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BIOL 3330 - microbio 2 > taxonomy and diversity > Flashcards

taxonomy and diversity Flashcards

1
Q

which organisms are cellular

A

fungi, protists, bacteria, archaea

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2
Q

which organisms are acellular

A

viruses, viroids, satellites, prions

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3
Q

what is the most inclusive level of the hierarchy

A

domain

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4
Q

list the domains

A

Archaea, Bacteria, Eukarya

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5
Q

list the order of the hierarchy

A

kingdom, domain, phylum, class, order, family, genus, species

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6
Q

T or F: bacteria has no kingdom

A

true

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7
Q

for bacteria, class ends in __

A

ia

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8
Q

for bacteria, order ends in __

A

ales

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9
Q

for bacteria, family ends in __

A

aea

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10
Q

what can each species be divided into

A

strains

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11
Q

what is the type strain

A

the holder of the species named, and it’s usually one of the first stains studied and this the most characterized (but it may not be the most representative member)

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12
Q

what do we call strains that differ via biochemical/physiological ways

A

biovar

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13
Q

what do we call strains that differ via morphology

A

morphovar

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14
Q

what do we call strains that have antigenic differences

A

serovar

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15
Q

how is the genus and species of newly isolated microbes determined

A

based on the polyphasic taxonomy. Components include phenetic and genotypic charcaterizations

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16
Q

what are phenetic differences based upon + what traits of the microbe are these

A

phenotype: morphology and physiology

17
Q

what are genotypic differences based upon + what traits of the microbe are these

A

genes and genomes: average nucleotide identity, rRNA genes

18
Q

what are the two approaches to identifying an unknown microorganism

A

classical and molecular

19
Q

what characteristics does the classical approach look at

A

morphological, physiological/metabolic, biochemical, and ecological characteristics

20
Q

the classical approach forms the basis for ___ classification

A

phenetic

21
Q

the molecular approach forms the basis for ___ classification

A

genotypic

22
Q

how do we use the molecular approach to identify microbes

A

involves sequencing of one or a few genes, or the entire genome

23
Q

give an example of the molecular approach to identifying unknown microbes

A

sequencing of the gene encoding for the 16S SSU rRNA

24
Q

which hierarchical group does 16S rRNA sequencing help us determine

A

genus

25
Q

list 3 advantages of 16S rRNA sequencing

A
  • rRNA is found in all microorganisms
  • the rRNA is very important, so these genes change very slowly over time (don’t tolerate mutations)
  • they do not appear to have been involved in HGT
26
Q

how many nucleotides is the 16S rRNA gene

A

1540 nt

27
Q

what types of regions does the 16S rRNA include

A

variable and conserved

28
Q

role of the variable regions in 16S rRNA?

A

they contain signature sequences that are found in specific groups of organisms

29
Q

role of the conserved regions in 16S rRNA?

A

they’re found in all members belonging to domain bacteria

30
Q

list 2 ways in which an organism can be identified to the species level

A

average nucleotide identity (ANI) and determination of the G + C content

31
Q

how does average nucleotide identity (ANI) work?

A

gene by gene comparison following whole-genome sequencing is performed between the unknown and known organisms. Calculation of the fraction of identical nucleotides is determined

32
Q

ANI values between an unknown and known of ___% indicate that the organisms are members of the same species

A

95-96%

33
Q

how is determination of the G+C content done?

A

using whole genome sequencing data, the percentage of based in the DNA that are G and C is determined, giving a percentage of GC content

34
Q

how is the GC% data used to identify the species of an organism?

A

-if two bacteria differ by more than 10% GC content, they’re probably not related (different genus)
- within a genus, variations among bacteria are less than 10%
- the GC content among strains of a species will be constant

35
Q

how would one identify levels below species?

A

make use of Multilocus sequence analysis (MLSA)

36
Q

describe multilocus sequence analysis

A

multiple genes of two organisms (5-7 housekeeping genes) are sequenced and compared. If two microbial isolates have the same sequence for multiple genes than there is strong evidence to suggest the two strains are related (or even in the same strain)

37
Q

what is wgMLSA

A

MLSA data paired with whole-genome sequencing

BIOL 3330 - microbio 2 (8 decks)

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