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MICR 2420 > Symbioses and Microbes > Flashcards

Symbioses and Microbes Flashcards

1
Q

what is MUTUALISM?

A

both species BENEFIT - may fail to grow independently

ex. lichens consist of fungi and algae that grow together

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2
Q

what is SYNERGISM?

A

both species BENEFIT, but can easily separate and grow independently

ex. human colonic bacteria and methanogens

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3
Q

what is COMMENSALISM?

A

one species benefits, the other is neither benefitted nor harmed

ex. Beggiatoa bacteria

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4
Q

what is AMENSALISM?

A

one species benefits, the other is harmed; NONSPECIFIC

ex. sterptomyces bacteria secrete antibiotics that lyse other species

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5
Q

what is PARASITISM?

A

one species benefits, the other is harmed (the host); OBLIGATORY for the parasite

ex. Legionella pneumophila

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6
Q

what is the cow and rumen microbe an example of?

A

SYNERGISM
each partner benefits
partners can be separated (not easily)

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7
Q

what are the similarities between macrophages and amebas?

A

molecular mechanisms involved in:
directional motility
recognition
binding
englufment
phagolysosome processing of bacteria

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8
Q

what is endosymbiosis?

A

species are infected by INTRACELLULAR BACTERIA

parasitic or mutualistic relationship - hard to tell

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9
Q

give an example of endosymbiosis

A

WOLBACHIA AND MOSQUITOES

bacteria competes with malaria parasites for colonization
lessens malarial load in the insect
bacterial infection lessens lifetime of species

REDUCES TRANSMISSION OF MOSQUITO BORNE DISEASE

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10
Q

how can we determine what species are present in a biome?

A
  1. culture
  2. DNA sequencing
  3. RNA sequencing
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11
Q

what is the problem with culture plates?

A

many bacterial strains cannot survive on agar

some bacteria are fastidious (have complex nutritional/environmental needs)

some need other species to survive

some may be non-viable, or viable but non-culturable

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12
Q

what is high-throughput culture or “culturomics”?

A

uses AI and ROBOTS

automatic adaptive isolation and biobanking

allows picking thousands of colonies into multi-well plates

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13
Q

what is RNA sequencing?

A

USE mRNA

extract it from a community, transcribe to DNA

barcode and sequence, match transcripts to known genomes

tells us who’s alive: dead cells do not transcribe RNA

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14
Q

what are METAGENOMES?

A

PREDICTIVE

use softwara to annotate genes and predict possible functions

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15
Q

what are PROTEOMICS?

A

DIRECT

extract and sequence proteins using mass-spec, use computer to match peptides to proteins and proteins to genes

regulation of metabolism, dissociated very fast

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16
Q

what is METALBOLOMICS/METABONOMICS?

A

DIRECT

extract all molecules in a sample

subject sample to mass-spec or NMR spec

match compound signatures from obtained spectra to standards

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17
Q

what is METATRANSCRIPTOMICS?

A

RNA sequencing

mRNA content reflects active transcription - what cells are doing in response to their environment

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18
Q

what is lipidome?

A

all the lipid molecules in a sample

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19
Q

what is secretome?

A

all the secreted products of a cell

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20
Q

what is resistome?

A

antimicrobial resistance genes in a sample

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21
Q

what is pheonome?

A

all phenotypic data from species within a sample

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22
Q

how do microbes vary under different conditions?

A

an omics analysis will only yield a snapshot

microbiomes are DYNAMIC systems - change in response to the environment

need to do studies LONGITUDINALLY

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23
Q

what is multi-omics integration?

A

integrate host genomics, transcriptomics, metabolomics, and epigenomics to see how host and microbiome interact

enormous ramifications because everyone’s microbiome is different

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24
Q

what are marine and aquatic microbes?

A

oceans and freshwater are full of microbes

bacteria and algae are primary producers

ALVIN: submersible vessel, went to depths of ocean and gathered info

sea is mostly unstudied - used to think it is unstable

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25
Q

what are the layers of the ocean?

A

NEUSTON (10micons): surface, MAJORITY of microbial life

COSTAL SHELF: full of debris

EUPHOTIC ZONE: light can penetrate

APHOTIC ZONE: no light

BENTHOS: depth, where techtonic plates, very high pressure

water temperature becomes a constant 4 degrees C at a certain depth, approaches 0 at benthos due to salt content

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26
Q

what does oligotrophic mean?

A

low in plant nutrients, high amounts of dissolved O2

OCEAN MICROBES

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27
Q

who was HOLGER JANNASCH?

A

discovered that ocean microbes are unculturable

need to view microbes under microscope

discovered that decomposition in the ocean takes 100x longer than land

argued against dumping sewage into the ocean

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28
Q

describe the sinking of Alvin

A

alvin was a submarine

sank in in OCTOBER 1968 when a cable snapped during deployment

stayed ~150m deep from ~1yr before it was rediscovered

found a still intact sandwich, which slows metabolic rate in the ocean

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29
Q

what did the sorcerer II global ocean expedition find?

A

estimated 25000 different microbes per litre of sea water

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30
Q

what can be found in a singular drop of sea water?

A

10 million viruses

1 million bacteria

1 thousand small protists

31
Q

what did Tara Oceans discover?

A

in upper ocean layers, temperature determines microbiome composition
–> climate change can effect this

32
Q

what is the most abundant genome on earth?

A

PROCHLOROCOCCUS
accounts for half of ocean’s photosynthesis

33
Q

why was prochlorococcus so hard to culture?

A

has a SYMBIOTIC relationship with ALTEROMONAS

alteromonas produces CATALASE –> removes H2O2, a toxic biproduct of PROCHLOROCOCCUS’S metabolism

procholorcoccus lacks gene to make catalase, a smaller genome lets it replicate faster

rising CO2 levels reduces efficiency of catalase expression

34
Q

what microbes live in the benthos?

A

BAROPHILES (extreme pressure)
PSYCHROPHILES (extreme cold)
OLIGOTROPHS (nutrient depletion)

have extremely slow metabolic rates and heavy metal resistance genes

35
Q

what are hydrothermal vent system?

A

DEEP OCEAN OASIS
still have extreme pressure, but also extreme HEAT (allows slightly faster metabolism)
uses multiple oxidizing states of sulpher to respire (redox rxn)
full of life

36
Q

what other oases exist?

A

may be COLD
have sources of CARBON
ex. “cold seeps” (methane bubbles out of ocean surface), whale fall, shipwreaks

37
Q

what are the layers of soil?

A

organic horizon: organic matter undergoing decomposition

aerated horizon: decomposed organic particles and mineral (TOPSOIL)

eluviated horizon: insoluble particles, leached by rainwater, gritty, poor source of nutrients

B horizon: clay and minerals

water table

as you go down, less oxygen, more water

38
Q

what microbes can be found in each soil layer?

A

top soil: fungi, actinomyctes, slime molds

oxygenated layer: fungi (mycorrhizae), aerobic bacterial biofilms, aerobic bacterial filaments

prokaryotic domain: chemolithotrophs, anaerobic heterotrophs

bottom: anaerobes, endoliths, methanogens, chemolithotrophs

39
Q

what is the most harmful agriculture practice to soil?

A

application of manufactured fertilizer pellets (changes web –> microbes cannot survive without soil)

40
Q

what is humus?

A

rich source of nitrogen –> source of water, holds soil together, product of microbial digestion

41
Q

describe a soil particle

A

contains bacterial colonies, humic substances, polysaccharide secretion
9supports community, provides water), interact with each other and plant roots

42
Q

which province has the most diverse soil?

A

Manitoba

43
Q

what are streptomyces?

A

produce antibiotics, major genus of soil bacteria

44
Q

describe the symbiotic relationship between microbes and plan roots

A

microbes in rhizosphere protect plants from pathogens, fix nitrogen (diazotrophs)

plants provide nutrients to microbes

45
Q

what is the ectomycorrhizae

A

ECTO = OUTSIDE

forms a thick protective layer around roots
absorb nutrients
allows distant plants to communicate

benefits in agriculture: increase crop yield, makes healthier plants

46
Q

what is the endomycirrhizae

A

ENDO = INSIDE

fungi invade roots, forming arbsucles
lack sexual cycles, need plants to reproduce genes

extreme form of MUTUALISM

47
Q

what are endophytes?

A

grows within plant tissues
bacterial and fungal

bacterial cells adapt to grow in lumps to form a nitrogen fixing “organ” for host cell

leychemoglobin makes them pink –> carries O2

48
Q

what is a microbita

A

indicates the cell consortium (group of diverse microorganisms)

49
Q

what is a microbiome

A

refers to the genetic potential of the biota

50
Q

how many bacterial cells are in a person?

A

39 trillion

ratio: 1 human cell : 1.3 bacteria cells

200 bacterial species per person

51
Q

what disease can emerge from an imbalanced microbiome?

A

autism, colorectal cancer, T1D, depression. Parkinson’s

52
Q

describe the skin microbiome

A

difficult to colonize (dry, salty, acidic, protective oils)

10^12 microbes in moist areas (scalp, ears, armpits, genital, anal areas)

mostly gram POSITIVE bacteria
more resistant to salt and dryness (staphylcoccus epidermidis, cutibacterium acnes)

53
Q

what bacteria infects an infants mouth?

A

non-pathogenic neisseria (gram-negative cocci)

streptococcus (gram-positive cocci), lactobacillus (gram positive rods)

54
Q

what bacteria grows as teeth emerge?

A

prevotella and fusobacterium

streptococcus mutans (tooth enamel - converts sugar and acid to acid, causes tooth rot)

most bacteria are STRICT ANAEROBES –> use plaque

55
Q

what bacteria are found in the nose and oropharynx?

A

nose and nasopharynx: bacillota and actinomycetota –> gram positive, thick cell wall

nasopharynx: staphylococcus aureus and staph. epidermidis (some are better than others at keeping us healthy)

oropharynx: same as saliva

56
Q

describe the lung microbiome

A

mainly anaerobes

can differ in patients with COPD, CF, and asthma

mucocilliatory escalator sweeps inhaled particles towards throat –> really small microbes can get stuck and cause infection

57
Q

describe the urogenital tract

A

kidneys are near sterile

urethra contains S. epidermus and enterobacteriaceae
can cause UTIs

vaginal microbiota changes with menstrual cycle –> should not be diverse

lactobacillus secrete lactic acids –> protect from STIs, improve reproductive success

58
Q

describe the stomach microbiota

A

very low pH
few microbes survive

helicobacter pylori –> burrows into protective mucus, can cause ulcers (create urea buffer around itself)

hypochorydia: caused by malnourishment and PPIs –> can cause intestinal diseases

59
Q

describe the intestinal microbiome

A

contains feces
mostly anaerobes
most important microbiome in the colon
does as much work as liver

60
Q

why does everyone have a unique gut microbiome?

A

not the species that matter, but GENES
bacteria can easily uptake genes from different species

61
Q

what does the gut microbiome do?

A

regulate immune system
extracts energy from food
controls potential pathogens
makes essential metabolites (vitamins, cofactors)
improves intestinal function
removes toxins and carcinogens

62
Q

how do newborns acquire microbes?

A

fetus is STERILE
vaginal is very close to gut
get microbes from vaginal delivery
breastfeeding: sugars feed different microbes
interactions with environment

63
Q

how can we lose microbes?

A

C-section delivery
maternal antibiotics (ex. group B strep)
formula feeding (lack of ogliosaccarides)
indoor living
excessive sanitation
chemical preservation of food

64
Q

when does the microbiome become an adult microbiome

A

within 3 years of birth

65
Q

what is the missing microbiota hypothesis?

A

loss of microbiome in recent years due to changes in lifestyle
losing microbes faster than we can replace them

66
Q

what are ROBOGUTS?

A

a bioreactor used to emulate the human colonic environment

host free system, culture the uncultureable

67
Q

describe the compromised host

A

accidental penetration of the barrier or damage in the immune system can allow the microbiota to behave badly

microbes that breech the barrier are OPPORTUNISTIC pathogen/pathobionts

eg. inflammatory bowel disease

68
Q

what makes the microbiota protective?

A

COMPETITIVE EXCLUSION: niche prevents pathogens from growing

ENVIRONMENT MODIFICATION: lactobacillus colonization in the vagina makes it acdic

HOST STIMULATION: bacteroides fragilis stimulates a host cytokine, regulates immune system, prevents pathogens from growing

DIRECT PACIFICATION: secreted factors prevent expression of virulence genes from FBIs

69
Q

what is the gut-brain axis

A

signals between gut microbiome and brain, affects mood and behaviour

AV’s motto: “my microbes made me do it”

70
Q

what happens when the microbial balance is compromised?

A

containment breaches: bacterial penetration

niche disturbance: ex. exposure to xenobiotics

extinction events: ex. bifita bacteria loss since hunter/gatherer times

71
Q

describe obesity and the microbiome

A

obesity is associated with a less diverse microbiome

microbiome affects enegry regulation, metabolism, and fat storage

obesity is associated with inflammation: barrier function lost, increases tight junctions between epithelial cells in the gut, increased number of pro-inflammatory molecules

72
Q

what are gnotobiotic animals?

A

animals where the microbiota is known and defined

includes germ-free animals (very expensive, valuable for research)

73
Q

what abnormal physiology can be found in germ free animals?

A

poor immune system

lower cardiac output

need more calories to maintain body weight

stunted villi

enlarged ceca (part of gut with most microbes)

aggressive behaviour

misshapen mitochondria

74
Q

who is David Vetter?

A

boy in the bubble

SCID patient, impaired immune system

lived in completely sterile environment

died shortly after bone marrow transfusion due to complications with epsteine barr virus.

MICR 2420 (9 decks)

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