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Medical Microbiology > Gut flora and the Microbiome > Flashcards

Gut flora and the Microbiome Flashcards

1
Q

What is genomics?

A

Whole cell gene contents

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2
Q

What is transcriptomics?

A

Whole cell gene expression

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3
Q

What is proteomics?

A

Whole cell protein content

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4
Q

What is metabolomics?

A

Whole cell metabolite content

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5
Q

What is the microbiome?

A

A characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties
Refers to both microorganisms involved and their theatre of activity

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6
Q

What is the microbiota?

A

Ecological community of commensal and pathogenic microorganisms
Includes bacteria, archaea, protists, fungi and viruses

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7
Q

What is a biome?

A

A reasonably well-defined habitat which has distinct physiochemical properties

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8
Q

What is the weight of the human microbiome?

A

70kg

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9
Q

What is the weight of the bacteria microbiome?

A

1-3kg

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10
Q

Describe the human microbiome

A

Not only 1 microbiome
Each area/part of the body has a distinct microbiome with different compositions
Unique to each individual (even twins)

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11
Q

What may play a role in determining the microbiome?

A

Host genetics

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12
Q

Describe the gut microbiome

A

Significant variation between healthy individuals
Integral to host digestion
Approximately 400 species
Diversity throughout GI tract - changing pH, adhesion, nutrients

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13
Q

How can species be categorised in the gut microbiome?

A

Autochthonous
Allochthonous

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14
Q

Describe autochthonous species

A

Indigenous/resident
Colonise GI tract

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15
Q

Describe allochthonous species

A

Transient/passenger
Only colonise under abnormal conditions

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16
Q

What do the species in the gut microbiome do?

A

Provide unique and specific enzymes and biochemical pathways
Competitive exclusion of pathogens, protecting the host

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17
Q

What is the diagnostic role of the gut microbiome?

A

Can classify individuals as lean or obese with >90% accuracy
Changes in gut microbiome have been associated with multiple human illnesses - IBS, depression, cancer
Early life gut microbiomes linked to development of allergic conditions eg. asthma

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18
Q

How is the gut microbiome targeted for helping IBS?

A

Altering microbiota through dietary changes, probiotics or antibiotics can show benefit

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19
Q

What is the microbiota-gut-brain axis?

A

Network of connections, crucial to homeostasis
Changes in the gut may be linked to symptom perception in the brain

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20
Q

What factors can influence the brain?

A

Metabolic and immunological factors

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21
Q

How does the microbiota modulate behaviour?

A

Short chain fatty acids
Modulation of neuroendocrine system
Bacteroides, bifidobacterium can producegamma-aminobutyric acid (GABA)

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22
Q

What happens in IBS?

A

Inflammation in the gut, environmental and genetic risk factors
Alterations can be seen in gut microbiota

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23
Q

How does colorectal cancer differ from IBS?

A

Higher proportion of Pseudomonas. helicobacer and acinetobacter
Lower richness of beneficial bacteria eg. butyrate producing bacteria
Reduced abundance of Bifidobacterium species

24
Q

What interventions can be used for gut microbiome?

A

Prebiotics - non-digestable food ingredient to promote growth of beneficial organism
Probiotics - beneficial organisms
Synbiotics - micture of prebiotics and probiotics

25
Q

What is most commonly in probiotics?

A

Lactobacillus
Bifidobacterium

26
Q

What is an intervention that has proven to be effective for gut microbiome?

A

Faecal microbiota transplant (FMT) - example of probiotics

27
Q

What is antibiotic associated diarrhoea?

A

Related to overgrowth of C.diff

28
Q

What is susceptibility to C.diff infection associated with?

A

Decreased microbiota diversity

29
Q

What cures C.diff infection?

A

FMT

30
Q

How is FMT used to treat CDI?

A

Healthy donor, filter sample and administer by colonoscopy

31
Q

What happens to the gut microbiota after FMT?

A

Increased diversity
Increased abundance of various Firmicutes and Bacteroides
Decreased abundance of Proteobacteria

32
Q

How are psychiatric disease related to gut microbiome?

A

Dysbiosis increases translocation of gut bacteria into lymphoid tissue
Provokes an immune response
Activation of vagus nerve and spinal afferent neurons

33
Q

What are other associations to the gut microbiome?

A

Food allergies
Asthma
Obesity
Diabetes
Rheumatoid arthritis
CVD
Liver diseases

34
Q

What are technological approaches to assess the microbiome?

A

Targeted PCR amplification - 16S rRNA bacteria, internal transcribed spacer (ITS) 18S rRNA eukaryotes
Whole genome shotgun sequencing

35
Q

What is 16S rRNA?

A

Component of 30S small subunit of prokaryotic ribosome

36
Q

Describe prokaryotic ribosome

A

50S subunit - 5S, 23S
30S subunit - 16S

37
Q

Describe eukaryotic ribosome

A

60S subunit - 5S, 28S
40S subunit - 18S

38
Q

How is 16S targeted PCR amplification done?

A

Sample collection
DNA extraction
16S PCR amplification of whole sample
PCR products are sequenced
DNA sequences are analysed

39
Q

What 16S databases can be used?

A

Greengenes
Silva
RDP

40
Q

What are the 16S databases used for?

A

To separate samples into species/genus

41
Q

What is an operational taxonomic unit?

A

Used to classify groups of closely related individuals

42
Q

How are OTUs done?

A

Sequences are clustered according to their similarity

43
Q

What are the 2 types of diversity?

A

Alpha
Beta

44
Q

What is alpha diversity?

A

Diversity within a sample

45
Q

What is beta diversity?

A

Diversity between samples

46
Q

How can alpha diversity be measured?

A

Species richness
Species diversity

47
Q

What is species richness?

A

OTU count
Measure of how many different species can be detected in a microbial system

48
Q

How is species diversity measured?

A

Shannon index
Measure of how the microbes are balanced to each other and if there is species evenness (similar abundance level) or if some species dominate others

49
Q

How is beta diversity measured?

A

Bray-Curtis dissimilarity = based on abundance
Jaccard distance = based on presence or absence of species
UniFrac = based on phylogenetic trees

50
Q

How is a variable region chosen for 16S targeted PCR amplification?

A

Amplicon length
Phylogenetic signal

51
Q

What needs to be considered when deciding what controls to use?

A

16S rRNA gene found in all bacteria
Method is sensitive to contamination - environment, operator, reagents
Contamination is more important to consider for low biomass samples

52
Q

How can contamination be mitigated?

A

Randomise samples
Note batch numbers of reagents
Sequence negative controls

53
Q

How does whole genome shotgun workflow work?

A
54
Q

What are problems with Whole genome shotgun workflow?

A

Host cells often in excess in sample
No amplification step to enrich for bacterial DNA
Sample dependent

55
Q

How can enrichment be done without amplification?

A

Pre-extraction - differential lysis of mammalian cells, enrich for intact microbial cells, potential bias towards gram-positive bacteria
Post-extraction - enzymatic degradation of methylated molecules targets mammalian DNA, bias against AT rich bacterial genomes

Medical Microbiology (23 decks)

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