The Human Microbiota

Microorganisms of the human body

I. "We are not alone"

• The human body consists of ~ 10 - 100 trillion cells
• There are ~ 1 quadrillion bacteria inhabiting the human body
• Can we live without our microbiota?
  • Gnotobiotic animals: animals raised in a sterile environment
• Is the microbiota harmful or beneficial?
  • Microbiota as an organ: The human Microbiome project
    • helps regulate circadian rhythms!
  • Microbiota as a reservoir of antibiotic resistance
  • Probiotics: enhancing the microbiota
    • Lactobacillus prevents surgical wound infections
    • Lactococcus prevention of cholera
    • Christensella minuta and weight loss
  • Replacing the microbiota: fecal transplantation

II. The Nature of Symbiosis and other microbial interactions

    A. Mutualism 

1. Mammals: enteric bacteria produce Vitamin K

    B. Commensalism

1. Humans + resident microorganisms

    C.    Parasitism

1. Pathogens + host = disease

    D. Amensalism

1. Acid production by Lactobacillus
2. Bacteriocins and lantibiotics produced by bacteria

    E. Dysbiosis

Disturbance of normal microbiota + opportunistic pathogen = Disease

1. C. difficile / antibiotic-induced colitis

2. Akkermansia muciniphila (mucin-degrading microbes) / ulcerative colitis

3. Absence of gluten-digesting microbes / celiac disease

III. Normal Microbiota

A. Host factors that determine resident microbiota vs. transient microbiota

1. Physical Defense - barriers

   • Skin (keratinized stratified epithelium)

   • Mucous membranes (mucus)

2. Mechanical Defense - movements

   • Mucociliary action

   • Peristalsis

   • Chewing (mastication)

   • GI motility (grinding, peristalsis)

   • Fluid movement (urine, GI tract, mouth)

   • Shedding of epithelium

3. Biochemical Defense - secretions 

   • Lysozyme (tears, skin, saliva)

   • Organic acids (skin, vagina)

   • Hydrochloric acid (stomach)

   • Bile (intestine)

   • IgA (intestine, breast milk, saliva)

   • Mucus

   • Defensins/Antimicrobial peptides (lungs, urine)

   • Digestive enzymes (stomach, intestines)

   • Iron-binding proteins: lactoferrin

   • Bacteriocins - normal microbiota

B. External influences that shape the human microbiota

1. Personal hygiene: soaps, disinfectants

2. Environmental toxins: chlorinated water; smoking

3. Diet: sugars, fats, fiber

4. Antimicrobial drugs

   • Reduction of normal microbiota

   • Antibiotic-associated colitis (Clostridium difficile)

C. Changes in host environment affect normal microbiota

1. Teething: Fusobacterium, Streptococcus, Bacteroides

2. Breast feeding/weaning: Bifidobacterium --> enterobacteria

3. Puberty: Lactobacillus

4. Immune system status: Opportunistic infections 

   • HIV/AIDS

   • Genetic immune disorders

   • Malnutrition

   • Alcoholism

   • Cancer/Leukemia

   • Aging

5. Hospitalization

   • Oropharyngeal colonization by Gram-negatives

   • Sepsis via catheters, incisions

D. Bacterial factors help determine the normal human microbiota

1. Adhesion

   • Cell wall components

   • Pili/fimbriae

   • Capsules

   • Adhesins

2. Ability to use available nutrients

   • iron (transferrin)

   • fiber

   • Mucins/host proteins

3. Resistance to body defenses

E. The Normal Microbiota

1.    Skin    

• Staphylococcus, Bacillus, Candida, Propionibacterium acnes, Corynebacterium, Streptococcus,

2.     Nose    

• S. aureus, S. epidermis, Streptococcus pneumoniae, Haemophilus influenzae, diptheroids, anaerobes

3.    Oropharynx    

• S. aureus, S. epidermis, a-hemolytic streptococci, diphtheroids, Candida, Branhamella catarrhalis, anaerobes

4.    Mouth    

• Staphylococcus, Streptococcus spp., Fusobacterium, Veillonella, Actinomyces, Peptostreptococcus, Neisseria

5.     Conjunctiva    

• CoN Staphylococcus, Streptococcus pneumoniae, Haemophilus, Neisseria

6.     Stomach    

• Lactobacillus, Streptococcus – very low numbers; Helicobacter

7.    Small Intestine    

• Anaerobes (Peptostreptococcus, Prevotella, Bacteroides); Enterococcus

8.    Large Intestine    

• Bacteroides, Clostridium, Bifidobacterium, E. coli & other enterobacteria, Candida, Entamoeba
• Anaerobes outnumber facultative anaerobes 300:1

9.        Urinary tract    

• CoN Staphylococcus, Streptococcus, Lactobacillus

10.      Genital tract (female)    

• Lactobacillus, Gram-positives, Candida, Enterobacteria

11. External ear

• CoN Staphylococcus, Streptococcus, diphtheroids, Pseudomonas

Questions

1. What is the normal microbiota of the respiratory tract? Kidney? Blood?
2. What physical/chemical factors determine the resident microbiota at each site?

On-line resources/further reading

1. http://www.textbookofbacteriology.net/normalflora.html
2. https://www.researchgate.net/publication/51753203_Bacteriocin_Production_a_Probiotic_Trait

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