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microbiology 2 > microbes > Flashcards

microbes Flashcards

1
Q

microbiota

A

the micro organisms present in a specific site

bacteria, archaea, viruses, fungi, parasites

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2
Q

microbiome

A

microbial community that occupies a well defined habitat, including collective genome contained within the microbiota

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3
Q

prebiotic

A

a substrate that is selectively utilised by host microorganisms conferring a health benefit

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4
Q

probiotic

A

live microorganisms that, when administered in adequate amounts, confer a health benefit to the host

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5
Q

factors influencing microbial community composition

A
  • environmental parameters eg.O2 tension, pH, temperature, energy sources, toxins
  • interaction between microbes eg. cross feeding
  • rapid evolution and speciation (which may change species)
  • stochastic (unpredictable) forces eg. dispersal, dormancy
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6
Q

positive collaboration between microbes

A

cross-feeding

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7
Q

negative collaboration between microbes

A

eg. bacteria produce antibiotics (bacteriocins) that inhibits the growth of competing bacteria

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8
Q

dispersal

A

the way bacteria spread in communities eg. water spread, faecal oral etc.

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9
Q

intestinal microbiota and food intake

A

most complex polysaccharides are not digestible by the human gut, so they enter the colon and form a food source for the bacteria
bacteria (bifidobacterium and bactericides) have a diverse ability to break down different substrates and form secondary products

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10
Q

predictable changes in bacterial community composition with age

A

bacterial succession

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11
Q

dysbiosis

A

an imbalance in a microbial community associated with disease

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12
Q

blood of pathobionts

A

overgrowth of ambers of the commensal microbiota e.g enterobacteriaceae in inflammatory bowel disease

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13
Q

loss of commensals e. in antibiotic therapy

A

often accompanies by pathogen/pathobiont overgrowth eg. clostridiodes deficile associated with colitis
- replenishment may be effective in restoring balance

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14
Q

loss of divercity

A

low bacterial diversity has been documented in associstion with inflammatory bowel disease, HIV and type 1 diabetes mellitus

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15
Q

methods of measuring microbial communities

A

DNA, RNA, protein, metabolite

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16
Q

measuring microbiota using DNA

A

identifies which species are present - use next gen DNA sequencing

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17
Q

measuring microbiota RNA

A

measures abilities of microbiota by measuring activities and protein production - use RNA sequencing

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18
Q

measuring microbiota protein

A

measure proteins and produced by bacteria - mass spectrometry

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19
Q

measuring microbiota metabolites

A

measure metabolites produced by bacteria - mass spectroscopy

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20
Q

two types of sequencing microbiota

A

16s rRNA sequencing

whole metagenome shotgun sequencing

21
Q

whole meta genome shotgun sequencing

A

extract total nucleic acid and fragment into unordered sequence segments
massively parallel sequencing of fragments and assembly of sequence segments
results in a fully sequenced genome, but it is expensive and computationally complex

22
Q

16s rRNA sequencing

A
  • amplify a region of the bacterial chromosome, the 16s ribosomal RNA gene is used
  • gives read out of all the different sequence variants and their relative abundance
23
Q

why is the 16s ribosomal RNA gene used

A
  • present in all bacteria
  • phylogenetically informative, because it has variable regions which are characteristic for bacterial genera and species allowing a taxonomy to be assigned
  • also have conserved regions - consistent areas which the primers can bind to (bind to conserved regions which are the same in all bacteria, and amplify variable regions which differ between bacteria)
24
Q

measures of diversity

A
  • alpha diversity

- beta diversity

25
alpha diversity
measure of the mean diversity within a sample
26
beta diversity
measure of diversity between samples
27
hierarchical clustering
relative abundance of various taxa in each sample | distance matrices show phylogenetic relationships
28
principle coordinate analysis
visualising the level of similarity between samples in a dataset
29
diseases associated with dysbiotic microbiome
- atherosclerosis - obesity - inflammatory bowel disease - diabetes - liver disease - neurodegeneration - behaviour - metabolitesc syndrome - allergies - autoimmune disease
30
metabolic syndrome
a cluster of conditions that increase the risk of heart disease, stroke and diabetes includes high blood pressure, high blood sugar, excess body fat around the waist and abnormal cholesterol levels
31
diet low in animal fat and protein but high in plant fibres
microbiota related to metabolic health
32
diet high in animal fat and protein bu low in plant fibres
aberrant microbiota related to metabolic diseases
33
SCF
short chain fatty acids rpdocut of microbial degredation of indigestible polysaccharides positive health effects increase mucus expression and tight junction expression allowing enterocytes to adhere more closely and are less porous trigger the release of hormones from the epithelial cells - PYY and GLP-1 which regulate appetite and increase satiety
34
GLP-1
one of the hormones that increase satiety | promotor of glucose dependant insulin secretion
35
aberrant substances found in meat and eggs
L-carnitine and phosphatidylcholine are both constituents of red meat metabolised by intestinal bacteria, release trimethylamine (TMA)
36
TMA
trimethylamine | converted by liver enzymes to trimethylamine-N-oxide (TMAO), which promotes atherosclerosis
37
TMAO
metabolite of trimethylamine | promotes atherosclerosis
38
low mucus secretion
results in leaky epithelial barrier, which allows inflammatory PAMPS such as LPS (lipopolysaccharide) to cause metabolic endotoxaemia
39
metabolic endotoxaemia
heightened inflammatory and oxidant state often observed in obesity
40
hygiene hypothesis
- infections n early childhood prevent atopy in later life | - increased allergy in developed countries may be caused by high personal hygiene
41
PRR
pattern recognition receptors sense conserved microbial molecules PAMPS - found on both pathogens and commensals immune system sense commensals through PRRs under normal conditions, even though commensals separated from most immune cells by epithelial barriers
42
revision of the hygiene hypothesis
protection from allergic disease is mediated by early life exposure to commensals rather than pathogens
43
antibiotic therapy and the microbiota
although the composition of the gut microbiota varies between individuals, the community in each individual is relatively stable over time treatment with antibiotics has short term and long term effects on the microbiota
44
early life antibiotic therapy
associated with - increased type-1 diabetes - increased adiposity - increased risk of asthma in children
45
other members of the microbiota
fungi - can be identified and classified by sequencing a common nuclear ribosomal internal transcribed spacer region viruses - far more challenging to isolate and sequence due to the absence of conserved genes archea - human associated
46
methogenic archaea
amongst the most abundant microorganisms in the human gut | oral methogenic arch are associated with peridontal disease
47
factors impacting gut microbiota
- placenta - mode of delivery - gestational age - breast milk - geographical locations - family members - host interactions - material diet - weaning
48
untargeted microbiome directed interventions
- exercise - individualised nutrition - probiotics - faecal microbiota transplantation - probiotics - probiotics - synbiotics - postbiootics
49
targeted microbiome directed interventions
- bio-engineered commensals - drugs targetingg selected microbial metabolism - phage therapy - CRISPR-Cas9 based therapy

microbiology 2 (26 decks)

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