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