## 3 Results and Discussion
### Shotgun Metagenomic Analysis of M. gisevii MI-2 and Fermented Kombucha  
Comparative metagenomic analysis of _M. gisevii_ MI-2 and its fermented product--kombucha--provides insights into the evolution of microbial communities, metabolic shifts, and functional pathways that occur during fermentation. The composition of species in _M. gisevii_ MI-2 and kombucha L4-100 is shown in Table 6. The list of microorganisms is revealed in Supplementary Material S3 (Excel file). Three Kingdoms were identified in the _M. gisevii_ MI-2 sample and 4 in the kombucha L4-100 precipitate. More _Bacteria_ species (91) were obtained in kombucha, which shows the introduction of microorganisms into the product from plant raw materials and during the technological process. However, in terms of percentage, the bacteria content remained very similar in both samples at 81.07 and 82.60%. Eukaryotes identified more in the symbiotic system of _M. gisevii_ MI-2 than in kombucha (44 and 38 species, respectively). Nine viruses were found in _M. gisevii_ MI-2 (5 plant-specific and 4 bacterial phages). A total of 28 viruses were found in the kombucha; 5 plant-specific viruses remained during fermentation, and others were introduced during the fermentation process by various hostplants and bacteria. Having entered the _M. gisevii_ MI-2 microorganism complex from plant raw materials through a series of fermentations, plant viruses such as _Cauliflower mosaic virus_, _Dahlia mosaic virus_, _Figwort mosaic virus_, _Grapevine-associated calicivirus_, and _Rudbeckia flower distortion virus_ were able to establish themselves and survive (Figure 1C). One member from the archaea species _Candidatus Woesarchaeota_ archaeon was found in kombucha L4-100. It is widespread and abundant in soils, freshwater, sediments, and others [63]. Based on the abundance list of species (Supplementary Material S2 (Excel file) in each sample, Venn diagrams were constructed, and information was acquired about the Core-pan genome for eucaryotes, bacteria, and virus taxons (Figure 1; Supplementary Material S3 (Excel file)). After comparing the microbiota, 79.5% of eukaryotes, 92.5% of bacteria, and 77.8% of viruses identified in _M. gisevii_ MI-2 were also present in kombucha sediments. Specific to _M. gisevii_ MI-2 were 9 species of eucaryotes, and _3 Dentiscutata erythropus_, _Puccinia coronata_, and _Grosmannia calvigera_ detected only after fermentation in kombucha (Figure 1A). These fungi, _D. erythropus_ and _P. coronata_, are not typically associated with fermentation processes. Instead, each of them has a distinct ecological or  
pathological role. _D. erythropo_ is widespread in the soil and plays an essential ecological role as a detritivore, as first published in 2013 [64]. _P. coronata_ spores infect the alternate host buckthorn [65], which was the main biomass of fermented beverages. _G. clavigera_ is also a fungal pathogen of plants [PERSON] et al. [66]. However, _G. clavigera_ produces lignocellular enzymes and could grow using monoterpenes like limonene as the sole carbon source [67]. Consequently, _G. clavigera_ can degrade plant cellulose, so in theory, it could break down bacterial cellulose produced by _K. xylinus_, and using monoterpene limonene from buckhorn leaves. Unfortunately, until this described case, the interaction possibilities of these microorganisms were not studied because they inhabit very different ecosystems--forests and fermented tea, respectively. Results showed (Figure 1B) that 210 bacterial species from the _M. gisevii_ MI-2 metagenome were also detected in the metagenome of the fermented kombucha. Seventeen species were still in _M. gisevii_ MI-2 and did not migrate to the kombucha microflora. A wide range of bacteria (108) and viruses (21) species were introduced into kombucha with plant material or other food supplements during the fermentation process (Figure 1B,C).