L9.5 Microbial Taxonomy and the Evolution of Diversity

一、Introduction to Microbial Taxonomy

Taxonomy

• consists of three separate but interrelated parts

1. classification – arrangement of organisms into groups (taxa; s., taxon)

2. nomenclature – assignment of names to taxa

3. identification – determination of taxon to which an isolate belongs

Natural Classification 自然分类法

First classification in 18th century developed by Linnaeus

• based on anatomical（结构(上)的; 解剖的） characteristics

This approach to classification does not necessarily provide information on evolutionary relatedness

Polyphasic Taxonomy 多相分类法

Incorporates information from genetic, phenotypic, and phylogenetic analysis

Highest rank is domain

• Bacteria and Archaea – microbes only

• Eukarya – microbes and macroorganisms

Within domain

phylum, class, order, family, genus, species , epithet, some microbes have subspecies

1. Domain 界
2. Phylum 门
3. Class 纲
4. Order 目
5. Family 科
6. Genus 属
7. Species 种

1. Species

Definition

collection of strains that share many stable properties and differ significantly from other groups of strains

Another definition also suggested as a definition of species is:

• collection of organisms that share the same sequences in their core housekeeping genes

Example: Escherichia coli

2. Strains 系

Descended from a single, pure microbial culture

Vary from each other in many ways

• biovars（生物变型；生化变种） – differ biochemically and physiologically

• morphovars（形态变型 ） – differ morphologically

• serovars（血清变型） – differ in antigenic properties

Example：Escherichia coli K12

3. Type Strain 模式株，模式菌株

Usually one of first strains of a species studied

Often most fully characterized

Not necessarily most representative member of species

Example： Escherichia coli O1:K1:H7 U5/41

Binomial System of Nomenclature

Devised by Carolus Linnaeus

Each organism has two names：

• genus name – italicized and capitalized (e.g., Escherichia)

• species epithet（ (表示性质、特征等的)词语） – italicized but not capitalized (e.g., coli)

Can be abbreviated after first use (e.g., E. coli)

A new species cannot be recognized until it has been published in the International Journal of Systematic and Evolutionary Microbiology

二、Techniques for Determining Microbial Taxonomy and Phylogeny

Classical characteristics

1. morphological

2. physiological

3. biochemical

4. ecological

5. genetic

1. morphological

2. Ecological Characteristics

1. Life-cycle patterns

2. Symbiotic relationships

3. Ability to cause disease

4. Habitat preferences

5. Growth requirements

3. Molecular Characteristics

1. Nucleic acid base composition

2. Nucleic acid hybridization

3. Nucleic acid sequencing

4. Genomic fingerprinting

5. Amino acid sequencing

Nucleic Acid Base Composition

G + C content

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

usually determined from melting temperature ($T_{m}$)

variation within a genus usually <10%

Nucleic Acid Hybridization

DNA-DNA hybridization

• measure of sequence homology

Nucleic Acid Sequencing

Small subunit rRNAs (SSU rRNAs)

• 16S and 18S rRNA

• inferring microbial phylogenies and making taxonomic assignments at genus level

• 70% is cutoff value for species definition

Genomic Fingerprinting 基因组指纹

Requires analysis of genes that evolve more quickly than rRNA encoding genes

(1) multilocus sequence analysis (MLSA,多位点序列分析 )

• the sequencing and comparison of 5 to 7 housekeeping genes is done to prevent misleading results from analysis of one gene

(2) Restriction Fragment Length Polymorphism (RFLP)

Uses restriction enzymes to recognize specific nucleotide sequences

• cleavage patterns are compared

Ribotyping

similarity between rRNA genes is determined by RFLP rather than sequencing

(3) Single Nucleotide Polymorphism (SNP)

Looks at single nucleotide changes, or polymorphisms, in specific genes

Regions targeted because they are normally conserved, so single changes in a base pair reveal evolutionary change