Changes in microbial community structure during adaptation of kombucha symbiotic culture of bacteria and yeast to fermentation of sweet and acid whey

Whey is a liquid byproduct from the dairy industry that is not fully utilized and can be problematic to dispose of. Based on its composition, there is potential to upcycle whey into fermented beverages for human consumption. Most focus to date has been upon alcoholic fermentation to generate alcohol for distillation, or use of kefir grains to make acidic beverages. Kombucha fermentation is analogous to kefir, with a solid-state inoculum that is backslopped from one batch to the next, but yields a different profile of organic acids when applied to its typical substrate of tea sweetened with sucrose. Notably, some kombucha symbiotic cultures of bacteria and yeast (SCOBY) harbor a lactose-fermenting yeast species, Brettanomyces anomalus, rendering it possible that a SCOBY system could be adapted to lactose-containing whey substrates. The objective of this research was to apply a B. anomalus-containing kombucha SCOBY to the fermentation of sweet and acid whey. Sequential batch fermentations were performed to determine changes in microbial community structure and fermentation outcomes during adaptation to whey substrates. Metabarcoding targeting the fungal ITS2 region and the bacterial 16S V4–V5 domain was used to assess fungal and bacterial communities, respectively. We used ¹H nuclear magnetic resonance to determine the chemical composition of fermentations. The B. anomalus-containing kombucha SCOBY was able to perform repeat backslop-inoculated whey fermentation, with the major fermentation products being those characteristic to kombucha fermentation (acetic acid and ethanol). The whey-adapted SCOBY was characterized by replacement of the original main fungal taxa, Brettanomyces bruxellensis, by the lactose-fermenting B. anomalus, whereas the bacterial community remained more diverse.