Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Probiotics > Jan 2022 extenta > Flashcards

Jan 2022 extenta Flashcards

1
Q

Give one example of a probiotic strain commercially available. What species, genus, family
and division (phylum) does this strain belong to?

A

Strain: Lactobacillus plantarum 299V

Firmicutes
Bacilli
Lactobacilales
Lactobacillacea
Lactobacillus
Lactobacillus plantarum

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

Describe the health beneficial effects of the probiotic strain you have given under question 1a (299V).

A

Sold as Probi Mage

Outcompete pathogens
Induce immune response that protects from infections
Normalise stool
Relieve abdominal pain

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

Which mechanisms are causing the health-beneficial effects given in 1b?

A

It outcompetes pathogens by “sitting” in the adhesive sites that pathogens could have otherwise adhered to

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

Suggest a suitable prebiotic that the strain can be combined with and explain the synergistic
effect?

A

It can be combined with fingermillet porridge, as that serves as a good substrate for the microogranism and will help it grow.

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

Is the probiotic species given in 1a occurring spontaneously in any traditionally lactic acid
fermented foods, and in that case, which food(s)?

A

Yes, isolated from silage, sauerkraut, pickled vegetables and sourdough

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

Give a short summary of theoretical hazards that are discussed in connection with probiotics.
Is the probiotic strain of 1a safe?

A

Yes very safe and well known. For individuals with compromised immune system it is best to be careful with probiotics but otherwise very safe.
Theoretical hazards defined by WHO:
1. Systemic infections
2. Deleterious metabolic activities
3. Excessive immune stimulation in susceptible individuals
4. Gene transfer

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

To which bacterial cells are lipopolysaccharides (LPS) associated?

A

Gram negative. LPS contain lipid A which is an endotoxin and can induce immune response: endotoxins cause the production of cytokines, including tumor necrosis factor (TNF), interleukin (IL)-1, and IL-6; promote the release of prostaglandins and leukotrienes; and may trigger inflammation and septic shock

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

How can LPS (lipopolysaccharides) induce translocation?

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

Define “permeability” and “translocation” in connection to the gastro-intestinal tract.

A

With a thinner mucus layer bacteria may be able to permeate (thinner mucus layer means higher permeability of gut wall/ lumen) and translocate to the blood. This could mean the spread of endotoxins LPS from gram negative bacteria into the blood which leads to inflammation and could even lead to sepsis

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

How can probiotics decrease the risk of translocation?

A

Probiotics can outcompete pathogens such as the mucin-degrading Akkermansia. Without mucin degrading bacteria translocation is a lot less likely. Probiotics can also help regulate the immune system. With more beneficial bacteria there will be less pathogens and gram negative bacteria

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

T/F: Cytokines are always pro-inflammatory mediators

A

False, there are also anti-inflammatory cytokines

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

T/F: The 16S rRNA-gene is unique for each bacterial species.

A

It contains both conserved and hypervariable regions allowing it to be useful as we can have primers anneal to conserved regions and can classify bacteria based on the hypervariable regions

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

T/F: IBD = Inflammatory bowel disease

A

Yes

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

T/F: The bacterial strain is a population of genomically identical cells

A

True. ”A population of genetically identical cells”
- In other words: A strain is a population of organisms that descends from a single organism or pure culture isolate.

Strains within a species may differ from one another in many ways:
– Biovar: Strains that differ by biochemically and physiologically properties
– Morphovars: Strains that differ morphologically
– Serovars: Strains that differ in antigenic identity

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

T/F: The species are populations of organisms that have a high level of genetic similarity.

A

True.

”A population of organisms that have a high level of genetic similarity”. Organisms sharing ≥ 98 % of the
sequence in their house-keeping genes
- In other words: A bacterial species is a collection of strains that share many stable properties and differ significantly
from other groups of strains.

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

T/F: The genus is an aggregate of species sharing certain joint properties.

A

Could be false. Not really sure about the way the sentence is phrased. This is how they describe it in the taxonomy lecture. Strains with ≥ 97 % similarity by 16S rRNA comparison
- In other words: A well-defined group of one or more species that is clearly separated from other genera.

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

T/F: A suitable dose of probiotics is one million living bacteria per day.

A

Usually 1 billion is what probiotic supplements contain so I am guessing false.

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

T/F: qPCR can only quantify the total count of living bacteria.

A

No, qPCR uses genetic material so would not rely on whether they are alive or not.

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

T/F: Salmonella belongs to the family Enterobacteriaceae.

A

True

Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriacea
Salmonella

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

T/F: Staphylococcus belongs to the phylum Firmicutes.

A

True, gram positive

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

T/F: CFU = calculated formula of units.

A

False! Colony forming units

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

T/F: qPCR, PFGE and RAPD are culture-dependent techniques

A

Rapid amplified polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE). qPCR is not culture dependent so the answer must be false.

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

T/F: Health effects of probiotics should be documented on species level

A

Strain level as different strains can have different effects

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

T/F: If a probiotic species is not present on the QPS (qualified presumption of safety) list it must be evaluated as safe according to
Novel Food regulation

A

False, it is then regarded as unsafe

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

T/F: For qualification as probiotics, the microorganism must be supported by at least one human
clinical trial.

A

True. Here are the criteria:
In short, probiotic strains must be (i) sufficiently characterized; (ii) safe for the intended use; (iii) supported by at least one positive human clinical trial conducted according to generally accepted scientific standards; and (iv) alive in sufficient numbers in the product at an efficacious dose throughout shelf life.

26
Q

You have 80 faecal samples from celiac disease patients treated with the probiotic strain
Lactiplantibacillus plantarum 213. For compliance analysis, you and your colleagues want
to know if the given strain is present in the samples. At the lab, the following methods are
available: qPCR, T-RFLP, conventional culturing methods, RAPD and Sanger sequencing.
Choose two of the methods that can be used either combined or individually to answer the
research question and describe them in detail. Also explain the analysis of the data
acquired from the methods and the information you will get about the samples.

A

I would choose conventional culturing to see if the strain I am interested in is present in the samples. I would also do qPCR targeting the specific strain I am interested in, to see how much of it is present.

27
Q

What is T-RFLP?

A

Terminator restriction fragment length polymorphism. Based on restriction site closest to a labeled with a flourescent molecule. Based on PCR amplification. Sizes of fragments determined in electrophoresis.

28
Q

Describe in detail the procedure of using Illumina sequencing for 80 faecal samples from celiac disease patients treated with the probiotic strain
Lactiplantibacillus plantarum 213. Also explain the analysis of the data acquired from the methods and the information
you will get about the samples.

A

Using Illumina 16S gene sequencing we will get a lot of data about which bacteria are present down to species level. The obtained DNA fragments will be compared to a DNA database to identify which bacteria are present. This can be represented in different ways using tools such as QIIME2 to show relative abundance, alpha and beta diversity which can be visualised in a Bray Curtis Distance Matrix

DNA extraction
PCR 16S amplicon
PCR clean up
index PCR
PCR clean up
library quantification
library normalisation
pooling
denaturing and loading into Miseq
Getting sequences
Bioinformatics - alpha diversity, beta diversity, Bray curtis matrix, relative abundance of each species

29
Q

Why would you choose primers targeting conserved regions in the 16S rRNA gene for
identification of bacteria by PCR-based methods?

A

We need primers that will target a region we know. Therefore it is smart to use that conserved region.

30
Q

Describe in detail the acquisition of the human intestinal microbiota from gestation (pre-birth)
and during delivery of the child.

A

Delivery method plays a large role in which microorganisms colonise babies. Babies born vaginally will have more lactobacillus (associated with the vaginal microflora) while babies born with c-section will have more skin-related microorganisms from parents and midwives/doctors/nurses present at the birth. However research has shown that there are also bacteria present in umbilical chord and placenta, indicating that the baby also receives some microorganism from the mother earlier than delivery.

31
Q

Describe three factors that may affect the intestinal microbiota composition during the first
years of life.

A

Birth
Whether the baby is formula fed or breastfed. Breastmilk contain oligosaccharides that act as excellent prebiotics. Babies fed with välling and other products containing grains will get more endotoxins since many gram negative bacteria are present in grain and while they are nolonger alive after sterilisation of the food, endotoxins and spores will still be present.
The diet of the family will be a determining factor (also the diet of the breastfeeding mum). Hygiene will be an important factor too (pets in the family might affect the hygiene too). Use of antibiotics during the first years will also have an effect.

32
Q

Mention three external factors that may affect the microbiota composition while being an
adult.

A

Diet, lifestyle, exercise, stress, use of antibiotics, geographic location, illnesses

33
Q

Describe the composition of the microbiota in elderly and three factors that may affect its
composition.

A

Generally less diverse. Diet, lifestyle and illnesses will play an important role.

34
Q

Describe a clinical trial evaluating health benefits after consumption of water kefir by
healthy volunteers.
a) (7 points)
Mention one of the dominating bacteria in the product that are beneficial (on genus and
species level), suitable endpoints of the study, the experimental design, suitable intake and
the health benefits that may be obtained. Use maximum 300 words.

A

The microbial groups in the water kefir grain are lactic acid bacteria (LAB) (107 −108 CFU/g grain; mainly Lactobacillus sp., Lactococcus sp., Leuconostoc sp. and Streptococcus sp.). Suitable endpoints of the study would be to see a change in microbiome composition, a change in alpha diversity.

35
Q

Describe schematically the different steps in 16S rRNA gene analysis for identification of
the dominant bacterial species by sequencing in the sample of clinical trials of consumption of water kefir

A

After a sample has been taken
1) DNA extraction
2) PCR will be performed to create more copies of the DNA present, DNA amplification
3) Sequencing with Illumina
4) Bioinformatics

36
Q

Based on dominating species, should you recommend water kefir for prevention or
treatment for any disease? In that case, which disease?

A

gastrointestinal diseases like irritable bowel syndrome, some kinds of diarrhea, and ulcers caused by the infection H. pylori

37
Q

Choose 2 gram-negative bacteria and 2 gram-positive bacteria normally occurring as part
of the intestinal flora and name the different taxonomy levels for each bacterium from
phylum to species

A

Firmicutes
Bacilli
Lactobacillales
Lactobacillaceae
Lactobacillus
Lactobacillus acidophilus

Firmicutes
Bacilli
Lactobacillales
Streptoccocacea
Streptoccus

Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriacea
Escherichia
Escherichia coli

Proteobacteria
Gammaproteobacteria
Pasteurrelales
Pasteurracea
Actinobacillus

38
Q

Shortly describe the following words:
Next generation probiotic

A

A newly discovered bacteria that can provide health benefits, but does not have a history of being used in foods

39
Q

Describe: single arm trial

A

A single arm trial is one group of individuals being studied, no control group or groups with different “treatments”

40
Q

Describe: homofermentative

A

It means that the bacteria produces only one product. LAB producing only lactic acid. Heterofermentative LAB produce for instance acetic acid as well.

41
Q

Describe: Commensals

A

A commensal is an organism that uses food supplied in the internal or the external environment of the host, without establishing a close association with the host

42
Q

Describe: Transient microbiota

A

The term transient microbiota refers to microorganisms that are only temporarily found in the human body, and these may include pathogenic microorganisms. Hygiene and diet can alter both the resident and transient microbiota.

43
Q

Describe: Faecal transplantation

A

A fecal transplant is a procedure that transplants healthy gut bacteria via donor stool to a patient suffering from recurring infections with Clostridium difficiles

44
Q

Describe: universal primers

A

Universal primers are complementary to nucleotide sequences that are very common in a particular set of DNA molecules and cloning vectors. Thus, they are able to bind to a wide variety of DNA templates.

45
Q

Describe: Phylogenetic tree

A

a diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor.

46
Q

Describe the difference between a spontaneous and an induced fermentation and give
one example of each process.

A

Spontaneous fermentation occurs without a starter culture meaning that the microorganism is already present in the food or environment. An example is sourmilk made from raw cow milk. Induced fermentation is when a starter culture is added such as streptococcus thermophilus in the production of youghurt.

47
Q

Define “Lactic acid bacteria”

A

LAB are a group of bacteria that have same characteristics. They produce lactic acid from lactose. They are non-pathogenic and non-spore forming. Grow well at low pH.

48
Q

Mention 4 taxa included in the functional concept LAB.

A

Lactobacillus
Lactococcus
Pediococcus
Streptococcus (not sure)
Weissela

49
Q

Describe in detail 2 ways of how probiotic bacteria can induce an
immunological reaction.

A

Probiotics regulate host innate and adaptive immune responses by modulating the functions of dendritic cells, macrophages, and T and B lymphocytes [1,13]. One of the mechanisms of probiotics regulating immunomodulatory functions is through the activation of toll-like receptors.

50
Q

You have 100 fecal samples from diabetes type II patients treated with the probiotic strain
Lactiplantibacillus plantarum 213. At the lab, the following methods are available: NGS, qPCR,
conventional culturing methods, and flow cytometry.
For the questions below, choose between the methods that can be used either combined
or individually, to answer the research question and describe them in detail.
Also explain the information you will get about the samples.

Always keep in mind what is the easiest and cheapest method

a)
For compliance (if you have given a specific strain, you would like to see if the participants
Actually consumed it = proof of consumption)
analysis, you want to know if the given strain is present in the fecal samples?

A

PCR or sequencing
For PCR you need the specific primer of the strain
NGS is probably too expensive for this
Isolate colonies and identify those by PCR = Sanger sequencing
Either conventional culturing and then PCR or qPCR.
You just have to motivate it
To get the identity you have to use PCR.
If you choose conventional culturing you need to decide which media to use to culture

Compliance analysis: viable count, isolation of colonies and PCR, Sanger sequencing is a
good method for that

Compliance is all about finding the one you have been consuming in the fecal samples

51
Q

What method would you choose if you had to determine the number of living Enterobacteriaceae in faecal samples?

A

Culturing
Which media? VRBD a selective media for Enterobacteriaceae

52
Q

You want to determine if the probiotic product contains Lactiplantibacillus plantarum
as it is claimed on the product label?

A

First you culture it to see if it is living (and you will get the viable count).
You probably want to see how much of it you have too
Could use qPCR if you had the specific primer and a viability marker
PCR or sequencing

53
Q

You want to know if the probiotic product affected the microbiota composition in general?

A

NGS because here you want to see the composition in general (not on strain level but on genus level)

54
Q

Which growth media is good for lactic acid bacteria?

A

Rogosa (selective for lactobacillus)
MRS (non-selective, for all LAB)

55
Q

Which growth media is good for enterobacteriacea?

A

VRBD

56
Q

What is a very general growth media where many families can grow?

A

TSA

57
Q

What is a growth media for yeast?

A

Malt agar

58
Q

What is RAPD?

A

Random or Rapid Amplification of Polymorphic DNA. The segments amplified are random. So no need to know which primers to use.

59
Q

What is RFLP?

A

Restriction fragment lenght polymorphism. Using restriction enzymes to cut up DNA at restriction sites.

60
Q

Difference between Sanger sequencing and qPCR (real time PCR)?

A

Sanger sequencing and real-time PCR are complementary techniques with distinct applications. Sanger sequencing is focused on determining the nucleotide sequence, while real-time PCR is primarily used for quantifying DNA

Probiotics (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions