Unit 11- Microbiome

Question 1

What essential physiological functions does the human microbiome perform?

Answer 1

• Vitamin synthesis (e.g., vitamin K, B vitamins)
• Digestion of complex compounds
• Immune training
• Pathogen protection

The microbiome is often described as a newly discovered organ due to these functions.

Question 2

Differentiate between the innate genome and the adaptive genome.

Answer 2

• Innate genome: Fixed human DNA (~22,000 protein-coding genes)
• Adaptive genome: Microbiome’s vast gene pool (>8 million genes) capable of rapid change

The adaptive genome provides metabolic flexibility that the human genome alone cannot supply.

Question 3

What is the approximate microbial composition by body site?

Answer 3

• Gut: 29%
• Oral cavity: 26%
• Skin: 21%
• Respiratory tract: 14%
• Urogenital tract: 9%

Each body site has distinct microbial communities and functions.

Question 4

List the principles determining site-specific colonization.

Answer 4

• Oxygen availability
• pH
• Nutrient availability
• Moisture
• Immune surveillance
• Physical clearance

These factors create distinct ecological niches for microbial communities.

Question 5

What are the three complementary technologies used in the Human Microbiome Project (HMP)?

Answer 5

• 16S rRNA gene sequencing
• Shotgun metagenomics
• Metatranscriptomics

Each method has strengths and limitations, contributing to understanding the microbiome.

Question 6

How does mode of delivery influence early-life microbiome development?

Answer 6

• Vaginal birth: Exposes infants to maternal vaginal and gut microbes
• Cesarean delivery: Reduces exposure, leading to different microbial colonization

This affects gut microbiome maturation and immune system training.

Question 7

What are the clinical consequences of disrupted colonization during early life?

Answer 7

• Immune dysregulation
• Metabolic consequences
• Increased infection susceptibility
• Gastrointestinal disorders

Disruptions can lead to long-term health issues.

Question 8

Describe the timeline of microbiome development from birth to age 3.

Answer 8

• Rapid, unstable changes from birth to age 3
• Stabilizes into an adult-like community by age 3
• Maintains relative stability through adulthood

Diversity typically decreases later in life.

Question 9

What is the impact of breastfeeding on microbiome composition?

Answer 9

• Promotes high Bifidobacterium abundance
• Provides human milk oligosaccharides (HMOs) as prebiotics
• Contributes maternal microbes and immunological factors

These factors shape community assembly in the infant gut.

Question 10

What is the concept of functional redundancy in the microbiome?

Answer 10

• Different species can perform the same essential tasks
• Health is maintained through conserved functions, not specific species

Loss of function is more clinically important than loss of a particular species.

Question 11

Identify the major body sites that harbor microbial communities.

Answer 11

• Gut (highest density)
• Skin
• Oral cavity
• Vagina
• Upper airways

Each site has unique microbial compositions and densities.

Question 12

How do environmental factors determine microbiome composition?

Answer 12

• Oxygen levels
• pH
• Nutrient availability
• Moisture
• Host immunity
• Clearance mechanisms

These factors create distinct ecosystems at different body sites.

Question 13

What happens to the microbiome with reduced dietary fiber?

Answer 13

• Decline of fiber-fermenting bacteria
• Decreased SCFA production
• Increased inflammation risk

This shift can weaken the gut barrier and alter microbiome composition.

Question 14

True or false: The microbiome is considered an organ because it performs indispensable physiological functions.

Answer 14

TRUE

Its absence leads to system-wide dysfunction, as shown in germ-free animal studies.