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

Abstract

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.

The Buffer Capacity and Calcium Concentration of Water Influence the Microbial Species Diversity, Grain Growth, and Metabolite Production During Water Kefir Fermentation

“…This LAB species produces mainly D-lactic acid (Ludwig et al, 2009), and the proportions of D-lactic acid were indeed higher when the buffer capacity of the water was higher. The Oenococcus species found might represent a novel species, as its partial 16S rRNA gene sequence was only 97% identical to that of the closest known Oenococcus type strains, in particular O. kitaharae (Mattarelli et al, 2014), data that were also found via shotgun metagenomics of a water kefir microbial ecosystem (Verce et al, 2019). Its relative abundance was high at low pH values, which was conformed with the acidophilic nature of this LAB genus that occurs naturally in wine, cider, and related habitats (Ludwig et al, 2009).…”

Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India

“…The filtered metagenomic reads were used for taxonomical assignment by the Kaiju web server 1 for identification of bioremediation microbial species in the river sediment metagenome using NR protein database NCBI BLAST nr as reference database (Menzel et al, 2016;Cucio et al, 2018;Verce et al, 2019). Kaiju used Burrows-Wheeler transform algorithm for taxonomic classification on the protein-level.…”

Potential of Bacteria from Alternative Fermented Foods as Starter Cultures for the Production of Wheat Sourdoughs

“…hilgardii and Liql. nagelii , also Lacticaseibacillus paracasei , a LAB species similar to Liquorilactobacillus hordei/mali , and Oenococcus sicerae , bifidobacterial species ( Bifidobacterium aquikefiri ), and yeast species ( S. cerevisiae and Dekkera bruxellensis ) [ 38 , 39 , 44 , 50 , 51 , 75 , 76 , 77 ]. Moreover, LAB species frequently found in cereal fermentations are often animal-associated (e.g., gut microbiota; Liml.…”