Lecture13 Microbial classification Content q Definitions q Taxonomy

Lecture-13 Microbial classification

Content q. Definitions q Taxonomy q Systematics q. Phenotypic Analysis q. Genotypic Analysis q. Classification and Nomenclature

Definitions Taxonomy ◦ The science of identification, classification, and nomenclature Systematics ◦ The study of the diversity of organisms and their relationships ◦ Links phylogeny with taxonomy

Definitions The polyphasic approach to taxonomy uses three methods: 1. Phenotypic analysis 2. Genotypic analysis 3. Phylogenetic analysis

Approaches in taxonomy The polyphasic approach to taxonomy uses three methods: 1. Phenotypic analysis Examines the morphological, metabolic, physiological, and chemical characters of the cell 2. Genotypic analysis 3. Phylogenetic analysis © 2012 Pearson Education, Inc.

Approaches in taxonomy The polyphasic approach to Several methods of genotypic taxonomy uses three methods: analysis are available: 1. Phenotypic analysis 1. DNA–DNA hybridization 2. Genotypic analysis 2. DNA profiling 3. Phylogenetic analysis 3. Multilocus sequence typing (MLST) 4. GC ratio © 2012 Pearson Education, Inc.

Genotypic analysis

DNA–DNA hybridization

GC ratio

Approaches in taxonomy The polyphasic approach to taxonomy uses three methods: The means of estimating the relationships between microorganisms 2. Genotypic analysis o 16 S r. RNA gene sequences are useful in taxonomy; serve as “gold standard” for the identification and description of new species 3. Phylogenetic analysis o Whole-genome sequence analyses are becoming more common 1. Phenotypic analysis 1. Genome structure: size and number of chromosomes, GC ratio, etc. 2. Gene content 3. Gene order © 2012 Pearson Education, Inc.

Multigene Tree 16 S r. RNA Gene Tree Photobacterium damselae Photobacterium leiognathi Photobacterium mandapamensis 50 changes FS-2. 1 FS-4. 2 FS-3. 1 FS-5. 1 FS-2. 2 Photobacterium phosphoreum ATCC 11040 T FS-5. 2 Photobacterium angustum Photobacterium phosphoreum Photobacterium iliopiscarium ATCC 51761 NCIMB 13476 NCIMB 13478 NCIMB 13481 Photobacterium iliopiscarium ATCC 51760 T Photobacterium kishitanii chubb. 1. 1 ckamo. 3. 1 canat. 1. 2 hstri. 1. 1 calba. 1. 1 BAA-1194 T apros. 2. 1 ckamo. 1. 1 vlong. 3. 1 © 2012 Pearson Education, Inc. Photobacterium kishitanii

Classification and Nomenclature Classification Organization of organisms into groups on the basis of either phenotypic similarity or evolutionary relationship o Prokaryotes are given descriptive genus names and species epithets following the binomial system of nomenclature used throughout biology o Assignment of names for species and higher groups of prokaryotes is regulated by the International Code of Nomenclature of Bacteria o Major references in bacterial diversity: o Bergey’s Manual of Systematic Bacteriology o The Prokaryotes © 2012 Pearson Education, Inc.