--- module: 095-01 language: en chapter: 95 title: "Microbiome, Microbial Ecology, Evolution, and Host–Pathogen Co-adaptation" module_title: "Colonisation, anatomical niches, community assembly, and host–microbiome ecology" source_sha256: dec0ea0b0963b65f4b765498b18ecb67167115bb5110ecce5207c7f882ee4c1b --- # Colonisation, niches, and host ecology ## Definitions and context dependence ### Microbiome: communities, genes, products, interactions ### Microbiota refers to the organisms themselves ### Most residents harmless or beneficial in usual niche ### Same organism causes disease after context change #### Barrier breach #### Immune change #### Movement to a sterile compartment ## Site-specific burden and composition ### Skin: cool, dry, acidic, oxygenated, intermittent exposure ### Mouth: dense biofilms on teeth and mucosa ### Stomach: low biomass under acidity ### Colon: huge anaerobic community, slow transit, substrates ### Lower airway biomass low, shaped by aspiration and clearance ## Niche conditions and habitat construction ### Oxygen, pH, temperature, salt, water, nutrients, bile ### Microbes consume oxygen and shift pH #### Community constructs part of its own habitat ## Early colonisation, succession, and low-biomass caveats ### Begins around birth, not a single event ### Delivery mode, gestational age, feeding, antibiotics ### Maternal microbes contribute but are not the sole source ### Unstable early, site-specific over years ### Placental microbiome claims remain controversial ### Reagent and environmental contamination dominate low biomass ### Microbial DNA does not prove living colonisation ### Need controls, culture, microscopy, localisation, plausibility ## Community assembly and diversity metrics ### Dispersal introduces organisms ### Selection favours traits fitting the niche ### Drift randomly changes low-abundance populations ### Mutation and gene transfer generate variation ### Priority effects: early colonisers alter later establishment ### Different taxa can perform overlapping functions ### Alpha diversity: richness and evenness within a sample ### Beta diversity: difference between samples ### Higher diversity not universally healthier #### Low-diversity Lactobacillus vaginal states often healthy ### Metric choice and sequencing depth alter conclusions ## Spatial organisation and colonisation resistance ### Mucus separates luminal community from epithelium #### Inner colonic mucus resists penetration ### Secretory IgA excludes, retains, or shapes without inflammation ### Peptides, epithelial oxygen use, immune cells keep structure #### Loss of separation inflames without a new pathogen ### Colonisation resistance limits invaders #### Nutrient competition and attachment-site occupancy #### Bacteriocins, acidic metabolites, bile-acid transformation #### Antibiotics let C. difficile or resistant organisms expand ## Relationships, pathobionts, and interpretation ### Commensalism, mutualism, parasitism shift with context ### S. aureus colonises nose yet causes invasive disease ### Pathogenicity is an interaction, not a fixed property ### Pathobiont harms under altered host or community ### Opportunistic infection needs a defence defect ### Positive nonsterile culture may be carriage ## Site ecologies: oral, skin, vaginal ### Plaque: pellicle, early adhesion, coaggregation #### Frequent sugar selects acid-tolerant, demineralising communities ### Periodontitis: dysbiotic biofilm plus tissue destruction ### Skin differs by oily, moist, dry sites and follicles #### Atopic dermatitis: barrier, type-two, staphylococcal expansion ### Vaginal ecology: oestrogen, glycogen, lactate, antibiotics #### Bacterial vaginosis is polymicrobial, metabolite-altered #### Avoid labelling normal diversity as disease ## Microbial functions for the host ### Fermentation to short-chain fatty acids, gases, biomass ### Transformation of bile acids, amino acids, polyphenols, drugs ### Function depends on substrate and strain ### Immune development: germ-free animals altered, extrapolate cautiously ### Gut-brain signalling via vagal, immune, endocrine, tryptophan #### Human causal evidence limited and heterogeneous ### Virome: phages kill bacteria, move genes, alter competition ## Biofilms, exposures, and resilience ### Biofilm: surface community in self-produced matrix #### Tolerance differs from inherited resistance ### Diet changes activity fast, composition slowly #### Fibre supports saccharolytic fermentation ### Non-antibiotic drugs also reshape microbiota #### Microbes activate or inactivate drugs ### Ageing and illness change diet, transit, immunity, drugs #### Signature may be cause, consequence, or treatment effect ### Resilience is functional return; resistance is limited change #### Recovery may be functional without taxonomic return #### Repeated insults push alternative stable states #### One post-treatment sample cannot prove recovery ### Health is a resilient, location-compatible configuration