Quiz1

Question 1

Definition and difference between microbiome and microbiota?

Answer 1

Microbiome (or microbial community, consortia)- multi species system where organisms live together in a contiguous environment. Microbiota are the organisms in microbiome

Question 2

What is an isolate?

Answer 2

Isolate- population of microbial cells in pure culture derived from a single colony on an isolation plate and identified to the species level

Question 3

What is a strain?

Answer 3

Strain- a isolate/group of isolates exhibiting phenotypic and/or genotypic traits belonging to the same lineage, distinct from those of other isolates of the same species

Question 4

What is a clone?

Answer 4

Clone - a isolate/group of isolates descending from a common precursor strain by non-sexual reproduction exhibiting exhibiting phenotypic and/or genotypic traits characterized by a strain-typing method to belong to the same group

Question 5

Definition of species with respect to 16S sequence identity?

Answer 5

working species definition is 97% Identity in 16s=belongs to the same species

Question 6

taxonomic levels of Firmicutes Streptococcus mutans UA159?

Answer 6

Firmicutes-phylum, streptococcus - genus, S. mutans - species, UA159-strain

Question 7

Definition of dysbiosis?

Answer 7

-shift from healthy homeostasis to a disease state (oral diseases with bacterial etiology occur by dysbiosis)

Question 8

what makes oral diseases so complicated?

Answer 8

1) Its a polymicrobial disease.
- even pathogens can be detected in healthy subjects
- can have caries without S.mutans present
2) Everyone harbours variations in their microbial composition
- Same disease but don’t carry the same microbial species
- species can be the same in two oral samples but also in different amounts

Question 9

central dogma?

Answer 9

DNA→ mRNA→ Protein→ metabolites!
transcription, translation

Question 10

which “omic” technique is used to investigate DNA?

Answer 10

DNA is genomics, analyze nucleic acids

Question 11

which “omic” technique is used to investigate mRNA? what are they measured by?

Answer 11

mRNA is transcriptomics, analyzes nucleic acid, and are measured by arrays of DNA sequencing.

Question 12

which “omic” technique is used to investigate protein? what are they measured by?

Answer 12

Protein =proteomics. Proteomics (and metabolomics) are measured by mass spec.

Question 13

the overall slide for the omics?

Answer 13

Question 14

What is meta omics? how many species can be sequenced at once?

Answer 14

The “meta” omics is a characterization of all the genes/mRNA/Proteins/metabolites present in biological systems and is done for 100-1000s of species at once

Question 15

Limitations of 16S rRNA gene sequencing with respect to virulence? Why is 16s rRNA not enough?

Answer 15

16S rRNA ids the taxonomy and Phylogeny, but it doesn’t tell you what genes the bacteria has. Why is species id using 16sRNA not enough? 1) identical 16s rRNA gene does not necessarily mean same virulence genes and functions in the genome. 2) A single genetic marker is typically not enough to truly delineate strains or clones that have different virulence

Question 16

Definition of genome? What can bacterial genome consist of?

Answer 16

total genetic complement of an organism. Bacterial genome consists of chromosome (rarely a couple), and extracellular elements: plasmid, transposon insertional elements, prophage

Question 17

Role of mutation in bacterial genetics?

Answer 17

mutations can greatly impact virulence factors:
increases genetic variation in a population
genetic variation is distributed through recombination

Question 18

3 modes of acquisition or transferring of genes in bacteria?

Answer 18

Transformation-release of DNA by one cell and another cell picks it up, conjugation-transposon on a plasmid , transduction - through a phage

Question 19

Dentition of annotation with respect to bacterial genetics and the first 2 steps?

Answer 19

• process of attaching biological information to sequences
  1) id elements of the sequence
  2) assign biological information

Question 20

3 mechanisms that can result in the alteration of a gene and the outcome from this type of mutation?

Answer 20

gene deletion→ loss of function, gene duplication→ additional copy of a gene, gene shuffling → change of position on chromosome

Question 21

Ecological Plaque Hypothesis?

Answer 21

Carious disease can be attributed to change in the environment which disrupts homeostasis between the plaque microbiota and the host.

Question 22

How much saliva is produced per day on average? Saliva is also considered to be hypotonic with an average pH of _?

Answer 22

0.5-1.5 liters of saliva are secreted into the mouth each day.
Saliva is hypotonic with a pH of 6.7

Question 23

Mucus concentrates hundreds of different proteins, glycoproteins, and glycolipids and lipids present in saliva in order to form a protective film. What is this film called that coats the hard surfaces of teeth? How quickly does this film re-establish itself on the tooth surface after a professional cleaning?

Answer 23

Acquired pellicle. 30 seconds.

Question 24

What is Agglutination?

Answer 24

critical process in which bacteria become “trapped” in mucin and eventually cleared by swallowing.

Question 25

Define the Ecological Plaque Hypothesis in your own words.

Answer 25

A disease is a result of an imbalance of microorganisms caused by a change in the environmental conditions, which leads to a new dominant bacteria modifying the environment.

Question 26

What is metagenomics?

Answer 26

study of microbial population through the analyses of the total genome present.

Question 27

What are the 6 features of the 16S ribosomal RNA gene?

Answer 27

1. present in all microorganisms
2. together with ribosomal proteins make up the smaller ribosomal subunit essential for protein synthesis—> essential cellular function
3. essential regions can’t contain mutations, since these are lethal to the cell
4. Variable regions reflect evolution
5. gene is 1500 basepairs
6. >100,000 16s rRNA gene sequences in the database