## 3 Results and Discussion
### Identification of Microorganisms, Phylogeny, and Predominance  
Sixteen yeast and eight bacteria were identified during the fermentation of coffee varieties. The phylogenetic trees obtained using Bayesian and ML analysis contained the same clades (Figure 2). Phylogenetic analysis of the 16S rRNA gene revealed that isolates C23, C22, C20, and C18 formed a monophyletic group with high posterior Bayesian support (1) and ML bootstrap (97), closely related to species _ Bacillus albus_. On the other hand, isolate C24 clustered with a species of _Lactococcus garviaeae_, also with high posterior Bayesian support (1) and ML bootstrap (Figure 2A). The phylogenetic analysis of the 16 rRNA gene grouped isolates C17 and C19 with species of the genus _Staphylococcus_ (posterior/bootstrap = 1/100) and isolate C25 with species of the genus _Weissela_ (posterior/bootstrap = 1/100). The 16S rRNA gene could not discriminate between _Staphylococcus_ sp. and _Weissela_ species because only the V1 and V9 regions were used. Figure 1: Variation in the microbial population (log CFU.mL\({}^{-1}\)) of coffee cultivars during fermentation. The fermentation time is 48 h. (**A**) CA62; (**B**) A; (**C**) P2; (**D**) CP. (N: Natural fermentation; CA11: Fermentation inoculated with _S. cerevisiae_. LNF CA11; B10: Fermentation inoculated with _Kluyveromyces lactis_ B10.) Different lowercase letters indicate significant differences according to the Scott–Knott test (_p_ ¡ 0.05) when comparing the interaction between coffee variety and fermentation time. Different capital letters indicate a significant difference according to the Scott–Knott test (_p_ ¡ 0.05) when comparing the interaction between coffee variety and inoculation. Figure 2: Phylogenetic tree showing the relationships between the identified isolates and microorganisms. (**A**) Sequences of the 16S rRNA gene. The 16S rRNA gene from the _Escherichia coli_ strains was selected as the outgroup. (**B**) Sequences of the ITS rRNA gene. The ITS rRNA genes of strains of the genus _Debaryomyces_ sp. were selected as the outgroup. The tree was obtained using the neighbor joining (NJ)/maximum likelihood (ML) method of the Mega software package version 10.0 with a bootstrap value of n = 1000. Phylogenetic analyses of the ITS rRNA gene grouped isolate C9 together with species of the genus _Saccharomyces_ (posterior/bootstrap = -/89) and isolate C8 with species of the genus _Rhodutorula_ (posterior/bootstrap = 1/67) (Figure 2B). These isolates were only identified at the genus level as _Saccharomyces_ sp. and _Rhodutorula_ sp. Despite this, the gene was sufficient to identify isolates C16, C15, C14, and C13 at the species level as _Toraluspora delbrueckii_ (posterior/bootstrap = -/63); isolates C11 and C12 as _S. cerevisiae_ (posterior/bootstrap = -/63); isolates C5, C6, and C4 as _Pichia fluyveri_ (posterior/bootstrap = -/83); isolate C1 as _Hanseniaspora uavrum_ (posterior/bootstrap = -/83); isolate C7 as _Rhodosporidoolous ruineiae_ (posterior/bootstrap = -/78); and isolates C2 and C3 as _Meyerozyma caribbica_ (posterior/bootstrap = -/70). Given the identification of the microorganisms, it was possible to construct a bubble chart to show the presence and absence of the microorganisms throughout the fermentations varies according to the coffee variety analyzed and the type of starter culture used (Figure 3). Sixteen yeasts were isolated during the fermentation process. Analyzing their presence, it was observed that the identified species _M. caribbica_ C2 was the only yeast that was present in all established fermentation processes. Considering that the inoculation of starter  
Figure 3: Bubble plot showing the absence of microorganisms identified using the 16S rRNA and ITS genes during fermentation of different arabica coffee cultivars. ID: identification of microorganisms. The presence of yeast is represented in blue; the presence of bacteria is represented in green. (Microorganism present in N: (**A–H**); B10: (**I–P**); CA11: (**Q–X**)).