在内的食品发酵真菌的发酵微生物的物种形成和驯化已有文献记载，但细菌的情况尚未有报道，因为细菌进化速度较慢。食品发酵中的细菌物种形成需要发酵微生物在数百或数千年内保持菌株水平的持久性。通过记录在长达18年的时间里四个酸面团中有三个存在菌株水平的持久性，我们证明了即使可能性不大，但在数百或数千年内持续存在是有可能的。因此，我们不仅为面包店的发酵控制开辟了新的视角，还支持了尽管人类文化多样，但所有人都共享相同发酵微生物的可能性。
