taxonomy and diversity Flashcards
which organisms are cellular
fungi, protists, bacteria, archaea
which organisms are acellular
viruses, viroids, satellites, prions
what is the most inclusive level of the hierarchy
domain
list the domains
Archaea, Bacteria, Eukarya
list the order of the hierarchy
kingdom, domain, phylum, class, order, family, genus, species
T or F: bacteria has no kingdom
true
for bacteria, class ends in __
ia
for bacteria, order ends in __
ales
for bacteria, family ends in __
aea
what can each species be divided into
strains
what is the type strain
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)
what do we call strains that differ via biochemical/physiological ways
biovar
what do we call strains that differ via morphology
morphovar
what do we call strains that have antigenic differences
serovar
how is the genus and species of newly isolated microbes determined
based on the polyphasic taxonomy. Components include phenetic and genotypic charcaterizations
what are phenetic differences based upon + what traits of the microbe are these
phenotype: morphology and physiology
what are genotypic differences based upon + what traits of the microbe are these
genes and genomes: average nucleotide identity, rRNA genes
what are the two approaches to identifying an unknown microorganism
classical and molecular
what characteristics does the classical approach look at
morphological, physiological/metabolic, biochemical, and ecological characteristics
the classical approach forms the basis for ___ classification
phenetic
the molecular approach forms the basis for ___ classification
genotypic
how do we use the molecular approach to identify microbes
involves sequencing of one or a few genes, or the entire genome
give an example of the molecular approach to identifying unknown microbes
sequencing of the gene encoding for the 16S SSU rRNA
which hierarchical group does 16S rRNA sequencing help us determine
genus
list 3 advantages of 16S rRNA sequencing
- 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
how many nucleotides is the 16S rRNA gene
1540 nt
what types of regions does the 16S rRNA include
variable and conserved
role of the variable regions in 16S rRNA?
they contain signature sequences that are found in specific groups of organisms
role of the conserved regions in 16S rRNA?
they’re found in all members belonging to domain bacteria
list 2 ways in which an organism can be identified to the species level
average nucleotide identity (ANI) and determination of the G + C content
how does average nucleotide identity (ANI) work?
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
ANI values between an unknown and known of ___% indicate that the organisms are members of the same species
95-96%
how is determination of the G+C content done?
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
how is the GC% data used to identify the species of an organism?
-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
how would one identify levels below species?
make use of Multilocus sequence analysis (MLSA)
describe multilocus sequence analysis
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)
what is wgMLSA
MLSA data paired with whole-genome sequencing
