Metabolic reorganization shapes the dynamics of a water kefir microbial community

Chambeaudie, M.; Maze, D.; Cariou, M.; Duvernois-Berthet, E.; Mozziconacci, J.; Tulaeva, E.; Courel, M.; Delagoutte, E.; Lopes, F.; Lavelle, C.; Boule, J.-B.; Joubert, A.

doi:10.64898/2026.10.09.757983

bioRxiv · 10.64898/2026.10.09.757983

Metabolic reorganization shapes the dynamics of a water kefir microbial community

Chambeaudie, M.·Maze, D.·Cariou, M.·Duvernois-Berthet, E.·Mozziconacci, J.·Tulaeva, E.·Courel, M.·Delagoutte, E.·Lopes, F.·Lavelle, C.·Boule, J.-B.·Joubert, A.

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Abstract

Microbial fermentations emerge from the collective activity of interacting species whose relative abundances, metabolic functions, and environmental constraints continuously change over time. Water kefir provides a tractable model to investigate how multispecies communities coordinate their metabolic activities during fermentation. Here, we combined time-resolved community profiling, physicochemical measurements, metabolite quantification, and controlled co-culture assays to characterize the dynamics of a water kefir consortium comprising 19 detected microbial species. Our results reveal that water kefir fermentation is not adequately described as a simple succession of independently acting microbial groups. Instead, the community undergoes a reproducible reorganization of its collective metabolism around 20 h of fermentation. This transition marks a shift from an early regime characterized by the accumulation of soluble sugars and ethanol to a later regime dominated by enhanced sugar consumption and lactate production. Controlled interaction assays further showed that bacterial partners can alter carbon-use behaviour in Saccharomyces cerevisiae, highlighting the capacity of interspecies interactions to reshape metabolic phenotypes within the consortium. Together, these results support an ecological view of water kefir fermentation in which community-wide metabolic reorganization emerges from the interplay between microbial interactions, resource availability, and environmental change.

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Chambeaudie, M., Maze, D., Cariou, M., Duvernois-Berthet, E., Mozziconacci, J., Tulaeva, E., Courel, M., Delagoutte, E., Lopes, F., Lavelle, C., Boule, J.-B., Joubert, A.. 2026-10-12. Metabolic reorganization shapes the dynamics of a water kefir microbial community. https://doi.org/10.64898/2026.10.09.757983

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