This document provides detailed lecture notes on host-microbe interactions, covering the human microbiota and microbiome, their role in digestion, immunity, metabolism, and disease. Topics include the Human Microbiome Project, methods of microbiota identification (16S rRNA sequencing, metagenomics), early-life microbiome development, mucosal immunity, diet–microbiome interactions, inflammatory bowel disease, autoimmunity, the gut-brain axis, probiotics, and drug metabolism. The material integr...