Microbiomics/microbiota I Flashcards
What is meant with the ‘microbiota’?
Collection of micro-organisms
What is meant with the ‘metagenome’?
Collection of genomes of the microbiota
What is meant with the ‘microbiome’?
Community of microorganisms and host
On what DNA factor does metagenomics of bacteria often focus?
16S-ribosomal DNA
Why does human milk contain compounds that stimulate the growth of beneficial bacteria?
Humans have co-evolved with bacteria
How long does it take for the microbiota to establish?
~2 years
How can you easily intervene in the gut-microbiota? (3)
- Pre-biotics
- Pro-biotics
- Anti-biotics
What is symbiosis?
A close and long-term interaction between different organisms
On which two levels can ‘symbiosis’ be described?
- Individual microorganism vs. host
- Population of microorganisms vs. host
Which to symbiosis variants are there?
- Commensalism
- Mutualism
How do we call pathogenic microbes?
Pathobionts
What is meant with ‘dysbiosis’?
An imbalance/disruption in close and long term interactions
Which three ‘dysbiosis’ variants are there?
- Parasitism
- Amensalism
- Synecrosis
What is meant with ‘opportunism’?
Beneficial/commensal microbes may be pathogenic under certain circumstances
What is the keystone hypothesis?
Certain low-abundance microbial pathogens could remodel a normally benign microbiota into a dysbiotic one
An abundance of pathobionts is/is not always needed for dysbiosis
Is not
What are intrinsic factors that influence symbiotic vs. dysbiotic human microbiota? (2)
- Physiology
- Host genetics
Intrinsic factors: Name examples of physiology influencing symbiotic vs. dysbiotic human microbiota (2)
- Site
- Homeostasis (Temperature, pH, humidity, flushing)
Intrinsic factors: Name examples of host genetics influencing symbiotic vs. dysbiotic human microbiota (6)
- Metabolite absorption
- Cellular attachment site variation
- Host signaling molecules
- Hormones
- AMPs
- Host immune system
What are extrinsic factors influencing symbiotic vs. dysbiotic human microbiota? (8)
- Medical treatment/pesticides
- Food additives
- Recreational drugs
- Microplastics
- Industrial waste products
- Circadian rhythms
- Seasonal influences
- Aging
During the neonatal phase, there is a low/high a-diversity
Low
What is a-diversity?
Numbers of different bacterial species within an individual
During the neonatal phase, there is a low/high B-diversity
High
What is B-diversity?
Variation between individuals
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
High protein and animal fat diets lead to abundance of …
Bacteroides
High fiber diets lead to abundance of …
Prevotella
Mixed diets lead to abundance of …
Ruminococcus
What mechanisms could associate microbiota with obesity? (2)
- Mechanisms that increase energy uptake
- Mechanisms that decrease energy uptake
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
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
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
Autism spectrum disorder: Which GI disturbances do patients with ASD have? (4)
- Gut barrier disruption
- Constipation
- Abdominal pain
- Diarrhoea
C-section is/is not associated with ASD
Is
In what ways does the gut microbiota influence the gut-brain axis? (3)
- Production of neurotransmitters
- Production of SFCAs
- Production of tryptophan metabolites
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
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
What are follow-up experimental techniques after identification of an association? (3)
- In vitro
- In vivo
- Population-based functional studies
What is a problem with in vitro culturing?
Pure isolates of organisms needed –> bacteria evolved to thrive in presence of other bacteria (specialized niche)
Name two variants of difficult bacteria and what they need to thrive
- Some bacteria require (organ-)specific nutrients
- Some bacteria have community-dependences
What are two innovative culture models to be able to culture difficult bacteria?
- Diffusion growth chambers
- Continuous culture systems
For what purpose can ex-vivo tissue biopsies be used?
To culture bacteria that inhabit specific tissues
What is the problem with ex-vivo tissue biopsies?
No immune system -> tissue quickly broken down
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
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
Complex interactions between microbiota and … are needed (2)
- Immune system (innate, cellular)
- Cellular/tissues signaling at distance
Which models can be used to study the human microbiota? (8)
- Human
- NHP
- Pig
- Dog
- Rabbit
- Guinea pig
- Rat
- Mouse
Which of the model systems can be genetically modified? (4)
- Rabbit
- Guinae pig
- Rat
- Mouse
Why can’t you use zebrafish, nematodes and insects for microbiota studies?
Their microbiota are too different from mammals
What is coprophagy?
Herbivores eat their own droppings to increase nutrient intake -> affect microbiome
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
What are the limitations of mouse models for microbiota research? (2)
- Cross-talk between gut microbiota and host is host-specific
- Difficulties in simulation
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
Which two factors are required to prove associations in microbiota research?
- Large sample size
- Meta-studies
What is meant with ‘Kitome’?
Genetic material associated with kits and other laboratory product used during sample processing
What is a problem with the kitome?
Can influence the results of microbiota analysis
How can the kitome influence the results of microbiota analysis?
Introducing foreign sequences that don’t originate from the samples being studied
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
What is meant with ‘splashome’?
Environmental/laboratory contaminants that can be introduced to microbiome samples during collection, processing or analysis
What are solution for the influence of the splashome? (3)
- Negative controls
- Aseptic technique
- Laboratory decontamination procedures
