A 2  3 experimental design was set up with vegetable type (carrot / cabbage), cutting type (thin / rough), and salt concentration (0.8% / 1%) as factors. Vegetables were pressed down in 500 mL-jars and filled up with brine, and two independent jars used at 4 stages to characterise the microbial dynamics and biochemical changes by combining culturomics, 16S rRNA V5-V7 and gyrB metataxonomics, and targeted metabolomics.

Culturomics and metataxonomics results showed a similar succession of the main bacterial groups in both vegetables, with Enterobacteriaceae quickly replacing the initial microbiota, This work is openly licensed via CC BY 4.0.

1 further replaced within a few days by lactic acid bacteria, mainly represented by Leuconostoc sp. Cabbage and carrot fermentation rates quantitatively differed. Maximal Enterobacteriaceae counts were higher in cabbage (8 vs 7 logCFU/g), while lactic acid bacteria counts were higher in carrot (9 vs 8 logCFU/g). The acidification rate was faster in carrot (e.g. pH decreased to 3.8 in 40 h vs approx. 5.0 in 86 h in cabbage). Mannitol, lactic and acetic acids were the main metabolites produced in both vegetables, but concentrations were two-fold higher in carrot. Viable Enterobacteriaceae were not detected anymore after two-week fermentation, except for some roughly-cut cabbage samples. No pathogenic bacteria were detected. Taxonomic profiles varied according to the marker used, e.g. Leuconostoc was only detected with gyrB and viceversa for Clostridium. The gyrB marker provided a markedly better resolution at the specieslevel (for 97% of ASV vs only 20% for the 16S marker). Significant effects of cutting type, and not of NaCl concentration, were observed. Thinly-cut vegetables globally showed a quicker fermentation compared to roughly-cut ones and exhibited a higher titratable acidity, e.g. 0.8% vs 0.3%, respectively, in grated and sliced carrot at 64 h incubation. In line, a quicker production of acids and a quicker decrease of viable enterobacteria were observed in thinly-cut vegetables, in particular for cabbage, for which the surface generated by the cutting was ~20-fold greater in shredded cabbage than in leaf cabbage. Some leaf cabbage samples displayed atypical fermentations, with the presence of particular taxa and atypical metabolite profiles with high amounts of ethanol produced. These general trends were modulated by quantitative and qualitative differences between replicate jars.

This study confirms the highly diverse microbiota of spontaneously fermented vegetables and the tight competition between Enterobacteriaceae and lactic acid bacteria in their colonisation, and documents for the first time the effect of the type of cutting on the fermentation rate.