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MICRB 265 > Week 11 > Flashcards

Week 11 Flashcards

1
Q

microbiome (def.)

A

collection of microorganisms in environment

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2
Q

the ocean microbiome contains all the microbes that are _____ & the primary producers of _____

A

-responsible for nearly all the energy flux that occurs in oceans
-fuel (photosynthesis and chemosynthesis)

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3
Q

concentration of microbes in ocean microbiome

A

billions per little of sea water (both free living and complex communities)

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4
Q

the ocean microbiome is not a homogenous soup – it depend on _______

A

location, depth, season, temp, pH

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5
Q

____ has a massive impact on ocean microbiome

A

pollution (oil spills, microplastics)

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6
Q

Microbial biomass in soil is greatest where? smallest where?

A

-equator & rainforest
-desert

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7
Q

soil microbiome is dominated by _____ and less by ______

A

-bacteria & fungi
-protists & viruses

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8
Q

Bacteria plays a major role in recycling ______-> breakdown of dead ______

A

-organic matter
-plants and animals

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9
Q

Bacteria also play a major role in _______ and ____

A

-nutrient cycling (control nutrient availability in the environment)
-pH

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10
Q

Nutrients cycled by bacteria (4)

A
  • Phosphorus
  • Nitrogen
  • Sulfur
  • Iron
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11
Q

Bacteria produce large quantities of greenhouse gases (4)

A
  • methane (CH4)
  • carbon dioxide (CO2)
  • nitric oxide (NO)
  • nitrous oxide (N2O)
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12
Q

Rice fields account for _____ of global methane emissions
* Produced by ______ growing in flooded fields

A

-5-10%
-methanogens

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13
Q

Cable bacteria summary

A

-filmanetous, electrically conductive bacteria from family Desulfobulbaceae
-filaments transport e- over centimeter distances

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14
Q

Cable bacteria & rice fields

A
  1. cable bacteria deep in soil oxidize H2S to SO42- deep in soil
  2. transport e- to surface
  3. reduce O2 to water
    -this increase conc of SO42- in the soil
    -sulfate reducing bacteria outcompete other organisms for organic carbon (no food for methanogens)
    -bacteria reduce SO42- to H2S and cycle continues
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15
Q

Adding cable bacteria to plant pots growing rice reduces ________

A

methane emissions by >90%

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16
Q

___ animals have microbiomes. generally a complex mixture of __________. animal microbiome generally forms a _____ & varies widely between _______

A

-all
- archaea, bacteria, fungi, and viruses
-stable environment (resistant to disturbances)
-organisms and environment

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17
Q
  • Euprymna scolopes (bobtail squid) lives in a symbiotic relationship with _____
A

-Aliivibrio fischeri

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18
Q

Bobtail squid has a light organ which contains a _______

A

-network of unique reflector and lens tissues that help reflect and focus the light ventrally through the mantle

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19
Q

Quorum sensing in Aliivibrio fischeri

A
  • Bioluminescent Gram-negative, rod-shaped bacterium found globally in marine environments
  • Stimulated by AHL when cell density is high = produces light
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20
Q

enzymes that makes light + substrate for enzyme

A

-luciferase
-aldehydes

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21
Q

luxCDABE operon

A

luxCDE - produce aldehydes from fatty acids
lux
luxAB - luciferase

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22
Q

A. fischeri and the bobtail squid

A
  • The squid provides the bacteria with a sugar and amino acids
  • A. fischeri grows and uses quorum sensing to stimulate bioluminescence
  • The squid uses this bioluminescence to hide its silhouette when viewed from below by matching the amount of light hitting the top of the mantle (counter-illumination)
  • Bioluminescence demands a substantial amount of energy from a bacterial cell
23
Q

Colonization is specific for A. fischeri

A

-hatchlings of bobtail squid lack bacteria; need to carefully select for bacteria
-A. fischeri has flagella to move through ducts to the light organ (squid flushes ducts to eliminate non-motile bacteria)
-Squid halide peroxidase (uses H2O2 to oxidize halides) in ducts is antimicrobial -> A. fischeri possesses a periplasmic catalase → eliminates H2O2
- Squid produces nitric oxide (NO) (antimicrobial) in the light organ but A. fischeri produce NO inactivating enzymes

24
Q

Cellulose (def.)

A

linear polymer of β-1,4-linked glucose

25
Q

few organisms use cellulose as an energy source due to the ________

A

limited expression of cellulose-degrading enzymes (cellulases)

26
Q

_______ consume cellulose as plant fibre; depends on presence of ________

A

-Termites
-Trichonympha, a symbiotic protozoa

27
Q

Trichonympha internalize wood particles by _____ and partially digest them

A

phagocytosis

28
Q

Trichonympha contain both ___ and _____

A

-endo
-ectosymbionts

29
Q

Endo + Ectosymbionts of Trichonympha

A
  • Bacteria which help with nitrogen fixation (contain
    nitrogenase)
  • Conversion of sugar to energy by Trichonympha produces CO2 and H2, which contributes to making environment anoxic
  • Bacteria use H2 and CO2 to make acetate → AcCoA
30
Q

mutualism (def.)

A

organism A: benefit
organism B: benefit
obligatory interaction

31
Q

cooperation (def.)

A

organism A: benefit
organism B: benefit
non-obligatory interaction

32
Q

Commensalism (def.)

A

organism A: no effect
organism B: benefit

33
Q

Predation (def.)

A

organism A: dies
organism B: benefit
B eats A

34
Q

Parasitism (def.)

A

organism A: negative
organism B: benefit
Host/parasite co-exist

35
Q

amensalism (def.)

A

organism A: negative
organism B: no effect
release of toxic molecules

36
Q

competition (def.)

A

organism A: negative/small negative
organism B: benefit/small negative
competition for resources

37
Q

The human microbiome (def.)

A

-Combined microbes that live in and on humans (gut, skin, mouth)

38
Q

Microbes in human microbiome frequently identified by _______

A

gene encoding 16S rRNA

39
Q

Human microbiome is ____ to the individual and is formed within _____. more or less _____. different in different _________. necessary for ______

A

-unqiue
-the first 3 years
-stable
-areas of the body
-health

40
Q

Human microbiome responds to ______ but returns to normal when ______ is removed

A

-disturbances
-disturbance

41
Q

skin, saliva, urogenital tract are dominated by ________

A

gram + bacteria

42
Q

GI tract dominated by _____

A

gram - bacteria

43
Q

Despite this enormous inter-individual variety in microbiome, the symbiosis between microbes and humans results in a stable and common ______ and a well-balanced _______-> resistant to ______

A

-metabolic pattern
-physiological homeostasis
-exogenous microbes like pathogens

44
Q

Human microbiome depends on your _______

A
  • parents
  • diet
  • environment
  • genetics
  • health conditions
45
Q

Birth mode dictates _____

A

initial gut microbiome
- C section = microbes from skin
- Vaginal = microbes from vagina

46
Q

Infant microbiome changes after ____

A

birth regardless of mode of delivery (becomes more stables, generally end up similar between different delivery modes)

47
Q

When studying bacteria in microbiome, classification of bacteria by phylum does not provide enough information?

A

-phylum classification does not show if species are good, bad, or both

48
Q

Functional genomics (def.)

A

field of molecular biology that attempts to describe gene functions and interactions

49
Q

Metagenome (def.)

A

all the genes in an environmental sample; genes more common=activity needed/required for life

50
Q

KEGG (_____) + does what?

A

-Kyoto Encyclopedia of Genes and Genomes
-puts enzymes into categories based on metabolic pathway

51
Q

heat map tells us _____

A

which genes are enriched/depleted in different environments/microbiome

52
Q

CHILD Cohort Study

A

-3600 children in Manitoba
-study lots of variables & gut health/makeup
-mostly small correlations

53
Q

Caveats to microbiome research

A
  • Taxonomic information tells you nothing about function
  • Enzyme class information tells you nothing about outcomes
  • Soooooooooooooooooo many variables
  • Diving into metagenomic datasets to look for correlations is a computational nightmare
  • Mice are not humans
  • Correlation does not equal causation
54
Q

_____ change your diet/lifestyle or provide advice to others based on a single study

A

DO NOT

MICRB 265 (12 decks)

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