This thesis addresses modern approaches to studying the human microbiome, with an emphasis on comparing cultivation-based, molecular, and analytical methods and their integration into multi-omics analyses. The aim of the work is to present the advantages, limitations, and applicability of individual methods for determining the taxonomic composition, functional potential, and actual activity of microbial communities. Classical cultivation techniques are reviewed alongside molecular approaches such as PCR, qPCR, Sanger sequencing, and next-generation sequencing, including 16S rRNA amplicon sequencing and shotgun metagenomics, as well as advanced long-read sequencing technologies. Particular attention is given to indirect analytical methods, especially metabolomics and metaproteomics, which provide insight into metabolic pathways and expressed proteins of the microbiome. The thesis highlights that individual methods alone do not provide a comprehensive understanding of the microbiome due to limitations such as relative quantification, methodological biases, and the inability to distinguish between active and inactive microorganisms. The main conclusion is that integration of metagenomic, transcriptomic, proteomic, and metabolomic data enables more accurate interpretation of microbial structure, function, and host interactions, representing the most effective approach for investigating the role of the microbiome in health and disease.
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