Within the intricate tapestry of microbial communities, a single sample can encapsulate a wealth of genetic information derived from diverse sources - a spectrum spanning from organic matter like food to organic remnants such as faeces, or even sediment extracted from ecosystems. This genetic mosaic becomes a treasure trove containing fragments of DNA originating from a multitude of organisms including yeast, fungus, and bacteria, and even plants and animals. In this thesis, we embark on an exploration that promises to unravel intricate microbial tapestries, decode enigmatic assemblages, and confront the challenges woven into the fabric of metagenomic analysis. Through innovative approaches anchored in the mitochondrial realm, we strive to advance our understanding of microbial communities, their composition, and the intricacies of their coexistence.