Does strain-level persistence of lactobacilli in long term back-slopped sourdoughs inform on domestication of food-fermenting lactic acid bacteria?

Sourdoughs are maintained by back-slopping over long time periods. To determine strain-level persistence of bacteria, we characterized 4 sourdoughs from bakeries over a period of 3.3, 11, 18 and 19 years. One sourdough included isolates of Levilactobacillus spp. and Fructilactobacillus spp. that differed by fewer than 10 SNPs from the isolates obtained 3.3 years earlier and thus likely represent the same strain. Isolates of Lv. parabrevis differed by 200 – 300 SNPs, their genomes were under positive selection, indicating transmission from an external source. In two other sourdoughs, isolates of Fl. sanfranciscensis 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 Fl. sanfranciscensis from the fourth sourdough differed by 45 SNPs from the isolate obtained 19 years prior. We thus identified strain-level persistence in 3 out of 4 long-term back-slopped sourdoughs, making it possible that strains persisted over periods that are long enough to allow bacterial speciation and domestication.