8-1: The Human Microbiome

Question 1

How many bacterial genes are there for every human gene?

Answer 1

~100

Question 2

What is the human microbiota? What is another name for it?

Answer 2

Collection of microbes living in/on us. Also called “microbial flora”

Question 3

What is the human microbiome?

Answer 3

Microbiota and the environment they live in.

Question 4

What is dysbiosis?

Answer 4

Term used to describe microbiota that is unhealthy for the host. “out of balance” - loss of commensals, increase in microbes associated with disease.

Question 5

What does the majority of our knowledge regarding the microbiome come frome?

Answer 5

16s DNA shotgun sequencing and animal models

Question 6

What are some things we know very little about regarding microbiota?

Answer 6

Community dynamics, how microbes interact
Links between microbiota and disease: causal or correlative?
Mechanisms linking microbiota and disease
Ways to restore healthy microbiome to individuals with dysbiosis

Question 7

How are microbiota of people similar? How are they different?

Answer 7

Similar at phylum level, but also unique in each individual at species level

Question 8

Microbiota composition depends largely on which two factors?

Answer 8

Mostly environmental factors, some genetic component.

Question 9

At what age is microbiota established? What’s interesting about this?

Answer 9

Established at a young age, and very resilient to changes.

Question 10

What problems can microbiota resilience and loss of resilience lead to?

Answer 10

Loss of resilience can lead to dysbiosis, while resilience makes interventions in the microbiota difficult.

Question 11

Where are the microbes in/on our bodies?

Answer 11

Gastrointestinal tract (stomach, small intestine, colon)
Skin
Oral cavity/upper respiratory tract (mouth, nose, throat)
Urogenital tract (urethra, vagina)

Question 12

Most internal sites of the body are considered what?

Answer 12

Sterile - no bacteria

Question 13

How does microbiome vary by location?

Answer 13

Different parts of the skin, saliva, urogenital tract and GI tract have very different compositions of organisms

Question 14

Describe the composition of the stomach microbiota.

Answer 14

Low pH tends to keep numbers low, but a microbial community still exists

Question 15

What part of the GI tract has the densest microbial population?

Answer 15

Density increases as you progress through the GI tract, so the large intestine

Question 16

What factors vary throughout the GI microbiome?

Answer 16

pH, O2 and nutrients

Question 17

What protects the epithelium that lines intestines of the GI tract?

Answer 17

Mucous layer

Question 18

What is mucous?

Answer 18

Thick and slippery suspension that includes antimicrobial factors and mucin

Question 19

What is mucin?

Answer 19

Gel-like glycoprotein substance that serves as a barrier

Question 20

Where do most microbes remain in the GI tract?

Answer 20

Lumen and NOT in direct contact with host cells

Question 21

What feeds the GI tract population?

Answer 21

Nutrients in food, some of which we can’t digest

Question 22

What percent of fecal matter is made of bacteria?

Answer 22

30%!

Question 23

How is the gut microbiota variable?

Answer 23

Person-to-person differences, where the abundance of different genera varies by orders of magnitude
Even most abundant genera are missing from some people

Question 24

What are the three major phyla of the gut microbiota

Answer 24

1. Bacteroidetes: g(-)
2. Firmicutes: g(+)
3. Proteobacteria: facultative anaerobes. Maintain anaerobic environment by consuming any O2 present

Question 25

High proportions of which phyla is indicative of dysbiosis?

Answer 25

Proteobacteria

Question 26

What is the major form of metabolism in the gut? What is the minor form?

Answer 26

Major - Fermentation
Minor - aerobic respiration

Question 27

What are primary fermenters?

Answer 27

Usually Bacteriodetes. Break down diverse carbohydrates from food or mucin.

Question 28

What do primary fermenters produce?

Answer 28

Short chain fatty acids that are absorbed by the host, or fermentation products that feed other organisms (syntrophy)

Question 29

How is the gut microbiota important for human health? (4)

Answer 29

• Compete with pathogens to prevent colonization
• Digest food (eg. fiber to short chain fatty acids)
• Produce nutrients we can’t make (vitamins, AA)
• Promote healthy immune system

Question 30

What is the dominant symbiotic relationship we have with our gut flora?

Answer 30

mutualistic

Question 31

What can disruptions to microbiota early in life (eg. antibiotics) cause?

Answer 31

Asthma, allergies, etc

Question 32

What causes dental plaques?

Answer 32

Formation of biofilms on teeth

Question 33

What is Staphylococcus aureus responsible for?

Answer 33

It is an opportunistic pathogen that if exposed to cuts/wound, can lead to infection.

Question 34

What can S. aureus produce?

Answer 34

Potent virulence factors, causing life threatening infection

Question 35

What dominates vaginal microbiota? What do they do?

Answer 35

Lactobacillus species, which lower vaginal pH (~5) via fermentation end products (lactic acid) to preent infection

Question 36

What does low vaginal pH prevent? What happens when it is high?

Answer 36

Prevent infection with pathogens. Reduced lactobacillus increases pH allowing candida albicans to bloom, causing yeast infection

Question 37

What is a probiotic?

Answer 37

Live microorganisns that have a bacterial effect on the host. Consuming “good bacteria”.

Question 38

What is a prebiotic?

Answer 38

A substance, that when consumed, promotes the growth of beneficial microbes. Eg. fiber

Question 39

What are fecal transplants?

Answer 39

Fecal matter from a healthy donor transplanted into dysbiosis patient, to reintroduce normal/healthy microbiota.

Question 40

What infection can fecal transplants cure?

Answer 40

Clostridoides difficile infections