Microbiomes and Health

microbiome

combined genetic material of the microorganisms in a particular environment that can influence health and disease

Microbiota

ecological community of microorganisms: commensal, symbiotic, pathogenic

gut commensals

abundance of microbiological matter in the intestine

• 2 kg of body weight

• 60% dry weight of faeces

Microbiota of the GI Tract

4 Dominant Phyla

1. Bacteroidetes

2. Firmicutes

3. Proteobacteria

4. Actinobacteria

Gut Microbiota

Fundamental for digestion and gut immunity

• breakdown of complex carbohydrates

• production of short chain fatty acids

• synthesis of vitamins

*culture-based approach; metagenomics, 16s rRNA sequencing, metatranscriptomics

Gut Microbiota Development: Birth

• Birth (gut microbiota vaginal infections)

  • Vaginal: exposed to vaginal and intestinal microbes - seed baby’s gut

    • e.g. lactobacillus, bifidobacteria

  • Caesarean: skin and hospital microbes → delayed/altered development

    • e.g. staphylococcus, proponiobacterium

Gut Microbiota Development: Infant

Milk consumption: more stable and beneficial to formula - lower gut inflammation; immune tolerance

• acidic environment

• e.g. bidobacterium, lactobacillus

Solid Food Introduction: increase in microbial diversity and richness; increase SCFA

• e.g. bactericides, clostridia’s

Gut Microbiota Development: Toddler

Full adult diet: → increased complexity

• adult-like microbiota

Germ-free Mice Studies

*Absence of microbiota contributes to under-developed immunity

Defects in GALT (gut-associated lymphoid tissue)

• decrease in lymphoid follicles (peers patches)

Gut Barrier Immunity:

• Decrease mucus/AMP secretion

• Decrease intestinal epithelial lymphocytes

• decrease T cells and B cells in spleen

• decrease expression of TLRs on intestinal epithelium

Intestinal Epithelium

Single-cell (epithelial cells) layer lining inner surface of intestines - digestion, absorption, immune

• largest mucosal surface (400m2)

Barrier Defect = IBD, allergy, infection, inflammation, leaky gut, food intolerance

Intestinal Epithelium: Cell Types

• Enterocytes: nutrient-absorptive cells - form epithelium

• Paneth cells: secrete AMPs

• Endocrine cells: hormones that regulate digestion and appetite

• Goblet cells: mucin-secreting - protects lining

Intestinal Epithelium: Mucus Layer

Protective barrier produced by goblet cells

• contains:

  • glycoproteins “mucins”

  • digestive enzymes

  • antimicrobial proteins & antibodies

• separates epethelial from gut lumen

• limits pathogen invasion

Antimicrobial Peptides (AMPs)

small proteins of innate immune system found along intestinal epithelium

• produced by paneth cells - response to infection

• broad: anti fungal, antibacterial, anti parasitic, antiviral

Metagenomics

genetic material recovered from samples → analysis of microbial communities

1. 16S rRNA Sequencing: targets specific gene in bacteria to identify

2. Shotgun Metagenomics: sequences all DNA in sample

Microbiota: Age

Microbiota diversity declines with age: lower bifidobacterium, higher proteobacteria

• abundance of bifidobacteria = indicator of health

• → increased inflammation, weakened immunity, nutrient malabsorption

Hygiene Hypothesis

Lack of early childhood exposure to infectious agents, increases susceptibility to allergic diseases by suppressing natural development of immune system

Allergies

Imbalances in the gut microbiome (dysbiosis) can increase risk of developing allergies

• C-section, no breastfeeding, early antibiotic use

• Higher levels of ‘bad bacteria’: S. aureus, C. difficile

• Lower levels of ‘good bacteria’: bactericides, bifidobacteria

*Microbiota trains immune system to respond to ‘foreign’ antigens

Antibiotic Treatment

1. Salmonella Typhimurium: antibiotic → proliferate and induce inflammation

2. Pathogenic E.coli: accumulates after antibiotic treatment in mice

3. C. difficile: present at low numbers in health - treatment = increased and severe inflammation

Inflammatory Bowel Disease (IBD)

Disorders = chronic inflammation of the digestive tract

• e.g. Crohn's disease, ulcerative colitis

• linked:

  • dysbiosis

  • lack of breastfeeding

  • consumption of large amounts of fats

  • use of antibiotics

Enhancement of Gut Health

• probiotics: manipulate commensal bacteria

• introduces colonizing immunobiotic strains - AMPs prod

Probiotics

Live microorganisms that provide health benefits when consumed

• non-pathogenic & non-toxic

• resists gastric acid and bile

• attaches to epithelial cells

• adapts to native intestinal microbiota

• temp colonization of IT

Faecal Microbiota Transplantation (FMT)

intestinal microbiota transferred from healthy donor to patient → introduce stable microbial community in gut

• via stool banks

• human body weight outcomes = modest and unpredictable

Dysbiosis introduced via antibiotics

• normal microbiota disrupted → C.diffcile = advantage

Lung Environmental Conditions

• warm

• moist

• O2 rich

• few cm from oral cavity

Chronic Obstructive Pulmonary Disease (COPD)

common lung disease causing restricted airflow and breathing problems

• emphysema or chronic bronchitis

Unidirectional Travel

migration of microbes = unidirectional and serially interrupted by widely varying physical and chemical barriers

Bidirectional Travel

In the presence of vomiting or esophageal reflux

Lung Microbiome: pH

Microbe → cecum = endure acidic pH of stomach 2.0 and alkaline pH of duodenum 8.0

• compete for resources with densely populated resident microbiome

Lung Microbiome: Temperature

GI tract = uniform temp 37C through entire 9 meters of length

Mucosa of Res tract: gradient from ambient temperature at point of inhalation to core body temp in alveoli

Lung Microbiome: Mucosa Lining

Airway Bacteria = low

• lungs lined with lipid-rich surfactant that has bacteriostatic properties

Lung mucosa lined with mucus containing glycoproteins

• uses surfactant to limit bacteria

• **Designed to limit microbial growth

Lung Microbiome: Host-bacterial Interactions

Lungs exhibit a lot of extraluminal interactions between bacteria and host leukocytes

• result in divergent microbial communities

Respiratory Tract

Upper respiratory tract = primary source of lung microbiome

• LM mainly consists of transient microorganisms

• Health composition: microbial immigration (inhalation of bacteria) vs. elimination (cough, innate adaptive responses)

Microogranisms in Lungs

Sources:

• inhalation

• reflux and aspiration

• bloodstream

• nasopharyngeal aspiration

Oral Microbiome

microorganisms residing in the oral cavity that are the primary source of bacterial microbiota in the lungs

Diseased Lung Microbiome

• Higher microbial density

• Enriched with pathogens (Staphylococcus, Haemophilus)

• inflammation, impaired clearance, mucus

• e.g. Cystic Fibrosis, COPD, Asthma

Asthmatic Lung

characterized by inflammation and hyperreactivity = airway obstruction and difficulty in breathing

• increased proteobacteria

• increased streptococcus

COPD Lung

chronic inflammation and airflow limitation = progressive respiratory symptoms & increased risk of lung infections

• overgrowth of proteobacteria

• increased streptococcus and staphylococcus

COPD Exacerbations

The worsening of symptoms in a disease → dysbiosis

• increased mortadella

• microbial diversity drops

Stable → Exacerbation → Post-therapy → recovery

Treatment

• steroids, antibiotics

Cystic Fibrosis

disorder that leads to thick mucus production, recurrent respiratory infections, and progressive lung damage

• increased Proteobacteria and Actinobacteria

Lung, Oropharnyx, and Gut Microbiomes

Microbiomes are interconnected (oropharynx → lung = swallowing)

• Healthy microbiome: relegate immune system response via cytokines

• Dysbiosis: induce lung disease and damage

Gut-Lung Axis

Gut microbiome significantly influences lung health through immune modulation and systemic inflammation

• dysbiosis: gut → respiratory conditions = interconnected

Host-Microbiota Interactions: Respiratory Tract

Microbes enter lungs via micro-aspiration or dispersion

• host factors: birth mode, feeding, antibiotics, genetics shape lung

• Airway lining (epithelium) and immune cells (dendritic, T, B) interact

  • maintain tolerance and immune

  • produce AMPs and secretory lgA for defense

  • regulate inflammation

Airway Smapling Techniques

• Sputum (spontaneous or induced)

• Bronchoalveolar lavage

• Sterile tissue sample

• Protected endobronchial brush