Microbiomes—the collective assemblages of microorganisms and their genomes—form highly dynamic ecosystems that have broad impacts on host health and environmental balance. The concept of the microbiome has evolved from early microscopic observations to the modern system-level understanding made possible through culture-independent and high-throughput sequencing methods. Techniques such as 16S rRNA amplicon sequencing, shotgun metagenomics, metatranscriptomics, metabolomics, and metaproteomics have transformed our ability to characterize microbial communities, revealing their diversity, dynamics, and functional roles. The composition of microbiomes is affected by various factors that includes age, diet, host genetics, environmental conditions, and anthropogenic pressures such as antibiotics and pollutants. Dysbiosis, a disturbance in this balance, is linked to wide-ranging consequences across systems—from plant and animal disease, through compromised aquaculture production, to human disorders like colorectal cancer, obesity, allergies, inflammatory bowel disease, and neurodegeneration. This chapter provides an overview of microbiome discovery and evolution, details the major techniques used to study microbial communities, examines the factors that shape their structure, and highlights the role of dysbiosis in human health and disease.