Microbial Taxonomy

Question 1

what is taxonomy

Answer 1

Taxonomy is the science of defining GROUPS of biological organisms on the basis of shared characteristics and giving names to those groups

Question 2

what does modern taxonomy comprise of

Answer 2

1. Classification= the theory and process of ordering the organisms, on the basis of shared properties, into groups.
2. Nomenclature= giving names of appropriate taxonomic rank to the classified organisms.
3. Identification= obtaining data on the properties of the organism (characterization) and determination which species it belongs to.
   This is based on direct comparison to known taxonomic groups.

Question 3

why do we taxonomy

Answer 3

> 50,000+ known species, with assigned names
107-109 species in total, mostly without names
Potential for great confusion unless a logical system devised to organise them.

Question 4

who was Carl Linnaeus

Answer 4

created a system of naming plants and animals- we still use this system today
System was called binomial system, where each species of plant and animal is given a genus name followed by a specific name (species), both names are latin

Question 5

what is taxonomy based on

Answer 5

Traditionally based upon phenotypic properties:
-size and shape
-metabolism
-other biochemical/physical properties

Question 6

what is the basic taxonomic unit

Answer 6

speicies

Question 7

what is a species

Answer 7

-A group of organisms which are capable of interbreeding to produce viable offspring
-“a collection of similar strains that differ significantly from other strains so as to warrant recognition as a basic taxonomic unit”

Question 8

which is the genus and the species

Answer 8

genus= first word
species= second word
e.g Escherichia (genus) coli (species)

Question 9

what is the Binomial nomenclature and abbreviations for 3 organisms

Answer 9

Homo sapiens= H. sapiens
Escherichia coli= E.coli
Pseudomonas aeruginosa= P. aeruginosa

Question 10

what is a strain

Answer 10

Genetic variant within a species

Question 11

what are the levels of classification

Answer 11

Species
Genus
Family
Order
Class
Phylum
Division
Domain

(Bacteria, Archaea, Eukarya)

Question 12

why does Classification based on phenotype not work for bacteria

Answer 12

Morphological analysis does not work well for bacteria!
Many species look identical- need to look at other features

Question 13

what phenotypic characteristics are used to differentiate prokaryotes

Answer 13

-Gram reaction
-fermentation of sugars
-cell morphology
-growth on a specific compound
-possession of certain metabolic enzymes
Identification methods are usually based on sets of phenotypic characteristics
Clinical diagnosis

Question 14

look at diagram in booklet

Question 15

what are the problems with phenotype-based taxonomy

Answer 15

-Need to grow the organism to perform the tests!= Clear evidence that we cannot yet cultivate the majority of microorganisms.
-What tests to perform?=Pick different tests you can get different results and Almost nothing useful that can be applied across all species
-Alternatives needed!

Question 16

what was the new taxonomy in the late 1970s

Answer 16

Carl Woese and Norm Pace
Revolutionised taxonomy by taking a genetic approach
Studied “homologous” genes

Question 17

what do homologous genes have in common

Answer 17

have a common ancestor and Orthologs are homologous genes in different species yet retaining their original function

Question 18

what gene is present in every cell

Answer 18

a housekeeping gene is one required to maintain basic cellular function and so is typically expressed in all cell types of an organism

Question 19

how are procaryotes classified

Answer 19

-Prokaryotes can be classified using artificial or natural (phylogenetic) systems.

Question 20

how were prcayotes classified in the past

Answer 20

Historically, prokaryotes were classified on the basis of their phenotype (morphology, staining reactions, biochemistry, substrates/products, antigens etc). In other words a phenotypic characterization is based on the information carried in the products of the genes. These classification systems were artificial in that they often put organisms together that might not be genetically related

Question 21

how are procaryotes classified now

Answer 21

Modern characterization is based on the information carried in the genes i.e. the genome. This is genetic information and can also tell us something about the evolution of the organism. In other words phylogenetics.

Question 22

what are the advantages of phylogenetic analysis

Answer 22

-Every organism has it (eukaryotes have 18S rRNA, which is very closely related)
-It’s “highly conserved” (i.e. it doesn’t mutate quickly)
-There are regions which tolerate some changes- species markers!
-It doesn’t get transferred horizontally (or at least transfer is very rare)

Question 23

what is the 16s rRNA gene

Answer 23

-is a subunit of a ribosome found in all bacteria and archaea
-It is 1500 nucleotides long
-contains nine variable regions interspersed between conserved regions.
-useful taxonomic information in the nucleotide sequence

Question 24

What is the result of aligning all 16S/18S rRNA sequences?

Answer 24

A universal phylogeny: “The Tree of Life” (bacteria, archaea and eucarya)
Proposed by Woese et. al.

Question 25

what is The Hierarchy of Life

Answer 25

-Species are classified into domains Archaea, Bacteria, and Eukarya.
-Archaea and Bacteria consist of prokaryotic cells.
-Eukarya contain the protists and the kingdoms Plantae, Fungi, and Animalia.
-Protists include protozoa, algae and slime moulds

Question 26

what was the previous view on bacteria

Answer 26

-Bacteria and other microbes are “living fossils” in the course of evolution
-Primitive” microbes as “evolutionary dead-ends”

Question 27

what is Today’s dominant view

Answer 27

All organisms have evolved, and continue to evolve through time along divergent lines.

Question 28

what is bacterial nomenclature

Answer 28

-International code of nomenclature of bacteria.
-When “New” species described= characterised (biochemical/morphology/genetic) and named in accordance with the code
-“The International Journal of Systematic and Evolutionary Microbiology”
-“Bergey’s Manual of Systematic Bacteriology”
-deposited in Culture Collections= American Type Culture Collection (US)
National Collection of Industrial and Marine Bacteria (UK)

Question 29

what are type strains

Answer 29

-organisms whose properties define a species
-used as standards for comparison

Question 30

what is evolutionary history called

Answer 30

phylogeny= The universial tree of life shows the first living were microorganims and that microbes were the dominant life form for most history of life on earth

Question 31

What are procaryotic species

Answer 31

considered to be a group of strains that are characterized by a certain degree of phenotypic consistency, showing 70% of DNA–DNA binding and over 97% of 16S ribosomal RNA (rRNA) gene-sequence identity”