Summary of The Human Microbiome: Health and Disease

## Introduction The human microbiome is the community of microorganisms that live on and inside the human body. These microbes — bacteria, fungi, viruses, archaea and other microorganisms — coexist with human cells and contribute to many body functions. Studying the microbiome helps us understand how microbes influence nutrition, immunity, development and disease resistance. > Definition: The human microbiome is the collection of microorganisms and their genes that reside on the surface and within the human body, including skin, oral cavity, conjunctiva, gastrointestinal tract, and urogenital tract. ## Main Features of the Human Microbiome ### Composition - Includes **bacteria**, **fungi (mycobiome)**, **viruses (virome)**, **archaea**, and rarely observed protists. - Different body sites host distinct communities (skin vs. mouth vs. gut vs. urogenital tract). ### Gene Content and Function - The microbiome carries many microbial genes; sometimes called a “second human genome.” - Although species composition varies between people, core **metabolic pathways** at a given site are often conserved across healthy individuals. > Definition: Mycobiome — the fungal component of the human microbiome, often studied by sequencing 18S rRNA or whole-genome sequencing. ### Symbiosis and the Superorganism Concept - The human body plus its microbes can be viewed as a **superorganism**: human (eukaryotic) genes and microbial (prokaryotic) genes together influence physiology and health. ## Biological Roles and Examples ### Nutrient processing and metabolism - Microbes produce enzymes that break down complex dietary molecules (example: enzymes that help process plant polysaccharides like xyloglucans). - They contribute to synthesis of vitamins and certain amino acids de novo. - Microbial activity extracts additional energy from food (e.g., fermentation producing short-chain fatty acids such as butyrate). Did you know that xyloglucan is a major structural polysaccharide in plant cell walls, composed of a glucan backbone with xylose, galactose and fucose side residues? ### Immune system development and pathogen defense - Microbiome helps develop and mature the immune system and acts as a natural barrier against pathogens by: - Competing for nutrients and niche space - Producing antimicrobial compounds - Stimulating expression of mucins, secretory IgA and antimicrobial peptides ### Influence on prenatal development - Maternal microbiome can influence fetal nourishment, growth and the timing/length of pregnancy. Fun fact: Some body sites show more inter-individual variation in viral communities than in bacterial communities, which can make viral patterns useful in forensic applications. ## Human Microbiome Variation ### Across the lifespan - Microbiome develops rapidly in early life and typically stabilizes after about three years of age. - Species richness and diversity generally increase from birth through childhood and reach a more stable adult state. ### Across populations and lifestyles - Microbiome composition differs between populations, especially between industrialized and non-industrialized societies. - Lifestyle, diet, environment and geography all influence community composition. Table: Variation factors and effects | Factor | Typical effect on microbiome | |---|---| | Age | Increasing diversity during first 3 years, then stabilization | | Diet | Alters nutrient-usage pathways and species abundances | | Environment | Exposure to diverse microbes increases community richness | | Antibiotics | Can reduce diversity and disrupt community balance | ## Examples and Real-World Applications - Athlete microbiome example: Certain archaea such as *Methanobrevibacter smithii* remove H$_2$ via methanogenesis, which can improve fermentation efficiency and energy extraction in the gut; enriched metabolic interactions have been associated with higher athletic performance in some studies. - Antibiotic use example: Frequent or early-l