Techniques for Studying the Microbiome

The human body harbors an extensive microbiome crucial for maintaining health and well-being by supporting a robust immune system. Each bodily site provides a specific habitat capable of hosting trillions of microbial cells, with significant variations in species and strains across different body regions. Not only does the microbiome instruct the immune system in fighting infections but it also functions as a thermostat, contributing to the overall body homeostasis. Any disturbance in this delicate balance may lead to the loss of microbiotic tolerance, consequently triggering immune and autoimmune diseases. Numerous methodologies are available for microbiome study, encompassing cell culturing, sequencing techniques (such as 16S DNA, RNA, and gene marker analysis), metagenomic sequencing, metatranscriptomics, metaproteomics (utilizing nuclear magnetic resonance spectroscopy, mass spectrometry, and metabolomics), laser capture microdissection (LCM), fluorescence in situ hybridization (FISH), and computational biology tools. This chapter comprehensively discusses these technologies, alongside various techniques for microbiome collection from diverse body regions, including the gut, lungs, and other organs. Additionally, it covers methodologies employing animal models and ex vivo and in vivo sampling procedures, explores diverse techniques employed in studying the microbiome’s role in major diseases, and outlines how these principles can guide microbiome research in the forthcoming decade.