## 3 Results and Discussion
### Bacterial Population Profile in Sheep's Cheese
A large clade was formed with species from the LAB genera, such as _Streptococcus_ (pink), _Lactobacillus_, _Faecalibacterium_, _Lentilactobacillus_, _Lacticaseobacillus_, and _Lactococcus_ (turquoise green and lilac), sharing a common ancestor, as they share the same order as the _Lactobacillus_. Well-defined groupings were observed, such as _Pseudomonas_ (gray),  
Figure 3: Phylogenetic tree of the bacterial population identified in samples of sheep’s cheese sold in the southern region of Brazil. The circular phylogenetics tree was constructed using the maximum-likelihood method using 1000 bootstraps in the IQ-TREE program and visualized using the FigTree program. Each of the branches represents the evolutionary distance of the genomes represented at the ends. In constructing the phylogenetic tree, sequences of the 16S rRNA genes obtained in this study, amplified from sheep cheese samples, were used. Lactococcus_ (yellow), _Streptococcus_ (pink), _Lactobacillus_ (lilac), _Staphylococcus_ (light green), and _Acinetobacter_ (dark green) (Figure 3). Genetic proximity that drew attention was that of the light green clade, consisting of pathogenic bacteria of the genera _Alloococcus_, _Staphylococcus_, _Macrococcus_, and _Brochlor trix_, with lactic acid bacteria (red, lilac, and turquoise green clades), mainly of the genera _Lacticasebiacillus_, _Companilactobacillus_, _Limosilactobacillus_, _Lactiplantobacillus_, _Lentilactobacillus_, and _Loigalactobacillus_ (Figure 3). Additionally, a large clade in blue was generated with sequences that were not identified and was named Bacteria, which shares the same common ancestor as _Streptococcus_. Due to the high abundance of LABs in the bacterial population of cheeses and because they are responsible for the positive characteristics of dairy products, this group is always in evidence in studies and research. However, it is important to investigate in more detail the bacteria that have the potential to cause disease, whether those commonly investigated, which are identified in food quality control legislation, emerging pathogens, and even species that are harmful to health milk technology. Alpha diversity data were estimated using the Chao1, Simpson, and Shannon indices (Figure 4), given that the milk matrix supports a highly diverse microbiota due to its nutrient-rich nature [79]. From the analysis of bacterial population diversity in the cheeses, it is observed that the mean Chao1 index value is 53.4, ranging from 23.3 to 86.6 for samples ST056 and VF712, respectively. The samples RA127, VF712, and PT570 showed greater species diversity. The mean Simpson index was 0.350, and the Shannon index was 0.900. It can be seen in Figure 4 that 8 out of 13 samples had Chao1 index values above 50, indicating high species diversity. However, the same pattern does not hold for the Simpson and Shannon indices, indicating that the bacterial population does not maintain uniformity/richness and species abundance dominance. These findings reinforce the premise of previous studies that state the origin of the cheese influences the indices of richness, uniformity, and abundance of bacterial species [78]. Interestingly, the PT570 sample presented the highest values in all three indices analyzed, indicating it is a cheese with high diversity, uniformity/richness, and dominance of species abundance among all those analyzed. This cheese is produced with pasteurized milk, has a maturation period of 45 days (the youngest among  
Figure 4: Alpha diversity indices of samples of sheep’s cheese sold in the southern region of Brazil. Chao-1 diversity index: qualitative index based on the richness of species present in the sample; Shannon index: considers the uniformity in the abundance of species; Simpson index: based on the dominance of species abundance. average moisture content of 27%. [PERSON] et al. [80], in their study on Monascus cheese, also identified that there was higher alpha diversity in cheese samples with 10 days of maturation compared to those with 90 days, according to the Simpson index.