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Microbiology > Human Microbiome > Flashcards

Human Microbiome Flashcards

1) Understand the distribution and abundance of microbes on/in the human body (and which microbes are dominant in each area of the body). 2) Understand the human body as a series of microbial ecosystems 3) Review/know how physiological traits (e.g. fermentation) of select members of our microbiome affect Human health

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Biology 101 flashcards
1
Q

Microbiome/Microbiota (definition)

A

all the microbes associated with an organism (such as the human body) OR with a habitat (such as a type of soil).

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2
Q

Holobiont

A

An organism and all their associated microorganisms

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3
Q

Example of a “simple” microbiome

A

The microbiome of colonies of microbes (biological soil crusts) growing near a receding glacier in the high Arctic.

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4
Q

Human microbiome: our microbiome consists of…

A

the bacteria, archaea, viruses, and microeukaryotes that live in and on our bodies

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5
Q

Our microbiome contains ____ as many bacterial cells as human cells

A

10x
* Bacterial cells: total human cells = 1.3 (about equal)
* Bacterial cells: nucleated Human cells (RBCs removed) = 10:1
* > 10 trillion microbial cells in/on a human

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6
Q

amount of human genes vs. microbial genes

A

100 or 1000x more microbial genes
* 20,000 human genes
* 20 million microbial genes

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7
Q

bottom line of having 100 or 1000x more microbial genes than human genes

A

our microbiome provides us with important traits

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8
Q

What things are microbe-free in healthy animals

A

blood, organs, and cerebrospinal fluid

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9
Q

Our microbiome is necessary for…

A

optimal function of our body system

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10
Q

What happens if some members of the microbiome overgrow or escape their usual location

A

they can cause disease

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11
Q

Coevolution with our microbiome

Over millions of years, we coevolved together with bacteria through exposure to what

A

commensals, soil bacteria, food fermenting bacteria, etc

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12
Q

Which systems in our body have adapted evolutionarily such that they are dependent on these microorganisms in order to function optimally

A

immune and digestive system

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13
Q

Hygiene hypothesis

A

Essentially its good not to be too clean
* exposure to commensals, soil bacteria and fermenting bacteria led to a “good” microbiome which = proper development of our immune system
* Sterile, indoor lives and over-cleanliness might be responsible for many conditions such as allergies, chronic inflammatiory disease, and various immunological disorders

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14
Q

How is the normal microbiota of our bodies also viewed as par of our innate immunity to pathogens

A

By colonizing the available niches of our bodies and releasing primary and secondary metabolites, they make it very difficult for foreign pathogens to colonize our skin and mucosal surfaces.

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15
Q

handwashing removes what % of transient bacteria and what % of resident bacteria

A

90% of transient bacteria
40% of resident bacteria

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16
Q

Presence of skin microbiota inhibits infection by what

A

Staphylococcus aureus and other pathogens

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17
Q

Is handwashing good?

A

Overall, yes, but too many showers or use of antibacterial soup on the whole body can remove helpful bacteria

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18
Q

An epidemiologist investigating an outbreak of bacterial skin infections caused by Pseudomonas aeruginosa discovers that all the affected people were healthy young adults who had attended the same pool party. Testing revealed low levels of P. aeruginosa cells (and other hardy bacteria) in the pool, but that the level of chlorine in the water was three times higher than the recommended concentration. What is the best explanation for the outbreak?

A

The chorine in the pool killed too many of the natural skin microbiota, thus opening up niches for P. aeruginosa to colonize.

overall point: anything that removes or kills natural skin microbiota makes us susceptible to infection

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19
Q

Why do we compare the human body to a planet

A

From the perspective of microbes the human body is like a planet with many different environments that are colonized by different microbes. Each region (habitat) of the human body has a unique microbiome

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20
Q

How do we use Prevotella as an example of there not being necessarily the same species of the same genus across different body zones

A

vagina = Prevotella amnii
gut = Prevotella copri

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21
Q

The mouth, teeth, and throat are dominated by

Teeth has two

A

Streptococcus
* teeth = Streptococcus and Corynebacterium

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22
Q

The skin is dominated by

A

Gram + bacteria
* Firmicutes (Staphylococcus)
* Actinobacteria (Propionibacterium, Corynebacterium)

These also dominate the nose since these location are very similar!!

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23
Q

The vagina is dominated by

A

Lactobacillus

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24
Q

Example of coevolution in the mouth - digestion of starch

A

In the mouth Streptococcus gordonii captures humans amylases with Amylase binding proteins (Abps) to digest starch extracellularly leading to the production of lactic acid

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25
Q

Main Phyla associated with the human body

A
  • Bacteroidetes: Gram -, mainly break down polymers like cellulose (e.g. Prevotella, Bacteroides)
  • Actinobacteria: Gram +, cutibacterium (Prorionibacterium), Corynebacterium, etc
  • Firmicutes: both spore formers (Clostridiales), and non-spore formers (Staphylococcus, Streptococcus, Lactobacillus)
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26
Q

Why is the skin the most difficult place for microbes to live

A
  • Dry
  • Acidic (pH ~5.5)
  • Salt
  • Sebum (oily, waxy)
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27
Q

Would you expect to find more gram-positive or gram-negative bacteria on skin (and why)

A

Gram-positive: thicker cell wall, usually adapted to drier environments

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28
Q

What aspects of the skin are not uniform

A
  • pH
  • moisture availability
  • temperature
  • UV exposure
  • O2/CO2
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29
Q

Number of bacterial cells just on skin surface (forhead, armpit, back, forearm)

A

Forehead: 2x10^5
Armpit: 2x10^6
Back: 3x10^2
Forearm: 1x10^2

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30
Q

Where is the greatest diversity on the human face

A

inbetween the eye - third eye?

still very big diversity everywhere on the face

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31
Q

Which actinobacterial name can be remebered by thinking of Cuniform writing

A

Coryneform bacteria (Corynebacterium)
- resemble the wedge shaped characters

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32
Q

Which actinobacterial name can be remebered by Latin cutis = skin, cutin = waxy substancer in the “skin” of plants, and the word cuticle

A

Cutibacterium

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33
Q

skin propionibacterium are now known as

A

Cutibacterium

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34
Q

human skin microbiome is Gram…, high…, and Phylum…

A

Gram +, high GC, Phylum Actinobacteria

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35
Q

What makes up about 80% of the bacteria in hair follicles

A

Cutibacterium acnes

36
Q

What can Cutibacterium acnes ferment? Why is this important

A

can ferment lactic acid to propionate and can ferment glycerol
3 Glycerol -> propionate + acetate + lactate + 2 CO2
* This is important because sebum contains glycerol

37
Q

Cutibacteriums ability to ferment glycerol to produce propionic acid and other fatty acids does what to pH and the skin

A

lowers the pH and helps protect the skin from pathogens
* “skin probiotic”

38
Q

Cutibacterium acnes can also be a bad guy and cause

A

acne

39
Q

Sebaceous glands

A

open into hair follicles and secrete oily/waxy sebum, which lubricates the hair and skin of mammals

40
Q

In humans, sebaceous glands occur in the greatest number on the

A

face, scalp, and back

41
Q

What causes acne

A

increase production of sebum due to hormonal factors = blockage of duct that can lead to infection by Cutibacterium acnes
Leads to inflammation causing the characteristic acne lesions

42
Q

Cutibacterium acnes is a commensal bacterium living in hair follicles and can ferment glycerol in sebum to propionate, acetate, and lactate. This reduces the pH of the skin and inhibits the growth of …..
pathogens such as Staphylococcus aureus.
However, when there is excess sebum production, pores can become plugged and C. acnes can become an …..
pathogen by overgrowing and triggering an
inflammatory response.

A

opportunistic; opportunistic

43
Q

Relationship between Cutibacterium from skin and Propionibacterium from cheese

A

While both strains of Propionibacterium, Propionibacterium from cheese are different strains than Cutibacterium from skin - share a fairly recent common ancestor, but have each evolved to the biome that they live in - definitely not within the same genus

also true of the lactic acid bacteria that we talked about earlier in the course, that is strains of Lactobacillus in cheeses and yogurt are not the same strains found in/on the human body

44
Q

Herbivores in general depend more on……. in their guts compared to omnivores and carnivores

This is similar to

A

nitrogen fixation; similar to termites that depend on N-fixers to get their protein

45
Q

How does a cow that eats only dry hay get enough protein?

A

large fermentation vessel (Rumen) w/ many N-fixing bacteria and archaea
* they convert unusable nitrogen gas into a usable form that helps plants make protein
* when fed into the stomach, acid kills them and releases the amino acids which the cow then absorbs

46
Q

Location of fermentation chamber in cows and sheep (rumen) vs. humans and horses (cecum and large intestine)

A

Some animals (e.g. cows, sheep) have their major fermentation chamber (e.g. rumen) before the acidic stomach and some animals (e.g. humans, horses) have their fermentation chamber (cecum and large intestine) after the acidic stomach.

47
Q

Sites of fermentaiton in animals is also the site of most

A

N-fixation

48
Q

What is the equivalent (somewhat) of the Rumen in humans

A

tiny Cecum

49
Q

Along the length of the GI tract what increases, what decreases

A
  • microbial biomass increases
  • O2 levels decrease
50
Q

Characteristics of the small intestine
* major bacteria present
* what mainly happens here
* transit time

A
  • Enterococcaceae
  • Lactobacillales
  • Absorbance of many nutrients
  • Short transit time, antimicrobial compounds
51
Q

Characteristics of the large intestine (Colon)
* major bacteria present
* what mainly happens here
* transit time

A
  • Anaerobic decomposers like Bacteroides and Prevotella
  • Break down complex carbs and proteins into products that can be absorbed by the body
  • Long transit time
52
Q

Function of anaerobic decomposers like Bacteroides and Prevotella in the colon

A

to hydrolyze large glycans (e.g. cellulose and starch) using extracellular enzymes

53
Q

what makes up 60% of fecal mass

A

microbial cells

54
Q

function of anaerobes fermenting sugars in the colon

A

ferment sugars to short chain fatty acids (e.g. acetate) that feed other microbes and are taken up by our cells

55
Q

Function of facultative aerobes (e.g. E. coli) in the colon

A

scavenge all O2 keeping the lumen anaerobic

56
Q

Function of some fermenters (e.g. some Bacteroidetes) releasing peptides in the colon

A

peptides act as signals (neurotransmitters) to the brain and nervous system

57
Q

Main microbe components of the colon (large intestine) - Phylum, Gram, examples

A

2 main components
* Firmicutes (Gram +, lactobacillus, clostridium, christensenella)
* Bacteroidetes (Gram -, Bacteroides, Prevotella)

also many Proteobacteria (E.coli) and Actinobacteria (Bifidobacterium)

58
Q

Biochemical/metabolic contributions of intestinal microbes

A
  • vitamin synthesis
  • amino acid synthesis
  • organic acid production
  • breakdown of large polymers using extracellular enzymes
  • production of neurological agents
  • nitrogen fixation
  • gas production
  • odor production
59
Q

Bacteroides & depression

A

GABA-modulating bacteria of the human gut
* more GABA = less depressed

60
Q

The most abundant virus in the human colon infects what species

A

bacteroides

so important in all aspects of the colon

61
Q

Other than Bacteroides in the colon, where else did we talk about this species being dominant

A

Soil
* breakdown complex polysaccarides (starch, cellulose)

62
Q

ON FINAL

Vicuna dung gardens

A

decomposes, turns into soil and allows things to grow in nutrient poor environments
* dominanted by Bacteroides - but shifted from the anaerobes of the colon to aerobic Bacteroides found in soil
* First thought to be from the Vicuna, but turned out to be aerobic soil Bacteroidetes

63
Q

Archaea in the colon - mostly? do they work with in tandem with anything else?

A

Archaea make up 10-30% of microbes in the colon
mostly methanogens (Euryarchaeota)- many of them are living syntrophically with fermentative members of the Clostridiales

64
Q

Methanogenesis equation

A
65
Q

Syntrophic transfer of H2 by ethanol fermenter and methanogen

A

Ethanol fermenter produces H2 and Acetate, with is taken up by methanogen and used with CO2 to produce CH4

66
Q

M. smithii (methanogen in colon) is syntrophically associated with what? what does this allow

A

fermentative Clostridiales (producing H2)
Removal of H2 by M. smithii allows more fermentation and the production of more acetate

67
Q

Methanogens remove H2 = increased …. = increased …..

More methanogens = more

A

increased acetate = increased fat production

more flatulence (methane)

68
Q

Colon microbiome affects what in conjunction with diet

A

obesity!

69
Q
  • Microbiome from an obese human twin cause mouse to be
  • Microbiome from lean human twin caused mouse to be
  • Obese mice living with lean mice acquired
A
  • obese
  • lean
  • lean microbiome and lost weight
70
Q

Effect of Christensenella minuta on body fat

A

reduced body fat - correlated with BMI

71
Q

Christensenella minuta phylum and order

A

Phylum Firmicutes
Corder Clostridiales
* anti-inflammatory

72
Q

Are Archaea in the colon aerobic?

A

No!

73
Q

Characteristics of Bifidobacterium

A

Original probiotic
* Actinobacteria
* Named because of Y shape (Bifid)
* Ferment milk-based oligosaccharides (short chain polysaccharides)
* Important in early development of the gut microbiome and infant nutrition

74
Q

Successiuon of the human microbiome during infancy (breast-fed infant)

A
  • Bifidobacterium decrease as breast feeding stops ~12 months
  • Bacteroides increases as diet changes to plant-based saccharides

Bifidobacterium -> Bacteroides

75
Q

What is Bifidobacterium (Bifidus) added to

A

yogurt and other foods as a probiotic

76
Q

Probiotics

A
  • Live microorganisms which confers a health benefit when consumed
77
Q

Two main genera of probiotics

A
  • Lactobacillus and Bifidobacterium
78
Q

Ways probioitcs work

A
  • inactivation of bacterial toxins
  • competition with pathogens
  • up-regulation of immunity
  • suppression of inflammation
  • promotion of intensinal barrier function
79
Q

Prebiotics and how they work

A

Non-digestible food ingredient
* stimulate growth/acitivty of specific bacteria (e.g. Bifidobacterium)

80
Q

The human virome: what two things are also important members of the human microbiome

A

Bacteriophage and Archaeal viruses

81
Q

what aspect of the human virome leads to recycling of nutrient in the gut and may kill some pathogens

A

lysis of cells

82
Q

Lysogeny can lead to

A

good and bad traits
* enhanced triats
* Virulence such as toxins

83
Q

Thru what mechanism can phage enter our bodies thru the epithelial cells of the colon

A

transcytosis

84
Q

Why might transcytosis of phage particles occur

A
  • priming of immune system
  • circulating phage to kill bacteria
  • digesting phage as food source
  • Maybe no reason
85
Q

Mechanism of Bacteriophage adhering to mucus

A
  • phage adhere to mucus through Ig-like domains
  • Adherent phage form anti-microbial layer
  • Increased replicative success when adhered to mucus
86
Q
A

Microbiology (9 decks)

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