taxonomy and diversity

Question 1

which organisms are cellular

Answer 1

fungi, protists, bacteria, archaea

Question 2

which organisms are acellular

Answer 2

viruses, viroids, satellites, prions

Question 3

what is the most inclusive level of the hierarchy

Answer 3

domain

Question 4

list the domains

Answer 4

Archaea, Bacteria, Eukarya

Question 5

list the order of the hierarchy

Answer 5

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

Question 6

T or F: bacteria has no kingdom

Answer 6

true

Question 7

for bacteria, class ends in __

Answer 7

ia

Question 8

for bacteria, order ends in __

Answer 8

ales

Question 9

for bacteria, family ends in __

Answer 9

aea

Question 10

what can each species be divided into

Answer 10

strains

Question 11

what is the type strain

Answer 11

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)

Question 12

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

Answer 12

biovar

Question 13

what do we call strains that differ via morphology

Answer 13

morphovar

Question 14

what do we call strains that have antigenic differences

Answer 14

serovar

Question 15

how is the genus and species of newly isolated microbes determined

Answer 15

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

Question 16

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

Answer 16

phenotype: morphology and physiology

Question 17

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

Answer 17

genes and genomes: average nucleotide identity, rRNA genes

Question 18

what are the two approaches to identifying an unknown microorganism

Answer 18

classical and molecular

Question 19

what characteristics does the classical approach look at

Answer 19

morphological, physiological/metabolic, biochemical, and ecological characteristics

Question 20

the classical approach forms the basis for ___ classification

Answer 20

phenetic

Question 21

the molecular approach forms the basis for ___ classification

Answer 21

genotypic

Question 22

how do we use the molecular approach to identify microbes

Answer 22

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

Question 23

give an example of the molecular approach to identifying unknown microbes

Answer 23

sequencing of the gene encoding for the 16S SSU rRNA

Question 24

which hierarchical group does 16S rRNA sequencing help us determine

Answer 24

genus

Question 25

list 3 advantages of 16S rRNA sequencing

Answer 25

- 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

Question 26

how many nucleotides is the 16S rRNA gene

Answer 26

1540 nt

Question 27

what types of regions does the 16S rRNA include

Answer 27

variable and conserved

Question 28

role of the variable regions in 16S rRNA?

Answer 28

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

Question 29

role of the conserved regions in 16S rRNA?

Answer 29

they're found in all members belonging to domain bacteria

Question 30

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

Answer 30

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

Question 31

how does average nucleotide identity (ANI) work?

Answer 31

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

Question 32

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

Answer 32

95-96%

Question 33

how is determination of the G+C content done?

Answer 33

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

Question 34

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

Answer 34

-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

Question 35

how would one identify levels below species?

Answer 35

make use of Multilocus sequence analysis (MLSA)

Question 36

describe multilocus sequence analysis

Answer 36

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)

Question 37

what is wgMLSA

Answer 37

MLSA data paired with whole-genome sequencing