Acid-mediated selection and metabolic interactions drive robust assembly of sourdough starter communities across variable initial ratios.

Abstract

Achieving reproducible and robust outcomes in cereal-based fermentations remains challenging due to variability in starter composition and dynamic microbial interactions during fermentation. Here, we investigated how starting ratios shape the assembly dynamics of a defined three-species consortium in a well-mixed liquid cereal-based model system, comprising Lactiplantibacillus plantarum Lp100, Maudiozyma humilis Mh2, and Saccharomyces cerevisiae Sc4. By varying initial inoculation ratios over three orders of magnitude (1:1:1 to 1000:1:1), short-term batch cocultures exhibited pronounced ratio-dependent divergence during early growth, with Sc4 showing a graded response to initial abundance. Despite this early divergence, all communities reproducibly converged by 48 h to a similar composition of approximately 10:1:1 (Lp100:Mh2:Sc4), indicating strong constraints on community assembly under liquid cereal-based fermentation conditions. This convergence was associated with environmental modification and asymmetric resource use. Lp100 imposed acidification and preferentially depleted specific nutrients, establishing early competitive asymmetry. Time-resolved metabolomics revealed that community assembly proceeded through distinct metabolic phases, characterized by early nitrogen‑carbon niche partitioning, metabolite-associated interactions among community members. Consistently, extracellular metabolites associated with Lp100, together with residual nutrients, may contribute to the observed growth of yeast. Together, these results demonstrate that acid-mediated environmental filtering and asymmetric metabolic interactions impose strong constraints on microbial community assembly, leading to robust and reproducible fermentation outcomes largely independent of initial inoculation ratios. This work provides a mechanistic framework for understanding microbial stability in liquid cereal-based fermentation systems, and offers guidance for the rational design of resil