Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what is SYNERGISM?

A

both species BENEFIT, but can easily separate and grow independently

ex. human colonic bacteria and methanogens

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what is COMMENSALISM?

A

one species benefits, the other is neither benefitted nor harmed

ex. Beggiatoa bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what is AMENSALISM?

A

one species benefits, the other is harmed; NONSPECIFIC

ex. sterptomyces bacteria secrete antibiotics that lyse other species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what is PARASITISM?

A

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

ex. Legionella pneumophila

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is the cow and rumen microbe an example of?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what are the similarities between macrophages and amebas?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what is endosymbiosis?

A

species are infected by INTRACELLULAR BACTERIA

parasitic or mutualistic relationship - hard to tell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

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

A
  1. culture
  2. DNA sequencing
  3. RNA sequencing
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what are METAGENOMES?

A

PREDICTIVE

use softwara to annotate genes and predict possible functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what is METATRANSCRIPTOMICS?

A

RNA sequencing

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what is lipidome?

A

all the lipid molecules in a sample

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what is secretome?

A

all the secreted products of a cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what is resistome?

A

antimicrobial resistance genes in a sample

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what is pheonome?

A

all phenotypic data from species within a sample

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
what are the layers of the ocean?
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
26
what does oligotrophic mean?
low in plant nutrients, high amounts of dissolved O2 OCEAN MICROBES
27
who was HOLGER JANNASCH?
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
28
describe the sinking of Alvin
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
29
what did the sorcerer II global ocean expedition find?
estimated 25000 different microbes per litre of sea water
30
what can be found in a singular drop of sea water?
10 million viruses 1 million bacteria 1 thousand small protists
31
what did Tara Oceans discover?
in upper ocean layers, temperature determines microbiome composition --> climate change can effect this
32
what is the most abundant genome on earth?
PROCHLOROCOCCUS accounts for half of ocean's photosynthesis
33
why was prochlorococcus so hard to culture?
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
what microbes live in the benthos?
BAROPHILES (extreme pressure) PSYCHROPHILES (extreme cold) OLIGOTROPHS (nutrient depletion) have extremely slow metabolic rates and heavy metal resistance genes
35
what are hydrothermal vent system?
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
what other oases exist?
may be COLD have sources of CARBON ex. "cold seeps" (methane bubbles out of ocean surface), whale fall, shipwreaks
37
what are the layers of soil?
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
what microbes can be found in each soil layer?
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
what is the most harmful agriculture practice to soil?
application of manufactured fertilizer pellets (changes web --> microbes cannot survive without soil)
40
what is humus?
rich source of nitrogen --> source of water, holds soil together, product of microbial digestion
41
describe a soil particle
contains bacterial colonies, humic substances, polysaccharide secretion 9supports community, provides water), interact with each other and plant roots
42
which province has the most diverse soil?
Manitoba
43
what are streptomyces?
produce antibiotics, major genus of soil bacteria
44
describe the symbiotic relationship between microbes and plan roots
microbes in rhizosphere protect plants from pathogens, fix nitrogen (diazotrophs) plants provide nutrients to microbes
45
what is the ectomycorrhizae
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
what is the endomycirrhizae
ENDO = INSIDE fungi invade roots, forming arbsucles lack sexual cycles, need plants to reproduce genes extreme form of MUTUALISM
47
what are endophytes?
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
what is a microbita
indicates the cell consortium (group of diverse microorganisms)
49
what is a microbiome
refers to the genetic potential of the biota
50
how many bacterial cells are in a person?
39 trillion ratio: 1 human cell : 1.3 bacteria cells 200 bacterial species per person
51
what disease can emerge from an imbalanced microbiome?
autism, colorectal cancer, T1D, depression. Parkinson's
52
describe the skin microbiome
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
what bacteria infects an infants mouth?
non-pathogenic neisseria (gram-negative cocci) streptococcus (gram-positive cocci), lactobacillus (gram positive rods)
54
what bacteria grows as teeth emerge?
prevotella and fusobacterium streptococcus mutans (tooth enamel - converts sugar and acid to acid, causes tooth rot) most bacteria are STRICT ANAEROBES --> use plaque
55
what bacteria are found in the nose and oropharynx?
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
describe the lung microbiome
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
describe the urogenital tract
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
describe the stomach microbiota
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
describe the intestinal microbiome
contains feces mostly anaerobes most important microbiome in the colon does as much work as liver
60
why does everyone have a unique gut microbiome?
not the species that matter, but GENES bacteria can easily uptake genes from different species
61
what does the gut microbiome do?
regulate immune system extracts energy from food controls potential pathogens makes essential metabolites (vitamins, cofactors) improves intestinal function removes toxins and carcinogens
62
how do newborns acquire microbes?
fetus is STERILE vaginal is very close to gut get microbes from vaginal delivery breastfeeding: sugars feed different microbes interactions with environment
63
how can we lose microbes?
C-section delivery maternal antibiotics (ex. group B strep) formula feeding (lack of ogliosaccarides) indoor living excessive sanitation chemical preservation of food
64
when does the microbiome become an adult microbiome
within 3 years of birth
65
what is the missing microbiota hypothesis?
loss of microbiome in recent years due to changes in lifestyle losing microbes faster than we can replace them
66
what are ROBOGUTS?
a bioreactor used to emulate the human colonic environment host free system, culture the uncultureable
67
describe the compromised host
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
what makes the microbiota protective?
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
what is the gut-brain axis
signals between gut microbiome and brain, affects mood and behaviour AV's motto: "my microbes made me do it"
70
what happens when the microbial balance is compromised?
containment breaches: bacterial penetration niche disturbance: ex. exposure to xenobiotics extinction events: ex. bifita bacteria loss since hunter/gatherer times
71
describe obesity and the microbiome
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
what are gnotobiotic animals?
animals where the microbiota is known and defined includes germ-free animals (very expensive, valuable for research)
73
what abnormal physiology can be found in germ free animals?
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
who is David Vetter?
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)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions