Eukaryotic microbes, particularly Saccharomyces cerevisiae, are increasingly being studied for their beneficial properties. High throughput sequencing has made it possible to sequence and annotate the genome in many Saccharomyces species. The analysis of complex microbial species present in the sample mix can be performed using metagenomic sequencing. An important approach in determining the genetic composition of microbial genomes, which is difficult to define in total, has been highlighted by metagenomics. Rapid advances in sequencing technologies, like sequencing of genomes and metagenomes, as well as developments in the field of bioinformatics that help to analyze sequence data, have enabled a wide range of questions to be investigated. The study aims to perform a metagenomic analysis to check the reliability of mapping-based methods in the context of metagenomic sequencing of rat fecal samples, in particular when native bacteria are mixed with two species of yeasts, namely the yeast PY0001 and the DNA of Candida albicans. For the processing of vast amounts of sequencing data, metagenomic research relies heavily on software tools. These tools allow for the analysis of DNA from complex microbes and provide insight which is focused on monitoring yeast species in the presences of other microbes in the given samples. We have focused on the bioinformatics aspects of analyzing metagenomic data sets. The pipeline was successful in identifying strains and shown effectiveness, despite the challenges of a combination of species. The results of the phylogenomic networks carried out in this study have shown that inclusion of yeast alone and yeast plus fecal sample within analyses did not create major problems with the dataset when we applied the pipeline. So, in conclusion further analysis can be continue to operate the same pipeline even if you have close related yeasts or have bacterial DNA nearby. The relevance of the used pipeline for advancing metagenomic research efforts is reinforced by its resilience and adaptability.