biostudies-literatureBreselge SInstitute for the Advancement of Food and Nutritional SciencesScience Foundation IrelandFood for Health IrelandHRB/SFIIrish Department of Agriculture, Food and the MarineEuropean Union's Horizon EuropeEuropean Union's Horizon 2020265https://www.ebi.ac.uk/biostudies/studies/S-EPMC12690108biostudies-literatureUnknown9(1)Water kefir (WK) is a fermented beverage produced by a complex symbiotic community of microbes, including yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). Here, we combined shotgun metagenomics, NMR metabolomics, GC-MS volatile organic compound (VOC) analysis, and metaproteomics to investigate microbial succession, functional dynamics, and the roles of yeasts and Zymomonas in WK fermentations representative of two WK types, i.e., one dominated by yeast-LAB-AAB and another by Zymomonas. Metagenomic profiling revealed that yeast-LAB-AAB communities exhibited dynamic microbial succession, whereas Zymomonas-dominated communities remained stable. Despite differing microbial compositions, both fermentations maintained consistent global metabolic functions, although specializedNPJ science of foodWater kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.PMC12690108NA-AGFOODDEVELAUTH20201216TC/2018/0025101060218818368USIRL-2019-1SFI/16/RC/3835SFI/12/RC/2273_P2Breselge SYin XKilcawley KPorcellato DSkibinska Ide Paula Dias Moreira LBrennan LCotter PDfalseWater kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.Water kefir (WK) is a fermented beverage produced by a complex symbiotic community of microbes, including yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). Here, we combined shotgun metagenomics, NMR metabolomics, GC-MS volatile organic compound (VOC) analysis, and metaproteomics to investigate microbial succession, functional dynamics, and the roles of yeasts and Zymomonas in WK fermentations representative of two WK types, i.e., one dominated by yeast-LAB-AAB and another by Zymomonas. Metagenomic profiling revealed that yeast-LAB-AAB communities exhibited dynamic microbial succession, whereas Zymomonas-dominated communities remained stable. Despite differing microbial compositions, both fermentations maintained consistent global metabolic functions, although specialized2025-01-01T00:00:00Z2025 Dec2026-06-06T00:12:10.938Z2026-05-23T03:13:57.209ZS-EPMC126901084136625310.1038/s41538-025-00624-3