Microbiomes

Question 1

microbiome

Answer 1

entire habitat including the microorganisms, their genomes, and the surrounding environmental conditions

Question 2

microbiota

Answer 2

assembly of microorganisms present in a defined environment established using marker genes (16S or 18S ribosomal NA or other) and genomic regions, amplified and sequenced from biological samples

Question 3

metagenome

Answer 3

collection of genomes and genes from members of a microbiota which is obtained via shotgun sequencing (followed by assembly or mapping to a knowledge database)

Question 4

How are microbiomes related to everything around it?

Answer 4

Question 5

Major Factors which Shape the Microbiome

Answer 5

diet, antibiotic use, host genetics, age, sex
also environmental conditions, xenobiotics, and stress

Question 6

Are microbiomes unique?

Answer 6

yes, to the species, to the individual, to specific body sites within the individual

Question 7

Diseases which can affect the Microbiome

Answer 7

autism spectrum disorder, infectious diseases, Type 2 diabetes, atherosclerosis, liver cirrhosis, depression, asthma, obesity, cancer, IBD

Question 8

5 Major Functions of the Microbiome

Answer 8

1. Immune Stimulation
2. Production of Micronutrients
3. Digestion
4. Defense
5. Detox

Question 9

4 Components of Microbiome Defense Against Incoming Pathogens

Answer 9

1. Competitive Exclusion
2. Physical Barrier
3. Chemical Warfare
4. Biologic Warfare

Question 10

competitive exclusion

Answer 10

microbes “win” and prevent colonization by pathogens

Question 11

physical barrier defense

Answer 11

tightens tight junctions, but also increasing mucus thickness (especially in the gut) to prevent colonization of pathogens

Question 12

chemical warfare

Answer 12

microbes can secrete AMPs, or toxins, or secondary bile acids

Question 13

bacteriophage

Answer 13

virus that infects bacteria

Question 14

primary bile acids

Answer 14

from the host; emulsify fat

Question 15

secondary bile acids

Answer 15

from microbes

Question 16

What species depend on microbiome for digestion?

Answer 16

ruminants

Question 17

cellulase

Answer 17

enzyme that vertebrates don’t have, so depend on microbial metabolism to breakdown plant matter

Question 18

short chain fatty acids

Answer 18

fermentation products [of microbes] that provides nutrients and energy for gut cells which promote the balance between inflammatory and anti-inflammatory signals, particularly at high concentrations

Question 19

examples of short chain fatty acids

Answer 19

acetate, propionate, butyrate

Question 20

How does the microbiome of the gut affect the rest of the body?

Answer 20

short chain fatty acids and other microbial metabolites can extend the reach outside the gut via endocrine signaling, behavior, immune development, etc.

Question 21

What vitamins can be synthesized by microbes?

Answer 21

Vitamin B12, other B vitamins, Vitamin K

Question 22

What percent of the daily requirement of vitamin K can be produced by your microbiome?

Answer 22

0.002 - 15%

Question 23

What vitamin can ONLY be synthesized by microbes?

Answer 23

vitamin B12

Question 24

How does the microbiome affect the immune system?

Answer 24

stimulates development of mucosally-associated lymphoid tissues (like GALT)

also increases barrier function, increases AMP secretion, provides tolerogenic environment

Question 25

IBD and Microbiome

Answer 25

microbiome is an INITIATING trigger in a flare up of IBD

a dec. in tolerance inducing microbes –> inc. inflammation –> inc. pathogens –> dec. barrier function –> inc. immune activation

Question 26

xenobiotic

Answer 26

chemical substance found within an organism that is not naturally produced or expected to be present within an organism (for example, a medication)

Question 27

Are xenobiotics good or bad?

Answer 27

can be either

Question 28

Bryant’s Woodrat

Answer 28

adorable little thing which eats a lot of creosote bushes which is normally incredibly toxic but these guys have the microbiota to handle it

Question 29

antibiotic

Answer 29

a substance which kills or disrupts the growth of a bacteria

Question 30

Antibiotics and Microbiome

Answer 30

antibiotics can cause long-term alterations in microbiome that can lead to disease

Question 31

Probiotic

Answer 31

LIVE microorganisms which when administered in adequate amounts can confer a health benefit on the host

Question 32

3 Examples of Probiotics

Answer 32

1. Enterococcus faecium
2. Bifidobacterium
   bifidum
3. Lactobacillus plantarum

Question 33

Are probiotics FDA approved?

Answer 33

no

Question 34

Prebiotic

Answer 34

a substance which induces the growth or specific metabolism of a beneficial microorganism

Question 35

Examples of Prebiotics

Answer 35

fiber, breast milk, oligosaccharides

Question 36

Synbiotics

Answer 36

combination of pre and post biotics

Question 37

postbiotic

Answer 37

soluble product(s) secreted by or released from a live microorganism that provides a health benefit

Question 38

Example of Postbiotics

Answer 38

Vitamins B and K, amino acids, AMPs

Question 39

Fecal Microbial Transplant (FMT)

Answer 39

transplantation of feal microbiota from healthy donor to recepient

Question 40

importance of screening donor in FMT

Answer 40

infections of recipient can result, potentially fatal!

Question 41

Potential Applications of FMT or other microbe transplantation

Answer 41

Human: C. diff, ulcerative colitis, cancer, non-alcoholic fatty liver disease

Animals: C. diff, ruminal indigestion, acute diarrhea (dogs), IBD

Question 42

Killed probiotics are considered what?

Answer 42

postbiotics