Microbiomes etc Flashcards
1
Q
- What is a microbiome?
A
a. The The entire habitat, including the microbes (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions
2
Q
- What is Microbiota?
A
a. Bacteria, archaea, fungi, protists, and algae
3
Q
- What is a biome?
A
a. A reasonably well defined habitat which has distinct bio-physio-chemical properties
4
Q
- What microbial structural elements are there (4)?
A
a. Proteins/peptides
b. Lipids
c. Polysaccharides
d. Nucleic acids : DNA and RNA
5
Q
- What type of mucleic acid material is there within the microbiome?
A
a. DNA?RNA
b. Mobile genetic elements
c. Viruses/phages relic DNA
6
Q
Why do bacteria act differently on agar then in the eviroment
A
this is not how they behave normally so this will cause their phenotypes to change
7
Q
- What are the internal/external structural elements of the microbiome?
A
a. Environmental conditions
8
Q
- What microbial metabolites are there within a microbiome?
A
a. Signalling molecules
b. Toxins
c. Organic molecules
9
Q
- Why is using the term microflora incorrect and you should use microbiota?
A
a. The assemblage of microorganisms presents within a defined environment. Sometimes microflora is used but as microorganisms are not plants this is wrong.
10
Q
- What are metataxonomics?
A
a. High-throughput processing used to characterise the entire microbiota. Typically uses marker genes such as the 16S rRNA gene.
11
Q
- What is a Metagenome?
A
a. The collection of genomes and genes from the members of the microbiota.
12
Q
- What is metabolomics/metabonomics?
A
a. The collection of metabolite profiles within a single sample/location and how they are impacted by external factors.
13
Q
- What are meta transcriptomics?
A
a. The analysis of a suite of messenger RNA from a sample/system. Gives information on the regulation and expression of genes.
14
Q
- What are Metaproteomics?
A
a. Large-scale characterisation of the entire protein complement of a sample at a given time.
15
Q
- What percentage of microbes can be cultured?
A
a. 1-5%
16
Q
- What is a biofilm?
A
a. A biofilm is a structured community of microbial cells enclosed in a self-produced extracellular polymeric matrix (EPS) and adherent to inert or living surfaces
17
Q
- What do Pseudomonas fluorescens biofilms that grow on the surface of plant roots prevent?
A
a. The growth of fungal pathogens
18
Q
- What are the four main benefits to biofilms?
A
a. Protection
b. Stability
c. Nutrients
d. Community
19
Q
- How do biofilms create protection (6)?
A
a. Antibiotics
b. Toxins
c. Antibodies
d. Phage attack
e. Predation
f. Environment
20
Q
- How do biofilms create stability (3)?
A
a. Stable growth
b. Environment
c. ‘normal’ growth
21
Q
- How do biofilms aid in nutrients (5)?
A
a. Concentration
b. Trace compounds
c. Waste products
d. Reduces gene range
e. Cooperation
22
Q
- How does community affect biofilms (3)?
A
a. Gene transfer
b. Signal transduction
c. Quorum sensing
23
Q
- How do biofilms develop (3)?
A
a. Adhesion
b. Maturation
c. Dispersion
24
Q
- What type of structure does Corynebacterium and cocci in plaque form?
A
a. Corncob
25
24. When there is low density of microbial cells there is ________ and when there is high density of cells then there is _________ behaviour.
a. Individual
| b. Group
26
25. What are the three types of Quorum activity?
a. Quorum sensing
b. Quorum sensing competitive inhibition
c. Quorum quenching
27
26. Biofilms can either be ___________ or _________.
a. Cooperative
| b. Competitive
28
27. What ways can biofilms be studied (7)?
a. Microscopy
b. Cultoromics
c. Metabarcoding
d. Metagenomics
e. Metatranscriptomics
f. Metaproteomics
g. Metabolomics
29
28. What two scales are to be considered when studying biofilms?
a. Temporal
| b. Spatial
30
29. What is the holobiont?
a. is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit
31
30. What disease states are affected by microbiomes (3)?
a. Dysbiosis
b. Low diversity
c. Variable
32
31. What healthy states are affected by microbiomes?
a. Eubiosis
b. High diversity
c. Uniform
33
32. What are healthy interactions with microbiomes?
a. Obligate symbiosis
b. Vertical inheritance
c. Metabolic collaborations
34
33. What is antagonistic coevolution?
a. Parasitic
| b. Diseased state
35
34. What is mutulatistic coevolutoion?
a. Positive interactions healthy state
36
35. There are 5 types of microbial holobionts, one is a pathogen, one a symbiont. What are the other three?
a. Opputunistic pathogen
b. Pathobionts
c. Commensals
37
1. What is genomics the study of?
a. Genes
38
2. What are transcriptomics the study of?
a. mRNA
39
3. What are proteomics the study of?
a. Proteins
40
4. What are metabolomics the study of?
a. Metabolites
41
5. What is the definition of metabolomics?
a. The study of chemical processes involving live metabolites, the small molecules substrates, intermediates, and products of metabolism within a system. Typically requires identification and quantification of all metabolites.
42
6. What is metabolite fingerprinting?
a. The creation of a spectral fingerprint from a sample. This doesn’t involve the identification or quantification of metabolites
43
7. What is metabolite profiling?
a. Focus on the analysis of a large group of metabolites that is either related to a specific metabolic pathway or a class of compounds.
44
8. What is targeted metabolomics?
a. Involved the quantitative measurement of known metabolites from defined metabolic process, such as amino acids.
45
9. What is metabonomics?
a. The study of how the metabolome of an organism is impacted by external factors such as diet , environment, toxins etc.
46
10. What does NMR stand for?
a. Nuclear magnetic resonance
47
11. Are the sample that enter a mass spec and NMR dry or wet?
a. Dry
48
12. What type of container are samples of NMR placed in?
a. Glass
49
13. What is a “Sweep” in NMR?
a. When the magnets create the alignment
50
14. What is a “Shift” in NMR?
a. The alignment of the atoms after a sweep takes place
51
15. What type of solvents must the NMR and Mass spec samples be mixed with?
a. Polar
52
16. What is an isotope?
a. Same atom different neutrons
53
17. What makes isotopes useful for NMR?
a. They have a unique spin
54
18. What is precession in relation to NMR?
a. the change of spin induced from the magnets in the NMR
55
19. What effect do the electron clouds of a molecule have on the effects of spinning in a NMR?
a. The higher electron density the higher the shielding
56
20. How is the spin in the NMR calculated?
a. The amount of electric current created in the coil
57
21. What is a frequency spectrum (NMR)?
a. The frequency assigned to a specific isotopes electric current
58
22. What is a chemical shift (NMR)?
a. The differences in the chemical structure of the nuclei
59
23. What is J-coupling (NMR)?
a. When electrons from neighbouring atoms affects another atom
60
24. What are the benefits of NMR(4)?
a. Highly reproducible results
b. Non-destructiuve analysis of samples
c. Ideal for structural characterisation
d. Relatively cheap to run
61
25. What are the drawbacks of NMR (4)?
a. Limited sensitivity for metabolite
b. Limited sensitivity reduces range of measurable metabolites
c. Very expensive capital expenditure for equipment
62
What are samples kept at -80C?
Prevent further cell metabolism ans keep at sample taking state
63
What are proteins to big to be use in?
Mass Spec
64
26. What does Mass Spec analyse?
a. Analysis of ions within a vacuum
| b. Measure the Mass of the different ions
65
27. How are the ions separated in a Mass Spec?
a. To a mass to charge ratio
66
28. What do the Quadropoles then use to filter?
a. Electric charge
67
29. What separates based on speed of travel?
a. Time of flight
68
30. Mass Spec gives us Mass-to-Charge (____/____) against _______
a. M/Z
| b. Intensity
69
31. What are the different types of measuring in mass spec?
a. Direct infusion MS
b. Matrix Assisted Laser desorption Ionisation MS
c. Liquid Chromatography MS
d. Gas Chromatography MS
e. Ambient Ionisation MS
70
32. What is direct infusion Mass Spec and what are the steps(3)?
a. Sample extracted into solvent
b. Extract injected directly into MS over two minutes
c. Typically linked to an electrospray ionisation
71
33. What is considered the easiest method of Mass spec?
a. Direct infusion MS
72
34. What is the downfall of Direct infusion MS?
a. Gives a limited fingerprint
73
35. What is Matrix Assisted Laser desorption Ionisation MS and what are the steps (5)?
a. Sample is spotted onto a stainless steel plate
b. A matrix is added on top and provides protons
c. Matrix adsorbs energy from lases (UV or Nd:YAG)
d. This results in an energy ‘cloud’ of ions to erupt
e. Analysed using the time-of-flight
74
36. What is time of flight?
a. Time of flight (ToF) is the measurement of the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.) to travel a distance through a medium.
75
37. What is Liquid Chromatography MS and what are the steps(3)?
a. Samples contents are separated first
b. Molecules move through columns at different speeds
c. Created a 3D data set based on retention times
76
38. What is Gas chromatography and the steps (4)?
a. Samples are extracted and derivatised so that they are volatile
b. The samples are then heated and enter into a column inside an oven
c. Different metabolites progress through at different speeds
d. Created a 3D data set
77
39. What is ambient ionisation MS and what are the steps(4)?
a. Generation of ions in a standard atmosphere
b. Ions captured and transferred through a tube hit by a laser
c. Aerosol is transferred to solvent matrix
d. Hits collision surface
78
40. What are the benefits of ambient ionisation MAS?
a. Opens up a wide range of application areas
b. Allows analysis in almost real time
c. Mainy different AIM varieties
79
41. What is the Ambient ionisation MS used in queens?
a. REIMS
80
42. What types of Mass Spec Imaging are there?
a. Maldi
b. Desi
c. SIMS
81
43. What is a MALDI?
a. Uses a laser beam
| b. Desorbed ionized singly charged molecules
82
44. What is a DESI?
a. Charged solvent droplets
| b. ESI-like ionised molecules
83
45. What is a SIMS?
a. Primary Ion beam
| b. Secondary ions
84
46. How do we analyse metabolomics data?
a. Normalization transformation scaling
b. Multivariate analysis
c. Univariate analysis
d. Database searching
e. Biochemical pathways
85
47. What is tandem Mass Spec?
a. The targeted metabolomics experiment with tandem mass spectrometry measures defined ion transitions from known metabolites
86
Is NMR reproducable?
YES, very godd reproduction
87
Is Mass spec a sensitive measure?
YES, it cries A LOT
88
1. What is the definition of health at its most basic level?
a. The absence of disease
89
2. What is personalised health care?
a. Using metabolomic footprints to understand health requirements
90
3. What are lung cancer symptoms (8)?
a. A cough that has lasted for 2-3 weeks
b. Cough not getting better but worse
c. Chest infections keep coming back
d. Coughing up blood
e. Ache when breathing and coughing
f. Persistent breathlessness
g. Persistent tired and lack of energy
h. Loss of appetite and unexplained wight gain
91
4. How can metabolomics be used to diagnose lung cancer?
a. Using sputum tests
| b. Identify biomarkers
92
5. What is the accuracy of detecting lung cancer using metabolomics?
a. 80%
93
6. What do smokers produce that healthy people do not?
a. Sputum
94
7. What is gestational diabetes?
a. Diabetes when pregnant
95
8. How many pregnant women are affected by gestational diabetes?
a. 10%
96
9. What puts you at risk of gestational diabetes?
a. BMI over 30
b. Prevoulsy had a baby that weighed more then 4.5 kilos (10lbs)
c. Had gestational dibates before
d. Parent or sibling has disbetes
e. Non-white
97
10. What does aetiology meam?
a. The cause, set of causes, or manner of causation of a disease or condition
98
11. What is a heterogeneous medical condition?
a. medical term referring to a medical condition with several etiologies (root causes), such as hepatitis or diabetes.
99
12. What is an Exposome?
a. The exposome can be defined as the measure of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources. Understanding how exposures from our environment, diet, lifestyle, etc.
100
13. What is breath analysis using metobolomics good for?
a. Lung cancer
101
14. What can breath analysers detect?
a. Volatile compounds
| b. Give non-invasive biomarkers for the disease
102
15. What is a major issue with breath analysis?
a. They are not very reproducible
103
16. What can nutritional metabolomics be used for?
a. Understand the complexity of diet
b. Correlation of diet and health
c. Determine what a person has eaten
104
17. What is a benefit of metabelomics complared to traditional nutritional studies?
a. Prevents the requirement for diet records
105
18. How is sampling conducted for nnutritional metabolomics?
a. Urine
| b. Shite
106
19. Ways to ensure a robust experimental design in metabolomics (4).
a. Statistical power and sample size
b. Batch affect
c. External Cross validation
d. Internal cross validation
107
20. What are the benefits of metabolomics in human research?
a. End-point genome
b. Understanding underlying biochemistry
c. Potentially smaller number of targets
d. Represents phenotype of organism
e. Essential for study of systems biology
f. Wide analytical range
g. Fairly low per sample cost
108
21. What are the draw backs of metabolomics?
a. Difficult for upstream regulation
b. Metabolites involved in multiple pathways
c. Unknown metabolites
d. Impacted by wide range of factors
e. Does not represent all of the systems biology
f. No technique can detect all metabolites
g. Very high capital expenditure
109
Metabolomics allws the _______ detection of disease when there are no _______
a. early
| b. symptoms
110
Metabolomics can be used as a ___________ tool to determine health
screening
111
What is detected in the early stages of illness and late stages of illness?
biomarkers
112
If disease is detected early why can be done using metbolomics to aid this?
Change current pathway and return to homeostasis
113
Metabolomics is a _______ area of study, which makes it difficult to maintain sampling througout.
longitudinal
114
What screening is not very consistant?
Mass Spec
115
1. Mass spec is used to __________ microorganisms that have been genetically engineered?
a. Screens
116
2. What is the bottleneck of biotechnology?
a. The screening processes
117
3. What is the synthetic biology life cycle?
a. Design
b. Build
c. Test
d. Learn
118
4. What screening methods are there?
a. Colourmetric
b. OD
c. Elisa
d. Mass Spec
119
5. Elisa allow the detection of _________ which leads to a change in adsorbance
a. Antibody
120
6. What tpyes of mass spec are typically used for screening?
a. Typically LC-MS or GCMS used to detect product
121
7. What are the new Mass specs that have been developed for screening?
a. REIMS
b. EchoMS
c. Reaction DESI
122
8. What does REIMS stand for?
a. Rapid Evaporative Ionisation MS
123
9. How does REIMS work?
a. Ambient ionisation
b. Rapid laser heating
c. Evaporation contains ions which can be analysed
124
10. What is Betulinic acid, where is it naturally found, what properties does it have, ?
a. Naturally occurring pentacyclic triterpenoid
b. Found in the bark of White Birch trees
c. Shown to have antiretroviral, antimalarial, anti-inflammatory, and anticancer properties
125
11. You need to keep a balance of ________ expression and ______ concentration
a. Gene
| b. Substrate
126
12. Checking for naturally occurring _________ _________ will allow you to develop synthetic organism
a. Gene expression
127
13. What is a scrambled libraries?
a. Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution
128
14. What is an issue with scrambled libraies?
a. It impairs unintended genes
129
15. Reims cost _______ then LC-MS
a. Less
130
16. What compounds can reims not beable to detech with REIMS?
a. Large molecules
131
17. What is echo MS?
a. Acustic
b. Tranfers nano sized droplets into a MS
c. Only takes 1/3 of a second
d. Very high throughput
132
18. How many samples can be scanned using ECHO?
a. 100,000 in a week
133
19. What is DESI
a. Desorption Electrospray Ionisation MS (DESI-MS)
134
20. What samples can you not use in adesi?
a. Corrosive samples
135
1. Metabolomics and metataxonomics were used to investigate the efficacy of FMT, the study showed elevated levels of __________ prior to the FMT which causes C. difficile to germinate, and found a reduction of _________ after the treatment.
a. Taurocholic acid
| b. taxons
136
2. What is one way to investigate HMO in breast milk and the micobiome?
a. Fractionate the milk
| b. Use a chemostat system to model the effect on gut microbiome
137
3. What is the different steps of the research framework for microbiome and metabolome research (6)?
a. Observational study
b. Hypothesis based on metaboloites
c. Metaflux/cellculture study
d. Model oragnaism study
e. Intervention study/gene depletion study
f. Clinical trial
138
1. What ways can the human microbiome be commercialised (4)?
a. Sequencing your gut flora
b. Creating microbiomes for people
c. Medications for dysbiosis
d. Biotechnologies
139
2. Who are uBiome?
a. Startup testing shite
b. Got a $600 investment
c. Went bankrupt
d. Investigated by the FBI
140
3. What are the three case studies covered in the manipulating the microbiome lectures relating to?
a. Difficile treatment
b. Human mil
c. Covid-19
141
4. Chloridoids difficile is part of the ______ microbiota.
a. Gut
142
5. What eradicates microbiota in the gut?
a. Antibiotics
143
6. What do vegetative C. difficile produce?
a. Toxins
144
7. What is the mortality rate when infected with Chloridoids difficile?
a. 10-20%
145
8. What is a treatment method for recurrent Chloridoids difficile?
a. Faecal microbiome transplant
146
9. What are potential issues with faecal transplants (6)?
a. In 2019, E. coli introduced: introduce other bugs
i. They could be resistant
b. Can the pill be standardised?
c. Administration route
d. Patients think its gross
e. Need annual treatment
f. Toxins in transplant
147
10. Youngster et al, 2016 showed a cure rate of _______ after ______ treatments.
a. 91%
| b. 2
148
11. In what year did the FDA suspend clinical trials of feacal transplants?
a. 2019
149
12. Where does a baby first get their microbiota?
a. THEIR MA’s DOOT
150
13. Who was the first to link the gut microbiome and health?
a. Escherich
151
14. If breast feeding how long does the microbiome of the breast milk supply the main source of the microbiome of the baby?
a. Up until 14 month
152
15. After breast feeding what his the second highest influence on the microbiome of infants?
a. The household and siblings
153
16. How many microorganisms are thought to be in breast milk?
a. 700 species
154
17. What are the possible routes of infection of the breast milk?
a. Hormonal changes: increase the tits, then more permeable to bacteria
b. Mammary epithelium
c. Internalised in circulatory system ends up in the cells
155
18. What is found in breast milk that is not eaten by the infants?
a. Oligosaccharides
156
19. What are the 4 commponents to breast milk?
a. Protein
b. Fat
c. Lactose
d. Oligiosaccharides
157
20. How many oligosaccharides are found in breast milk g/L?
a. 5-15
158
21. How many different types of oligosaccharides are there in breast milk?
a. +100
159
22. What role does the ooliogosaccharides play if not used?
a. Feeds bifidobacteris
b. Acts as a decoy for pathogens
c. Potential roles outside of the gut
160
23. What is one of the most abundant HMO?
a. 2’-fucosyllactose
161
1. What human microbiomes are there (4)?
a. Oral microbiome
b. Skim microbiome
c. Digestive tract microbiome
d. Uritnetia microbiome
162
2. What microorganisms might you find within the human microbiomes?
a. Archaea
b. Bacteria
c. Viruses
d. Fungi
e. Parasite
163
3. What are the two previous methods used for studying the human microbiome?
a. Clone library sequence
| b. Terminal restriction fragment length polymorphism
164
4. What are the four main approaches to study the human microbiome?
a. DNA
b. RNA
c. Protein
d. Metabolite
165
5. What does DNA based approaches in the human microbiome allow you study (5)?
a. 16s RNA
b. 18S
c. gene sequence
d. Who is there?
e. What can they do?
166
6. What does RNA based approaches in the human microbiome allow you study (3)?
a. Metatranscriptomics
b. What pathways are used
c. How do they respond
167
7. What does Protein based approaches in the human microbiome allow you study (3)?
a. How are they interacting with the host?
b. What proteins are being produced
c. Metaproteomics
168
8. What does metabolite-based approaches in the human microbiome allow you study (3)?
a. What are the chemical outcomes of their activity?
| b. Metabolomics
169
9. What is Metataxomics also referred to as?
a. 16S rRNA gene amplicon sequencing
170
10. Universil ________ amplify conserved regions of 16S rRNA genes and each sample is given a different _____ for tracing sequencing reads.
a. Primers
| b. Barcodes
171
11. What does OUT stand for?
a. Operational taxonomic unit
172
12. Metataxonomics can give _____ to genus level.
a. OUT
173
13. Is statistical modelling easy or difficult in metataxonomics?
a. Difficult
174
14. Is the data from metataxonomics quantitative or qualitative?
a. Qualitative
175
15. Metataxonomics studies are robust (T/F)?
a. False
176
16. What is always difficult when completing a Metataxomic study?
a. Taxonomic identification
177
17. How many base pars does B. anthracis and B thuringienis differ by in their 16S gene?
a. 9bp
178
18. What can Metataxomic not tell you about the microbial community?
a. What they are doing
179
19. The data analysis of metagenomics is complicated (T/F)?
a. True
180
20. To assign function there what does there need to be?
a. A database entry
181
21. Host _______ can be a complicating factor in metagenomics.
a. DNA
182
22. When using Metatranscriptomics it gives a snapshot of the active ________.
a. mRNA
183
23. What is the majority of genetic material collected in humans in Metatranscriptomics?
a. mRNA
184
24. What are the majority of non-human mRNA collected in Metatranscriptomics?
a. Ribosomal
185
25. During metaproteomics the protein sequence is determined and then _________ matched.
a. Database
186
26. What do ribosomal proteins give you _________ composition in metaproteomics?
a. Taxonomic
187
27. In metaproteomics non-ribosomal proteins give you what kind of information?
a. Functional information
188
28. What method is considered the cross-kingdom interaction?
a. .Metabolomics
189
29. What is one of the issues with Metabolomics?
a. Finding the source of the metabolite
190
30. What is fluxomics?
a. is the study of comprehensive flux in the metabolic network of a cell,
191
31. How is fluxomic studied?
a. Isotope labelling to track metabolism
b. Labelled energy source fed in at time point
c. Labelling is incorporated and measured
d. Shows where energy is going in the system
192
32. Why is culturomics important?
a. Isolates are required for hypothesis testing
193
33. What must be replication in culturomics?
a. The environment of the microbe
194
34. DNA extraction kits are not produced sterile (T/F).
a. True
195
35. Sampling _________ for DNA/RNA, proteins, and metabolites.
a. Differs
196
36. What is difficult to establish in microbiome studies?
a. Cause and effect
197
When the microbiome is taken out of the body what happens to the microbes?
they go into shock and then they change gene and protein expression
