Four spontaneous rye sourdough fermentations were performed over a period of ten days with daily
back-slopping. Samples taken at all refreshment steps were used for culture-dependent and cultureindependent
characterization of the microbiota present. Furthermore, an extensive metabolite target
analysis was performed through a combination of various chromatographic methods, including liquid
chromatography coupled to mass spectrometry (LC/MS) and gas chromatography coupled to mass
spectrometry (GC/MS). Spearman’s rank correlation coefficients were calculated and a principal
component analysis (PCA) was performed on the data obtained in this study combined with data
obtained previously for wheat and spelt sourdoughs. In general, the establishment of a stable microbial
ecosystem occurred through a three-phase evolution, with mainly Lactobacillus plantarum and
Lactobacillus fermentum dominating the rye sourdough ecosystems. PCA revealed that ornithine and
mannitol were positively correlated with rye sourdoughs, contributing to bacterial competitiveness at
the onset of sourdough production. Wheat and spelt sourdoughs showed a high degree of similarity,
although certain compounds (e.g. indolelactic acid) appeared to be specific for spelt sourdoughs. The
production of amino acid metabolites, mainly hydroxy acids (e.g. phenyllactic acid) and alcohols (e.g. 3-
methyl-1-butanol), contributed to the equilibration of the redox balance and further enhanced the
competitiveness of dominant species in stable sourdoughs.