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Water kefir is a fruity, sour, slightly alcoholic and carbonated beverage, which is made by fermentation of an aqueous sucrose solution in the presence of dried figs and water kefir grains. These polysaccharide grains contain lactic acid bacteria (LAB), yeasts, and sometimes bifidobacteria and/or acetic acid bacteria, which consume sucrose to produce exopolysaccharides, lactic acid, acetic acid, ethanol, and carbon dioxide. Shotgun metagenomic sequencing was used to examine the microbial species diversity present at two time points during water kefir fermentation in detail, both in the water kefir liquor and on the water kefir grains, hence representing four samples.  Lactobacillus harbinensis, Lactobacillus hilgardii, Lactobacillus nagelii, Lactobacillus paracasei , and a  Lactobacillus  species similar to  Lactobacillus hordei/mali  were present in the water kefir examined, along with  Bifidobacterium aquikefiri  and two yeast species, namely  Saccharomyces cerevisiae  and  Dekkera bruxellensis . In addition, evidence for a novel  Oenococcus  species related to  Oenococcus oeni  and  Oenococcus kitaharae  was found. Its genome was derived from the metagenome and made available under the name of  Candidatus  Oenococcus aquikefiri. Through functional analysis of the four metagenomic data sets, it was possible to link the production of lactic acid, acetic acid, ethanol, and carbon dioxide to subgroups of the microbial species found. In particular, the production of mannitol from fructose was linked to  L. hilgardii, Candidatus  O. aquikefiri, and  B. aquikefiri , whereas glycerol production was associated with  S. cerevisiae . Also, there were indications of cross-feeding, for instance in the case of amino acid supply. Few bacterial species could synthesize a limited number of cofactors, making them reliant on the figs or  S. cerevisiae . The LAB species in turn were found to be capable of contributing to water kefir grain growth, as dextransucrase-encoding genes were attributed to  L. hilgardii, L. hordei / mali , and  Candidatus  O. aquikefiri.

Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species