<p><span style="color: rgb(42, 42, 42); font-family: Merriweather, serif; font-size: 15px; background-color: rgb(239, 242, 247);">The primary aim of this article is to determine the changes in the microbial community within the current water kefir grains when developed in a protein-supplemented environment through metagenomic analysis. Supplied nutrients directly alter structures that contain complex microbial communities in nature. Considering the much more complex human intestinal microbiota, there are numerous articles indicating changes due to nutrition. This study validates this system on a micro scale. The second objective is to create alternatives for the current water kefir beverage and increase its consumption. The properties of these beverages were determined through chemical, sugar composition, microbiological, and sensory analyses. The research identified that the microbial content in water kefir grains changes, resulting in a high biomass structure due to the increased presence of bacteria producing excessive exopolysaccharides. Based on all analysis findings, the ginger and basil-flavored beverage group was determined to be the most suitable product. Further research is required to optimize other flavor components.</span></p>