4/28/2025 Notes | BIOL 412

Topic: Human Microbiome

• review “things to focus on” slide from lecture (Ch. 23)

• read Ch. 24

OUTCOME

• different habitats w/in the human body

• differences in microbial composition

• distinguish between patterns demonstrating a core microbiome and those demonstrating variability

• “healthy” vs “unhealthy” microbiome in literature

SUMMARY

• major habitats

• case study: GI tract

• variability

SYMBIOSIS BETWEEN HUMAN AND MICROBES

• microbiome: all microorganisms living in a particular environment; can refer to organisms themselves or to their combined genetic material

• symbiosis: prolonged, intimate relationship between two organisms

• Human Microbiome (HM): all microorganisms living in or on humans

  • newly-emerging research due to health applications (last 20 years)

HUMAN MICROBIOME RESEARCH

• started with funding by governments

• we can’t study human microbiome without studying multiple humans and comparing across populations

• 3-10 microbial cells : 1 human cell

• think about abundance, diversity, and function

• advances in the field relies on molecular sequencing and bioinformatics

  • mostly studied using amplicon sequencing in Illumina MiSeq platforms focusing on 16s rRNA gene and shotgun metagenomic approaches

    • amplicon sequencing: PCR on one section of RNA at a time

• main findings

  • four main habitats

    • GI tract

    • skin

      • includes nose, ears, and exterior

    • oral

    • urogenital (vagina)

  • core microbiome

  • variability

  • health and disease

FOUR HABITATS

• composition

  • all have differences in composition and diversity

  • saliva is very diverse, with others less so

• skin

  • extreme environment

    • dry, waxy, salty

    • exposed to UV rays (mutagen)

    • interacts with secretions

  • dominated by staphylococcus and propionibacterium

  • estimated abundance of bacteria: 21%

• saliva

  • largest diversity

  • dominated by streptococcus

  • lysozymes constrain growth of Gram positives

  • food pulses

  • interacts with tooth biofilms

  • constant colonists

  • estimated abundance of bacteria: 26%

• urogenital tract

  • dominated by lactobacillus

    • production of acid drops pH

  • little immigration due to acid

  • high competition

  • estimated abundance of bacteria: 9%

• gastrointestinal tract

  • most studied

  • dominated by bacteroidetes and firmicutes

  • estimated abundance of bacteria: 29%

GASTROINTESTINAL TRACT

• dramatic change in microbial composition

  • diet

  • region & ethnicity

• ~10^14 cells/gram

• produces ~100mL of gas a day

• nutrients are shared between microbes and human

  • Vitamin K

  • Vitamin B12

  • steroids

• takes ~24hrs to pass from mouth to anus

• 2 bacterial doublings per day (on average)

• gradient of pH

  • very acidic (2-4) —> neutral (7)

• gradient of oxygen levels

  • high levels (aerobic) —> low levels (anareobic)

    • community metabolism changes

• major regions

  • stomach

    • proteobacteria, bacteroidetes, actinobacteria, fusobacteria

    • Helicobacter pylori

      • biofilm-forming

      • 50% of population, is decreasing

      • 4 flagella

        • can’t create ulcers w/out flagella

      • Gram negative

    • abundance: ~10^4 cells/mL of content

    • acidic (pH=2)

    • digestion (break-down of food structure)

      • physical activity

      • chemical activity

  • small intestine

    • depends on diet

      • Bacteroides (meat)

      • coliforms and Lactobacillus (vegetarian)

    • abundance increases throughout tract

    • anoxic at end

  • large intestine

    • specialist anaerobic

    • Bacteroides OR Prevotella (not both, one or the other)

    • E. coli

    • 10^11 cells/mL

    • fermentation and methanogenesis

      • methanogenic archaea living in large intestine

      • Bacteroidetes + Gram-positives = 90%

• microhabitats

  • ex. lumen vs mucosal layer

• relies on fecal research and mouse models

  • identified 3500-35000 of species

  • 200-300 species per individual human

  • 10^13 cells / day are expelled

  • majority of info relies on fecal samples

GUT HEALTH

• gut microbiota regulates host energy balance via singaling metabolites

  • can affect weight and obesity incidence

• some causation relating to obesity and gut microbiota

• Dysbiosis

• Inflammatory Bowel Disease asociated with genetic abundance