Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Microbiome > MHD2 Methods to characterise the microbiome > Flashcards

MHD2 Methods to characterise the microbiome Flashcards

1
Q

What factors determine what microbiota will be present?

A

nutrient availability
pH
temperature
atmospheric conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the taxonomic hierarchy mnemonic?

A

Delicious KP Crisps Often Follow Good Sex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the taxonomic hierarchy

A 
Domain – Bacteria
Kingdom – Bacteria 
Phylum – Proteobacteria
Class – Gammaproteobacteria
Order – Enterobacteriales
Family – Enterobacteriaceae
Genus – Escherichia
Species – Coli
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are the major phyla present in a human?

Angry flies probably fart badly

A 
Actinobacteria
Firmicutes
Proteobacteria
Fusobacteria
Bacterioidetes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Where are Actinobacteria found?

A

Nares (nostrils), Skin retroaurical crease (inner elbow), Skin antecubital fossa (ear)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Give two examples of Actinobacteria

A

o Corynebacterium

o Propionibacterium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Where are Proteobacteria found?

A

Saliva, Nares, Tongue, Tonsils, Skin antecubital fossa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Where are Bacterioidetes found?

A

Gut stool, Saliva, Gingiva (gums), Tonsils, Tongue

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Where are Fusobacteria found?

A

Saliva, Tongue, Tonsils

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Where are Firmicutes found?

A

Vagina, Gut stool, Saliva, Gingiva, Nares, Tongue, Tonsils

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Give 3 examples of Firmicutes

A

o Lactobacillus
o Staphylococcus
o Streptococcus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What methods can be used to characterise microbiota?

A

By isolating the individual prokaryotes, viruses, fungi and parasites and using phenotypic or genotypic methods for analysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Which bacterial genus of the Neisseria family CAN grow on Thayer-Martin medium?

A

Within the Neisseria family. N. gonorrhoeae and N. meningitis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Which bacterial genus of the Neisseria family CANNOT grow on Thayer-Martin medium?

A

N. flavescens, N. sicca, and N. subflava

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Which between N. gonorrhoeae and N. meningitidis cannot use maltose?

A

N. gonorrhoeae cannot

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What genotypic tests can be used to classify new species of bacteria?

A

16S rRNA gene sequencing is used to determine whether the new species shares less than 97% nucleotide sequence similarity with the 16S rRNA sequences of all the known species of bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is phylogeny the study of?

A

The evolutionary history of an organism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How does phylogeny studying work?

A

Molecular sequence data is used in order to determine which organisms share a common ancestor by examining genetic properties

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is systematics?

A

The study of the diversity of organisms and their relationships

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is used to accurately name species in two terms

A

binomial nomenclature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How was microbial characterisation first performed?

A

Cultivation methods: to distinguish 6 types of bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What conditions do obligate aerobic bacteria grow in?

A

same O2 level as the atmosphere

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What conditions do obligate anaerobic bacteria grow in?

A

complete absence of O2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What conditions do facultative anaerobic bacteria grow in?

A

presence or absence of O2, but prefer O2 presence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What conditions do micro-aerophile bacteria grow in?
low levels of O2
26
What conditions do capnophile bacteria grow in?
increased levels of CO2
27
What conditions do aero-tolerant bacteria grow in?
Equally well in O2 presence of absence
28
What other phenotypical tests are there?
- gram-staining - cell-shape - susceptibility to various antimicrobials - characterising cell-wall fatty acids - biochemical tests to observe the gases and short-chain fatty acids produced from sugar and glucose fermentation.
29
Rather than phenotypic methods, what is more accurate?
molecular-based methods should be used alongside phenotypic one
30
What is a combination of phenotypic and molecular based approaches called?
Polyphasic approach
31
Name two biochemical test kits
- API strips | - Biolog systems
32
How can you control which type of bacteria grow?
Culture media atmospheric conditions incubation temperature Media can be either agar or broth based and have varying nutrient compositions
33
Why are agar plates more useful than broth based?
Most bacteria can be isolated and each colony observed is potentially derived from a different single bacterium
34
How are bacteria cultured?
Mixed cultures are recovered from samples of microbiota and individual colonies are purified before identification using phenotypic and genotypic tests
35
What type of media is used to increase the probability of isolating specific bacterial groups?
Selective media
36
Give 2 examples of selective media
MacConkey agar | Man-Rogosa-Sharpe agar
37
What does MacConkey agar distinguish between?
Gram-negative and gram-positive as it inhibits gram-positive species
38
How does MacConkey agar inhibit gram-positive species?
it contains bile salts and crystal violet
39
What type of medium is MacConkey also known as? Why?
'Differential medium' | It can distinguish species that ferment lactose as it contains the pH indicator neutral red.
40
What can API 20E strips be used to identify?
Isolated colonies
41
Name three lactose-positive colonies and what colour they turn MacConkey agar
Escherichia, Enterobacter, Klebsiella | pink
42
Name three lactose-negative colonies, and what colour colonies do they have on MacConkey agar?
Salmonella, Proteus, Shigella | white
43
When is chromogenic agar used? why?
in clinical and commercial laboratories to distinguish bacteria which are closely-related, as it allows differentiation.
44
What type of medium is Columbia blood agar?
rich, non-selective medium
45
What types of microbes does Columbia blood agar allow to grow?
Theoretically allows all types of microbes to grow
46
What bacteria can you isolate with Columbia blood agar?
Allows the isolation of fastidious (fussy) aerobic and anaerobic bacteria with complex nutritional requires.
47
What type of agar is nutrient agar and what types of bacteria can it isolate?
It is an example of a non-selective medium that can isolate non-fastidious aerobes and anaerobes
48
How is chocolate agar produced?
By heating blood agar to cause the blood cells to burst and release NAD and heamin into the medium
49
What does chocolate agar allow to grow?
very fastidious bacteria, such as Neisseria meningitidis (i.e. the bacterium lacks enzymes necessary for lysing red blood cells)
50
The isolation and growth of anaerobic bacteria requires what specialist equipment?
- Hungate tubes - Sealed cabinet - Gas pack
51
How do hungate tubes aid the growing of anaerobic bacteria?
They are used to prepare anaerobic broth medium, anaerobic bacteria added using a needle inserted into the rubber stopper of the tube. The anaerobic environment in the tube is maintained by creating the rubber seal by heating.
52
How does a sealed cabinet | aid the growing of anaerobic bacteria?
It is used to isolate and grow obligately anaerobic and microaerophilic bacteria in anaerobic conditions
53
How does a gas pack aid the growing of anaerobic bacteria?
It is used to maintain atmospheric conditions in gas jars to isolate and grow facultative, oxygen-tolerant anaerobes, or capnophiles
54
What is the problem with studying bacteria from the gastrointestinal tract by collecting faecal samples?
these are not representative of the microbiota in the GI tract as a whole, specifically with regard to more proximal regions of the tract.
55
Explain why faecal samples are not representative of the gut microbiota as a whole? Give an example
The same strain of bacteria can metabolise substances differently when found in different regions of the GI tract, which is seen in the way E.coli in the faeces and the caecum have varying concentrations of their metabolites.
56
What bacteria dominates the vaginal microbiota?
Lactobacillus
57
Why may thrush of bacterial vaginosis develop?
If the vaginal microbiota environment is disrupted by antibiotics of infection
58
How can lactobacillus be isolated?
Using the selective medium Man-Rogosa-Sharpe agar
59
What species does the mouth contain?
Streptococci (aerobic or anaerobic) and Bacteroidetes (fastidious obligatory anaerobic bacteria.)
60
Who do Bacteroidetes survive in the mouth?
Bacteroidetes live in cavities and the gaps between teeth which are oxygen-free and contain food debris for the species to survive.
61
What allows Bacteroidetes and Proteobacteria to be present in the faeces?
the colon is an anaerobic, nutrient-rich environment
62
What type of anaerobic are proteobacteria?
facultative anaerobic
63
Why is the isolation of novel bacteria important?
in microbiology as gaps in our knowledge of microbial diversity and function can be filled by isolating as many bacteria and archaea as possible.
64
What do metagenomic studies do?
sequence and annotate all the genes in all the DNA of the microbiota
65
No function has been found for how many of the microbial genes cultivated?
50%
66
What % of the gut microbiome has been cultivated?
75%
67
What advances have been made in culturing technology
Multiple culturing conditions, matrix-assisted laser desorption/ionisation, time of flight mass spectrometry, and sequence analysis to identify bacterial species.
68
Why do housekeeping genes change far more slowly over time?
They are essential for the proper functioning of a cell
69
What house keeping gene is used to distinguish individual prokaryote species?
16S ribosomal ribonucleic acid gene
70
When were archaea distinguished from bacteria and how?
in 1977 through phylogenetic analysis of 16S rRNA sequences
71
Why are rRNAs known as molecular clocks?
rRNAs are responsible for assembling the ribosome therefore their sequences change over time as translation is essential for life
72
How can PCR primers be designed for use in diversity studies?
There are large databases of 16S rRNA gene sequences
73
How do you ensure identification of bacteria up to genus level?
use PCR primers that flank the V3 and V4 variable regions as they amplify up to 450 nucleotides
74
Name a machine that can be used to sequence PCR products
The Illumina Miseq machine
75
What software can you use to process and analyse the PCR sequence products?
QIIME2, mothur, DADA2, phyloseq
76
When doing 16S rRNA sequencing, do you need to isolate the bacteria into pure cultures?
No
77
What are the pros of 16S rRNA sequencing?
inexpensiveness, small quantity of starting material required and availability of large public databases for analysis
78
What are the cons of 16S rRNA sequencing?
Bias: as many bacteria have more than one copy of 16S rRNA genes. Sample handling: atmospheric conditions and temperature must be maintained. Storage: of the samples by freezing can lead to the loss of Bacteroidetes-associated sequences and freeze-thaw cycles will affect the microbial composition present in the sample DNA extraction methods: can affect the results as bead-beating must be involved in order to minimise the underestimation of gram-positive populations.
79
Too vigorous an extraction method can cause what?
damage to genes
80
How can PCR biases arise?
``` differences in the specificity of the polymerases interfering substances contaminated reagents artefacts differential amplification ```
81
Why are negative controls integral in microbiota profiling studies?
DNA extraction kits have also been found to not be sterile, so can be a source of contamination
82
When are negative controls especially important during microbiota profiling studies?
In studies involving low-biomass samples from the nose, skin, lungs and vagina

Microbiome (10 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions