c17 lecture 3


Taxonomy vs phylogeny


T: Phenetic organization, based on phenotypes

P: Based on evolutionary relationships


Polyphasic Taxonomy


Incorporates various phenetic and phylogenetic information, with 16S RNA analysis


Ferdinand Cohn


Father of Bacteriology

Sorted bacteria based on morphology


Robert Koch on bacterial species designation:


Bacteria that maintain the characteristics when cultured in the same conditions should be designated a species


Biological classification


D P C O F G S


How do we define species for prokaryotes?


- Prokaryotes lack sexual reproduction -> cant use interbreeding

- Collection of strains, housekeeping genes


Biovar


Differ biochemically and physiologically


Morphovar


Differ morphologically


Serovar


Differ in antigenic properties


Type strain


First strain isolated, used as a reference


Binomial system of nomenclature for microbes


Genus species

G. Species


Pathotypes


Pathogenic strain of bacteria after recieving new genetic information through HGT


Phenetic classification system for microbes


Based on as many characteristics as possibleMorphologicalPhysiologicalEcologicalMolecular


Ecological characteristics of a microbe


Life cycle patternsSymbiotic relationshipsPathogenic abilityHabitatGrowth Requirements


6 analysis methods of molecular taxonomy


1) Nucleic acid base composition2) Nucleic acid hybridization3) Nucleic acid sequencing4) Genomic fingerprinting5) Proteins6) Fatty acids


G+C variation among prokaryotes


25-80%


G+C variation among a genus


<10%


Hybridization percentage and interpretation


0-25% = different genera25-75% = same genus, different species75-100% = same species


Most powerful and direct method for comparing genes and genomes?


Nucleic acid sequencing


3 main problems with phylogeny in microbes


1) Taxonomy not based on evolutive relationships

2) Asexual reproduction + HGT

3) No fossil record to support evolutive taxa