Week 1: Human Microbiome
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Microbe 3 bullet points
• Small, metabolically, genetically and structurally diverse organisms • Some can live anywhere • Essential for human health
Microbes influence___ 3 bullet points
• genetic diversity • normal physiology • health state
What is a microbiome? 3 bullet points definition, types(4), where on spectrum
• the microbial communities of an environment • Bacteria ・viruses・fungi・archaea • ← beneficial・commensal・pathogenic →
Where do these microbes live? Give examples of specific niches.
• in biomes, specific conditions(temp., moisture) and characteristic organisms • each biome has different microbes Ex: skin, mouth, armpit, stomach, intestines and vagina
Describe skin biome
desert, dry and high UV
Describe mouth biome
lake, wet, nutrient rich
Describe armpit biome
rain forest, moist, warm, humid
Describe stomach biome
acid lake
Describe intestine, vagina biomes
swamps
Which microbes live where? What determines where microbes live on/in humans?
ecological principles
Name ecological principles(4)
• selection/site specificity • succession • niche filling/founders effect • disturbance events(cyclic[diurnal, seasonal], catastrophic)
Selection/site specificity
• diff. microbes have diff. needs - diff. sites host diff microbes due to variation in: moisture, pH, nutrients, presence of other microbes
Selection/site specificity: How to characterize microbial environments? w/ examples
• abiotic: non-living factor of an ecosystem ex: temp., pH, moisture, nutrients, light, oxygen • biotic: living factor of an ecosystem ex: host immunology, microbial interaction
selection/site specificity: microbes change their environments due to___
• Due to metabolic “waste” product ex: pH・oxygen・sugars・etc • Due to ability to kill other microbes ex: Secrete toxins, antibiotics, antifungals, lyse, etc.
Niche filling/Founders effect: Unique microbiome for each person acquired___
• Acquired each generation: birth, foods, environment - “microbial signature”
Niche filling/Founders effect: in utero___
• babies have limited/no bacteria within the amniotic sac
Niche filling/Founders effect: Baby has limited___
• habitat space • nutrients this is where niche filling and founder effect come in
Founders effect
• Those species that get there first, fill specific spaces • Harder to remove once established • Redecorate- change the habitat
Niche filling: Baby as “bacterial magnet”:
• Open habitats for microbes to colonize • Repressed immune system • Surrounded by microbes(moms, other, environment)
Niche filling during:
• during labor when water breaks, vaginal microbes • during delivery; vaginally(vaginal and gut microbes) or scheduled C-section(skin microbes) • w/ first foods(skin, breast milk, formula) • skin to skin interactions(kangaroo, kissing, nursing)
Succession
• the process by which the structure of a biological community evolves over time
Baby primary succession
• niche colonized for the first time - birth-2/3 years
secondary succession
• recolonization of niche after major disturbance
Succession occurring through___
• Immune system development • Foods • Environmental influences(medicine, pathogens, daily exposures-soaps,etc.)