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TaxonomyContent

TaxonomyContent

Why Taxonomy?Why Taxonomy?

How to determine & classify a species

Domains versus KingdomsDomains versus Kingdoms

Phylogeny and evolution

Wh T ?Why Taxonomy?• Classification – Arrangement in groups or taxa g g p

(taxon = group)

• Nomenclature – Assigning names to taxa

• Identification – Determination of taxon to which an• Identification – Determination of taxon to which an

isolate belongs

(Most practical part of taxonomy)

Making sense of Nature

Classification

Comparison of species based on:

• Natural – anatomical characteristics• Phenetic – phenotypic characteristics• Genotypic – genetic characteristics• Genotypic – genetic characteristics• Phylogenetic – evolutionary links

Polyphasic TaxonomyPolyphasic Taxonomy

• used to determine the genus and species of a newly discovered procaryote

• incorporates information from genetic, h t i d h l ti l iphenotypic and phylogenetic analysis

genus – well defined group of one or more species that is clearly separate from other generathat is clearly separate from other genera

Defining procaryotic species & strains

• Definition species:– collection of strains that share many stable properties and

differ significantly from other groups of strains

• Alternative definition:ll ti f i th t h th i– collection of organisms that share the same sequences in

their core housekeeping genes

• Strain:descended from a single pure microbial culture- descended from a single, pure microbial culture

- Type strain: usually one of first strains of a species studied

Fig. 19.7 Hierarchical arrangement in Taxonomy.g. 9.7 e c c ge e o o y.

Binomial System of Nomenclature(Carl von Linné)

Numerical TaxonomyNumerical Taxonomy• To create phenetic classification systemsTo create phenetic classification systems• multistep process

– code information about properties of organismscode information about properties of organisms• e.g., 1 = has trait; 0 = doesn’t have trait

– use computer to compare organisms on 50 characters

– determine association coefficientt t i il it t i– construct similarity matrix

– identify phenons and construct dendograms

Association coefficients

• Simple matchingSimple matching coefficient (SSM)

• Jaccard coefficient– ignores characters g

that both lack

• dendogram – treelike diagram used to display resultsdendogram treelike diagram used to display results

• phenon – group of organisms with great similarity– phenons with 80% similarity = bacterial species– phenons with 80% similarity = bacterial species

similaritymatrix

rearranged andjoined to show l t

dendogrammatrix clusters

Figure 19.6

Techniques for Determining Microbial Taxonomy and Phylogeny

• Classical Characteristics• Classical CharacteristicsMorphological

EcologicalPh i l i lPhysiologicalBiochemical

Genetic

The largest bacterium: 600 μm by 80 μmThe largest bacterium: 600 μm by 80 μm

Ecological CharacteristicsEcological Characteristics

life-cycle patternslife-cycle patternssymbiotic relationshipsability to cause disease

habitat preferenceshabitat preferencesgrowth requirements

API 20E system for several physiological testsAPI 20E system for several physiological tests

Figure 35.6

Figure 35.5a. Classic dichotomous keys for clinically important genera.

Molecular CharacteristicsMolecular Characteristics

Comparison of proteinsNucleic acid base compositionNucleic acid base composition

Nucleic acid hybridizationyNucleic acid sequencing

N l i id b itiNucleic acid base composition

G + C content

- Mol% G + C = (G + C/G + C + A + T)100( )

Often determined from melting temperature (T )- Often determined from melting temperature (Tm)

- Variation within a genus usually < 10%

as temperature slowlyincreases, hydrogen bondsb k d t d

DNA issinglebreak, and strands

begin to separate

singlestranded

Figure 19.8 DNA melting curve.

Nucleic acid hybridizationNucleic acid hybridization

f h l• measure of sequence homology• common procedure:

bind nonradioacti e DNA– bind nonradioactive DNAto nitrocellulose filterincubate filter with radioactive– incubate filter with radioactivesingle-stranded DNA

– measure amount of radioactivemeasure amount of radioactiveDNA attached to filter

Figure 19.9

Nucleic acid sequencingNucleic acid sequencing

• most powerful and direct method for comparing genomesp g g

• sequences of 16S & 18S rRNA (SSU rRNAs) are used most often in phylogenetic studiesare used most often in phylogenetic studies

• complete chromosomes can now be sequenced and compared(BIOINFORMATICS !)(BIOINFORMATICS !)

Genetic AnalysisGenetic Analysis

• study of chromosomal gene exchange by transformation and conjugationtransformation and conjugation– these processes rarely cross genera

• plasmids can help to solve confusion in theplasmids can help to solve confusion in the analysis of phenotypic traits

Fig. 19.11 Overview Genomic fingerprinting technique.

Relative Taxonomic Resolution of Various Molecular Techniques

Figure 19.12

The Major Divisions of LifeThe Major Divisions of Life

• Currently held: 3 domains of life:–BacteriaBacteria–Archaea–Eucarya

• Scientists do not all agree aboutScientists do not all agree aboutthis way of the “Tree of Life”

The suggestedKingdomsKingdoms

Figure 19.14 Variations in Design of “Tree of Life”.

Figure 19.3 Universal Phylogenetic Tree.

Comparative Analysis of 16S rRNA sequences

• Oligonucleotide signature sequences– short conserved sequences specific for a phylogenetically

defined group of organisms

• Organisms relatedness = association coefficient (Sab)

th hi h th S l th l l l t d th– the higher the Sab value, the more closely related the organisms

Small Ribosomal Subunit rRNA

Fig. 19.10

Frequently used to create trees showing broad relationships

Universal PhylogeneticUniversal Phylogenetic Tree with Lateral Gene

TransferTransfer