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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
Q

What is a disadvantage of population studies with respect to the microbiota?

A

Perhaps only applies to the localized geographic area and the specific time period they were carried out

26
Q

High protein and animal fat diets lead to abundance of …

A

Bacteroides

27
Q

High fiber diets lead to abundance of …

A

Prevotella

28
Q

Mixed diets lead to abundance of …

A

Ruminococcus

29
Q

What mechanisms could associate microbiota with obesity? (2)

A
  • Mechanisms that increase energy uptake
  • Mechanisms that decrease energy uptake
30
Q

Obesity: What are examples of mechanisms that increase energy uptake? (4)

A
  • Increase in short-chain fatty acids
  • Increase in nutrient transport
  • Increase in fermentation enzymes
  • Increases interspecies H2 transfer
31
Q

Obesity: What are examples of mechanisms that decrease energy expenditure? (6)

A
  • Increase lipid synthesis and storage
  • Decrease bile acids
  • Decrease uncoupled mitochondrial function
  • Decrease thermogenesis
  • Decrease white adipose tissue browning
  • Decrease catabolic processes
32
Q

Some bacterial species are recognized as potential biomarkers for IBD in certain areas. Name these areas (4)

A
  • Screening and monitoring
  • Assessing disease activity
  • Predicting response to treatment
  • Predicting recurrence
33
Q

Autism spectrum disorder: Which GI disturbances do patients with ASD have? (4)

A
  • Gut barrier disruption
  • Constipation
  • Abdominal pain
  • Diarrhoea
34
Q

C-section is/is not associated with ASD

A

Is

35
Q

In what ways does the gut microbiota influence the gut-brain axis? (3)

A
  • Production of neurotransmitters
  • Production of SFCAs
  • Production of tryptophan metabolites
36
Q

What can be the negative effects of microbes on cancer development? (5)

A
  • Chronic inflammation
  • Impair of anti-tumour immune function
  • Induction of oncolytic transcriptional activity
  • Production of genotoxins
  • Local ROS production
37
Q

What are Koch’s postulates with respect to microbiota? (4)

A
  • 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
Q

What are follow-up experimental techniques after identification of an association? (3)

A
  • In vitro
  • In vivo
  • Population-based functional studies
39
Q

What is a problem with in vitro culturing?

A

Pure isolates of organisms needed –> bacteria evolved to thrive in presence of other bacteria (specialized niche)

40
Q

Name two variants of difficult bacteria and what they need to thrive

A
  • Some bacteria require (organ-)specific nutrients
  • Some bacteria have community-dependences
41
Q

What are two innovative culture models to be able to culture difficult bacteria?

A
  • Diffusion growth chambers
  • Continuous culture systems
42
Q

For what purpose can ex-vivo tissue biopsies be used?

A

To culture bacteria that inhabit specific tissues

43
Q

What is the problem with ex-vivo tissue biopsies?

A

No immune system -> tissue quickly broken down

44
Q

What are the advantages of in vitro organdies/ex vivo tissue biopsies? (4)

A
  • Free from external influences and confounding factors
  • More detailed and precise analyses
  • Reduced ethical concerns
  • Standardization & reproducibility
45
Q

What are limitations of in vitro organdies/ex-vivo tissue biopsies? (4)

A
  • Lack of complex interactions
  • Maintenance limits
  • Require specialized equipment and expertise
  • Essential to validate in animal or human studies
46
Q

Complex interactions between microbiota and … are needed (2)

A
  • Immune system (innate, cellular)
  • Cellular/tissues signaling at distance
47
Q

Which models can be used to study the human microbiota? (8)

A
  • Human
  • NHP
  • Pig
  • Dog
  • Rabbit
  • Guinea pig
  • Rat
  • Mouse
48
Q

Which of the model systems can be genetically modified? (4)

A
  • Rabbit
  • Guinae pig
  • Rat
  • Mouse
49
Q

Why can’t you use zebrafish, nematodes and insects for microbiota studies?

A

Their microbiota are too different from mammals

50
Q

What is coprophagy?

A

Herbivores eat their own droppings to increase nutrient intake -> affect microbiome

51
Q

What are the advantages of mouse models for microbiota research? (6)

A
  • 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
Q

What are the limitations of mouse models for microbiota research? (2)

A
  • Cross-talk between gut microbiota and host is host-specific
  • Difficulties in simulation
53
Q

What factors can be difficult to simulate in a mouse model for microbiota research? (6)

A
  • Human polygenic disease
  • Tissue healing -> vaginal/caesarian
  • Feeding -> breast/bottle
  • Diet
  • Medical history
  • Social activities
54
Q

Which two factors are required to prove associations in microbiota research?

A
  • Large sample size
  • Meta-studies
55
Q

What is meant with ‘Kitome’?

A

Genetic material associated with kits and other laboratory product used during sample processing

56
Q

What is a problem with the kitome?

A

Can influence the results of microbiota analysis

57
Q

How can the kitome influence the results of microbiota analysis?

A

Introducing foreign sequences that don’t originate from the samples being studied

58
Q

What are solutions for kitome influence on the results of microbiota research? (3)

A
  • Negative controls
  • Collecting data on previous contaminants
  • Buy guaranteed contaminant-free kits
59
Q

What is meant with ‘splashome’?

A

Environmental/laboratory contaminants that can be introduced to microbiome samples during collection, processing or analysis

60
Q

What are solution for the influence of the splashome? (3)

A
  • Negative controls
  • Aseptic technique
  • Laboratory decontamination procedures

I&I SC2 (13 decks)

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