Summary of Understanding the Human Microbiome

## Introduction The human microbiome at different body sites shows substantial variation in the species present between individuals and populations, while key metabolic activities remain conserved at a given healthy site. This material focuses on how composition and diversity of the human microbiome vary across populations, life stages, body sites, and environments — and on practical implications for health, environment, and research. > Definition: Microbiome — the community of microorganisms (bacteria, archaea, fungi, viruses) and their collective genetic material living in a defined environment, such as the human gut or household dust. ## 1. Composition versus Metabolic Activity ### What differs and what stays the same - Species composition can vary widely between individuals and across populations. Factors such as diet, lifestyle, geography, and environment shape which species are present. - Despite species-level differences, **core metabolic pathways** (e.g., fermentation, short-chain fatty acid production) at a given body site in healthy people often remain similar. This means different microbial species can perform equivalent functions (functional redundancy). > Definition: Functional redundancy — when multiple species perform similar metabolic roles in a community, so loss or change of some species does not necessarily alter overall function. ### Practical example - Two healthy individuals from different countries might not share many bacterial species in their gut, but both can still produce comparable amounts of short-chain fatty acids from dietary fibers because different microbes carry out similar fermentation pathways. ## 2. Population-level differences in the gut microbiome ### Patterns across human populations - Microbiomes from industrialized populations (e.g., urban USA) are distinct from non-industrialized, rural, or hunter-gatherer populations (e.g., Malawians, Guahibo, Yanomami). - As you compare broader taxonomic or evolutionary scales (e.g., humans vs. other primates vs. other vertebrates), population-level differences shrink and deeper host-related signals emerge. ### Table — Scale of microbiome differences | Comparison level | Observed pattern | Key driver(s) | |---|---:|---| | Within healthy human population | High species variability; conserved functions | Diet, age, environment | | Between human populations | Marked compositional differences (industrialized vs non-industrialized) | Lifestyle, diet, antibiotic exposure | | Humans vs non-human primates | Differences reduce; shared lineage effects visible | Host phylogeny, captivity | | Across vertebrates | Differences driven by deep evolutionary splits and lifestyle | Host physiology, long-term coevolution | ## 3. Age-related development of the gut microbiome ### Stages of microbiome maturation 1. Rapid change from birth to 3 years: species diversity and community composition develop quickly. 2. Stabilization after ~3 years: the composition becomes more persistent through adulthood. 3. Lifespan trends: species richness often continues to increase in childhood up to early adulthood and may vary with aging and lifestyle. > Definition: Species richness — the number of distinct microbial species detected in a community. ### Key observations (practical) - The largest inter-population differences are evident in children up to 3 years old. - Early-life exposures (mode of birth, diet, antibiotic use, environment) strongly influence long-term microbiome composition. ## 4. Non-bacterial members: Fungi and viruses ### The mycobiome (fungal community) - Fungi form a small but important part of human-associated communities. Sequencing approaches (e.g., 18S rRNA or whole-genome shotgun) are used to study them. - Candida species are commonly detected in human mycobiomes. ### Human virome and bacteriophages - Individuals typically carry a small number of distinct viral genomes at a given time (averaging a few viral genomes detectable per person).