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F24 Microbiomes > L10: Animal Microbiomes > Flashcards

L10: Animal Microbiomes Flashcards

1
Q

what is the complexity gradient of microbiome diversity

A
  1. Lepidoptera caterpillar gut
  2. Bobtail squid light organ
  3. Aphid bacteriocytes
  4. honeybee gut
  5. vertebrate gut
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2
Q

microbiome diversity - Lepidoptera caterpillar gut

A

no detectable resident microbiota

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3
Q

microbiome diversity - Bobtail squid light organ

A

single symbiont

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4
Q

microbiome diversity - Aphid bacteriocytes

A
  • 1-2 primary symbionts
  • a few microorganisms
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5
Q

microbiome diversity - honeybee gut

A

a few microorganisms

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6
Q

microbiome diversity - vertebrate gut

A

hundreds of microorganisms

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7
Q

what is the complexity gradient of model systems

A
  1. Hawaiian Bobtail squid
  2. fruit fly
  3. zebra fish
  4. mice
  5. humans
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8
Q

diversity of model systems - Hawaiian Bobtail squid

A

proteobacteria

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9
Q

diversity of model systems - fruit fly

A
  1. proteobacteria
  2. firmicutes
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10
Q

diversity of model systems - zebra fish

A
  1. proteobacteria
  2. fusobacteria
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11
Q

diversity of model systems - mice

A
  1. firmicutes
  2. bacteroidetes
  3. proteobacteria
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12
Q

diversity of model systems - humans

A
  1. firmicutes and bacteroidetes
  2. actinobacteria
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13
Q

examples of host-mictobiota co-adaptation mechanisms

A
  • corals and dinoflagellates
  • termites and wood decay
  • crop plants and root microbiome
  • cows and rumen microbiota
  • lab mice and gut microbiota
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14
Q

host-microbiota co-adaptation - corals and dinoflagellates

A

carbon provision in nutrient-poor waters

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15
Q

host-microbiota co-adaptation - termites and wood decay

A

lignocellulose degredation

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16
Q

host-microbiota co-adaptation - crop plants and root microbiota

A

nutrient provisiong

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17
Q

host-microbiota co-adaptation - cows and rumen microbiota

A

nutrient metabolism

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18
Q

host-microbiota co-adaptation - lab mice and gut microbiota

A

disease modeling

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19
Q

define phylosymbiosis

A

describes a pattern of symbiotic relationships where evolutionary history of a host organism correlates with the composition of its associated microbiome

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20
Q

phylosymbiosis - where is it not seen

A

microscopic marine invertebrates

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21
Q

define compartmentalization

A
  • separation of the cell interior in distinct compartments
  • can also separate microbes in space
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22
Q

how can compartmentalization drive the evolution of symbiotic cooperation

A

it can allow hosts to stabilize cooperation via:
- isolates symbionts and controls their reproduction
- reward cooperative symbionts and punish non-cooperative ones
- reduce direct conflict among different symbiont strains

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23
Q

gut microbiota - C. elegans

A
  1. protobacteria
  2. bacteroidetes
  3. firmicutes
  4. actinobacteria and acidobacteria (super small)
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24
Q

gut microbiota - Drosophila

A
  1. firmicutes
  2. protobacteria
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25
Q

gut microbiota - Honey bee

A
  1. firmicutes
  2. protobacteria
  3. bacteroidtes (very small)
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26
Q

gut microbiota - fish

A
  • has all families
    1. protobacteria
    2. others
    3. firmicutes
    4. bacteroidetes
    5. acidobacteria
    6. cremarchaeota
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27
Q

gut microbiota - mice

A
  1. firmicutes
  2. bacteroidetes
  3. protobacteria
  4. others
  5. cremarchaeota and acidobacteria (very small)
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28
Q

gut microbiota - humans

A
  • has all microbes
    1. firmicutes
    2. bacteroidetes
    3. protobacteria
    4. cremarchaeota
    5. acidobacteria
    6. others
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29
Q

explain the gut microbiota diversity in animals from most to least

A
  1. mammals
  2. fish
  3. reptile
  4. insect
  5. bird
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30
Q

host factors influencing gut microbiome

A
  • genotype
  • phenotype
  • vertical transmission
  • innate immunity
  • adaptive immunity
  • other mechanisms
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31
Q

host factors influencing gut microbiome - humans

A
  • genotype
  • phenotype
  • vertical transmission (expect vegetative reproduction)
  • innate immunity
  • adaptive immunity
  • other mechanisms (except coprophagy)
32
Q

host factors influencing gut microbiome - mice

A
  • genotype
  • phenotype
  • vertical transmission (except vegetative reproduction)
  • innate immunity
  • adaptive immunity
  • other mechanisms
33
Q

host factors influencing gut microbiome - fish

A
  • genotype
  • phenotype
  • vertical transmission (except maternal provisioning)
  • innate immunity (except PGRP)
  • adaptive immunity
  • other mechanisms (except coprophagy)
34
Q

host factors influencing gut microbiome - honey bees

A
  • genotype
  • phenotype
  • vertical transmission (except female germ cells and vegetative reproduction)
  • innate immunity (except NOD-like receptors)
  • NO adaptive immunity
  • other mechanisms
35
Q

host factors influencing gut microbiome - Drosophila

A
  • genotype
  • phenotype
  • NO vertical transmission
  • innate immunity (except NOD-like receptors)
  • NO adaptive immunity
  • other mechanisms
36
Q

host factors influencing gut microbiome - C. elegans

A
  • genotype
  • phenotype
  • vertical transmission (only female germ cells)
  • innate immunity (except PGRP and NOD-like receptors)
  • NO adaptive immunity
  • other mechanisms (except coprophagy)
37
Q

host factors influencing gut microbiome - Hydra

A
  • genotype
  • phenotype
  • vertical transmission (only vegetative reproduction)
  • innate immunity (except PGRP)
  • NO adaptive immunity
  • NO other mechanisms
38
Q

gut microbiota: diet and food levels - carnivores

A
  1. firmicutes and actinobacteria
  2. fusobacteria
39
Q

gut microbiota: diet and food levels - omnivores

A

proteobacteria

40
Q

gut microbiota: diet and food levels - herbivores

A
  1. firmicutes (99%)
  2. actinobacteria (1% - only 1 recorded)
41
Q

gut microbiota: diet and food levels - from most to least diverse

A
  1. herbivore
  2. omnivore (balanced diversity)
  3. carnivores
42
Q

Ant proventriculus case study - what is a proventriculus

A
  • a valve located between the crop and midgut of insects
  • blocks the enter of bacteria and particles ≥0.2 um into the mid- and hindgut
  • allows the passage of dissolved nutrients
43
Q

Ant proventriculus case study - explain the microbiome after the proventriculus

A
  • the mid-, hindgut, and rectum
  • has Opitutus sp. as the dominant microbe
44
Q

aphid bacteriome case study - what is a bacteriocyte

A

they are large cells that form the building blocks of the bacteriome

45
Q

aphid bacteriome case study - what is a bacteriome

A
  • specialized organ that host endosymbiotic bacteria
  • houses Buchnera spp.
46
Q

aphid bacteriome case study - what microbiome colonizes the aphid gut

A
  • facultative symbionts
  • gut-associated bacteria
  • bacterial pathogens
  • plant associated bacteria and pathogens
47
Q

aphid bacteriome case study - explain the Buchnera aphidicola bacteria

A
  • aphid ancestor and bacteria co-diversified
  • results in genome reduction
  • the bacteria engages in amino acid and vitamin provisioning
  • this provisioning is then maternally transmitted from bacteriocyte to progeny (children)
48
Q

Hawaiian bobtail squid and Vibrio fisherii case study - what does the squid use the bacteria for

A
  • Vibrio fisherii is contained within the Hawaiian bobtail squid’s light organ
  • the bacteria produces light for the squid to camouflage
49
Q

Hawaiian bobtail squid and Vibrio fisherii case study - explain the colonization process

A
  1. sterile (0 - 30 mins)
  2. permissive (30 - 60 mins)
  3. restrictive (60 - 120 mins)
  4. specific (past 120 mins)
50
Q

Hawaiian bobtail squid and Vibrio fisherii case study: colonization process - sterile

A
  • 0 mins: host hatches from egg
  • 30 mins: the bacteria’s cilia of surface epithelia begin to beat
51
Q

Hawaiian bobtail squid and Vibrio fisherii case study: colonization process - permissive

A
  • light organs are open to small numbers of bacteria or particles < 2um
  • 60 mins: host sheds mucus in response to bacterial peptidoglycan
52
Q

Hawaiian bobtail squid and Vibrio fisherii case study: colonization process - restrictive

A
  • initiation of bacterial aggregates (gram-negative bacteria)
  • bacteria and particles are removed by an unknown mechanism
53
Q

Hawaiian bobtail squid and Vibrio fisherii case study: colonization process - specific

A
  • only V. fisherii
  • V. fisherii aggregate above the pore and migrate to the duct before colonizing the light organ
54
Q

define bacterial quorum sensing

A

internal form of of communication that bacteria use to coordinate group behavior

55
Q

bacterial quorum sensing - define autoinducers

A

a chemical signal molecules that bacteria use in quorum sensing

56
Q

bacterial quorum sensing - how does it define the squid-vibrio symbiosis

A
  • at low cell density, bacteria produces autoinducers
  • via quorum sensing, bacteria move close and become high in density
  • high density than produces light
57
Q

explain compartmentalization in corals

A
  • mucus
  • tissue
    -skeleton
58
Q

compartmentalization in corals - mucus

A
  • 1st line of defense
  • has its own microbiome
59
Q

compartmentalization in corals - tissue

A
  • made of the: epidermis, mesoglea, gastrodermis, and mouth
  • has its own microbiome
  • has coral-associated microbial aggregates (CAMAs)
  • contains the phycosphere
60
Q

compartmentalization in corals: tissue - CAMAs

A
  • clusters of bacteria that form in the tissues of corals
  • contains Endoziocomonas (Gammaproteobacteria)
61
Q

compartmentalization in corals: CAMAs - Endoziocomonas

A
  • E. marisrubri 6c may have the ability to home in on suitable hosts via motility and chemotaxis
  • they then activate a cascade of mechanisms to evade or modulate host immune responses
62
Q

compartmentalization in corals: CAMAs - Endoziocomonas benefits

A
  • amino acid metabolism
  • biosynthesis and B vitamin provisioning
  • utilization of organic carbon sources by E. marisrubri 6c
63
Q

compartmentalization in corals: tissues - phycosphere

A
  • region around the Symbiodiniceae surface that is identified by the algae production of metabolites
  • within the tissues and inside the symbiosome
64
Q

compartmentalization in corals - skeleton

A
  • contains: endoliths and endolithic band
  • hotspot for bacterial diversity
  • has its own endolithic microbiome
  • has tissue and endolith nutrient exchange
65
Q

compartmentalization in corals: skeleton - bacterial diversity

A
  • has a low photosynthetically active radiation (PAR)
  • has stable near-infrared radiation (NIR) that is useable by bacteriochlorophyll
66
Q

compartmentalization in corals: skeleton bacterial - bacteriochlorophyll

A
  • a photosynthetic pigment found in certain bacteria
  • helps harvest light energy
67
Q

compartmentalization in corals: skeleton - nutrient exchange between endoliths and coral tissue

A

N and C nutrient exchange is increased in unhealthy/bleached corals

68
Q

compartmentalization in corals: nutrient exchange between endoliths and coral - low susceptibility to bleaching

A

usually has:
- greater diversity
- functional redundancy
- lower C and N assimilation (chemolithotrophy)

69
Q

compartmentalization in corals: nutrient exchange between endoliths and coral - high susceptibility to bleaching

A
  • lower diversity
  • higher C and N assimilation (photoautotrophy)
  • higher productivity
70
Q

explain the how microbes can provide a fast-response mechanism to rapid environmental change

A

from long to short:
1. genetic adaptation
2. epigenetic modification
3. acclimatization
4. algal symbionts
5. bacterial community

71
Q

how can we harness microbes to help organisms adapt

A
  • microbial transfer therapy
  • probiotics
72
Q

microbial dynamics - healthy coral

73
Q

microbial dynamics - unhealthy coral

A
  • opportunists
  • copiotrophs
  • presence of pathogens and pathobiome
74
Q

microbial dynamics: unhealthy coral - copiotrophs

A
  • organisms found in environments with abundant nutrients
  • specifically carbon
75
Q

microbial dynamics: unhealthy coral - pathobiome

A

community of microorganisms that interact with the host to cause disease

F24 Microbiomes (17 decks)

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