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I&I SC2 > Microbiomics/microbiota I > Flashcards

Microbiomics/microbiota I Flashcards

1
Q

What is meant with the ‘microbiota’?

A

Collection of micro-organisms

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2
Q

What is meant with the ‘metagenome’?

A

Collection of genomes of the microbiota

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3
Q

What is meant with the ‘microbiome’?

A

Community of microorganisms and host

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4
Q

On what DNA factor does metagenomics of bacteria often focus?

A

16S-ribosomal DNA

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5
Q

Why does human milk contain compounds that stimulate the growth of beneficial bacteria?

A

Humans have co-evolved with bacteria

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6
Q

How long does it take for the microbiota to establish?

A

~2 years

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7
Q

How can you easily intervene in the gut-microbiota? (3)

A
  • Pre-biotics
  • Pro-biotics
  • Anti-biotics
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8
Q

What is symbiosis?

A

A close and long-term interaction between different organisms

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9
Q

On which two levels can ‘symbiosis’ be described?

A
  • Individual microorganism vs. host
  • Population of microorganisms vs. host
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10
Q

Which to symbiosis variants are there?

A
  • Commensalism
  • Mutualism
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11
Q

How do we call pathogenic microbes?

A

Pathobionts

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12
Q

What is meant with ‘dysbiosis’?

A

An imbalance/disruption in close and long term interactions

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13
Q

Which three ‘dysbiosis’ variants are there?

A
  • Parasitism
  • Amensalism
  • Synecrosis
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14
Q

What is meant with ‘opportunism’?

A

Beneficial/commensal microbes may be pathogenic under certain circumstances

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15
Q

What is the keystone hypothesis?

A

Certain low-abundance microbial pathogens could remodel a normally benign microbiota into a dysbiotic one

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16
Q

An abundance of pathobionts is/is not always needed for dysbiosis

A

Is not

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17
Q

What are intrinsic factors that influence symbiotic vs. dysbiotic human microbiota? (2)

A
  • Physiology
  • Host genetics
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18
Q

Intrinsic factors: Name examples of physiology influencing symbiotic vs. dysbiotic human microbiota (2)

A
  • Site
  • Homeostasis (Temperature, pH, humidity, flushing)
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19
Q

Intrinsic factors: Name examples of host genetics influencing symbiotic vs. dysbiotic human microbiota (6)

A
  • Metabolite absorption
  • Cellular attachment site variation
  • Host signaling molecules
  • Hormones
  • AMPs
  • Host immune system
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20
Q

What are extrinsic factors influencing symbiotic vs. dysbiotic human microbiota? (8)

A
  • Medical treatment/pesticides
  • Food additives
  • Recreational drugs
  • Microplastics
  • Industrial waste products
  • Circadian rhythms
  • Seasonal influences
  • Aging
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21
Q

During the neonatal phase, there is a low/high a-diversity

A

Low

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22
Q

What is a-diversity?

A

Numbers of different bacterial species within an individual

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23
Q

During the neonatal phase, there is a low/high B-diversity

A

High

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24
Q

What is B-diversity?

A

Variation between individuals

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25
What is a disadvantage of population studies with respect to the microbiota?
Perhaps only applies to the localized geographic area and the specific time period they were carried out
26
High protein and animal fat diets lead to abundance of ...
Bacteroides
27
High fiber diets lead to abundance of ...
Prevotella
28
Mixed diets lead to abundance of ...
Ruminococcus
29
What mechanisms could associate microbiota with obesity? (2)
- Mechanisms that increase energy uptake - Mechanisms that decrease energy uptake
30
Obesity: What are examples of mechanisms that increase energy uptake? (4)
- Increase in short-chain fatty acids - Increase in nutrient transport - Increase in fermentation enzymes - Increases interspecies H2 transfer
31
Obesity: What are examples of mechanisms that decrease energy expenditure? (6)
- Increase lipid synthesis and storage - Decrease bile acids - Decrease uncoupled mitochondrial function - Decrease thermogenesis - Decrease white adipose tissue browning - Decrease catabolic processes
32
Some bacterial species are recognized as potential biomarkers for IBD in certain areas. Name these areas (4)
- Screening and monitoring - Assessing disease activity - Predicting response to treatment - Predicting recurrence
33
Autism spectrum disorder: Which GI disturbances do patients with ASD have? (4)
- Gut barrier disruption - Constipation - Abdominal pain - Diarrhoea
34
C-section is/is not associated with ASD
Is
35
In what ways does the gut microbiota influence the gut-brain axis? (3)
- Production of neurotransmitters - Production of SFCAs - Production of tryptophan metabolites
36
What can be the negative effects of microbes on cancer development? (5)
- Chronic inflammation - Impair of anti-tumour immune function - Induction of oncolytic transcriptional activity - Production of genotoxins - Local ROS production
37
What are Koch's postulates with respect to microbiota? (4)
- Must be found in abundance in suffering organisms, but not in healthy ones - Microorganism isolation from diseases organism and grown in pure culture - Cultured organism should cause disease - Re-isolation
38
What are follow-up experimental techniques after identification of an association? (3)
- In vitro - In vivo - Population-based functional studies
39
What is a problem with in vitro culturing?
Pure isolates of organisms needed --> bacteria evolved to thrive in presence of other bacteria (specialized niche)
40
Name two variants of difficult bacteria and what they need to thrive
- Some bacteria require (organ-)specific nutrients - Some bacteria have community-dependences
41
What are two innovative culture models to be able to culture difficult bacteria?
- Diffusion growth chambers - Continuous culture systems
42
For what purpose can ex-vivo tissue biopsies be used?
To culture bacteria that inhabit specific tissues
43
What is the problem with ex-vivo tissue biopsies?
No immune system -> tissue quickly broken down
44
What are the advantages of in vitro organdies/ex vivo tissue biopsies? (4)
- Free from external influences and confounding factors - More detailed and precise analyses - Reduced ethical concerns - Standardization & reproducibility
45
What are limitations of in vitro organdies/ex-vivo tissue biopsies? (4)
- Lack of complex interactions - Maintenance limits - Require specialized equipment and expertise - Essential to validate in animal or human studies
46
Complex interactions between microbiota and ... are needed (2)
- Immune system (innate, cellular) - Cellular/tissues signaling at distance
47
Which models can be used to study the human microbiota? (8)
- Human - NHP - Pig - Dog - Rabbit - Guinea pig - Rat - Mouse
48
Which of the model systems can be genetically modified? (4)
- Rabbit - Guinae pig - Rat - Mouse
49
Why can't you use zebrafish, nematodes and insects for microbiota studies?
Their microbiota are too different from mammals
50
What is coprophagy?
Herbivores eat their own droppings to increase nutrient intake -> affect microbiome
51
What are the advantages of mouse models for microbiota research? (6)
- Can be used for interventions not possible in humans - Comphrensive knowledge of mouse genome available - Low cost of maintenance - Omnivorous - KO mouse can be created to study pathways - Inbred
52
What are the limitations of mouse models for microbiota research? (2)
- Cross-talk between gut microbiota and host is host-specific - Difficulties in simulation
53
What factors can be difficult to simulate in a mouse model for microbiota research? (6)
- Human polygenic disease - Tissue healing -> vaginal/caesarian - Feeding -> breast/bottle - Diet - Medical history - Social activities
54
Which two factors are required to prove associations in microbiota research?
- Large sample size - Meta-studies
55
What is meant with 'Kitome'?
Genetic material associated with kits and other laboratory product used during sample processing
56
What is a problem with the kitome?
Can influence the results of microbiota analysis
57
How can the kitome influence the results of microbiota analysis?
Introducing foreign sequences that don't originate from the samples being studied
58
What are solutions for kitome influence on the results of microbiota research? (3)
- Negative controls - Collecting data on previous contaminants - Buy guaranteed contaminant-free kits
59
What is meant with 'splashome'?
Environmental/laboratory contaminants that can be introduced to microbiome samples during collection, processing or analysis
60
What are solution for the influence of the splashome? (3)
- Negative controls - Aseptic technique - Laboratory decontamination procedures

I&I SC2 (13 decks)

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