Lecture 2 PDF

Taxonomy, Classification, Nomenclature Prof. Wael Nabil Hozzein Taxonomy Includes the two disciplines of classification and nomenclature. The bacteria are classified in a hierarchic system based on phenotypic characteristics (morphological, physiological, and che...

Taxonomy, Classification, Nomenclature Prof. Wael Nabil Hozzein Taxonomy Includes the two disciplines of classification and nomenclature. The bacteria are classified in a hierarchic system based on phenotypic characteristics (morphological, physiological, and chemical characteristics). The basic unit is the species. Similar and related species are classified in a single genus and related genera are placed in a single family. Classification in yet higher taxa often takes practical considerations into account, e.g., division into “descriptive sections.” A species is designated by two Latin names, the first of which denotes the genus, both together characterizing the species. Family names end in -aceae. Classification Bacteria are grouped in the domain bacteria to separate them from the domains archaea and eucarya. Within their domain, bacteria are further broken down into taxonomic groups (taxa) based on relationships best elucidated by knowledge of the evolutionary facts. However, little is known about the phylogenetic relationships of bacteria, so their classification is often based on similarities among phenotypic characteristics (phenetic relationships). These characteristics are morphological, physiological (metabolic), or chemical (see Table 3.8) in nature. The role of chemical characteristics in classification is growing in importance, for instance, murein composition or the presence of certain fatty acids in the cell wall. DNA and RNA structure is highly important in classification. DNA composition can be roughly estimated by determining the proportions of the bases: mol/l of guanine + cytosine (GC). The GC content (in mol%). DNA-DNA hybrids, provides information on the similarity of different bacteria and thus about their degree of relationship. Another highly useful factor in determining phylogenetic relationship is the sequence analysis of the (16S/23S) rRNA or (16S/23S) rDNA. This genetic material contains highly conserved sequences found in all bacteria alongside sequences characteristic of the different taxa. In formal terms, the prokaryotes are classified in phyla, classes, orders, families, genera, and species, plus subtaxa if any. Morphological characteristics: Microscopic morphology: » Cell shape e.g. coccus » Size » Arrangement.e.g. clusters, chain » Staining e.g. Gram + or Gram - » Capsule characteristic » Spore morphology e.g. round, oval, terminal » Flagellar arrangement e.g. monotrichous Colonial morphology Colonial appearance like color, shape, texture, margin, elevation …etc. Biochemical tests Examples - Fermentation/oxidation of carbohydrates - Enzyme activities - Metabolism of organic acids, lipids, proteins and amino acids. - pH or redox range of growth -Tolerance of chemical agents In short, these tests collectively define nutritional and physiological interaction of the organism with its environment.  Identifying Bacteria Dichotomous keys used for Morphological identification of organisms characteristics: Useful for identifying eukaryotes Differential staining: Gram staining, acid-fast staining Biochemical tests: Determines presence of bacterial enzymes A clinical microbiology lab report form Nomenclature The rules of bacterial nomenclature are set out in the International Code for the Nomenclature of Bacteria. A species is designated with two Latinized names, the first of which characterizes the genus and the second the species. Family names always end in -aceae. Taxonomic names approved by the “International Committee of Systematic Bacteriology” are considered official. In medical practice, short handles have become popular in many cases, for instance gonococci instead of Neisseria gonorrheae or pneumococci (or even “strep pneumos”) instead of Streptococcus pneumoniae. Scientific Binomial Source of Genus Name Source of Specific Epithet Klebsiella pneumoniae Honors Edwin Klebs The disease Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in mice (muri-) Streptococcus pyogenes Chains of cells (strepto-) Forms pus (pyo-) Trypanosoma cruzi Corkscrew-like Honors Oswaldo Cruz (trypano-, borer; soma-, body) Hierarchy Species Genus Family Order Class Division Phylum Kingdom (1969) Domain (80’s)  Taxonomy Science of Classification of organisms Hopes to show relationships among organisms Is a way to provide universal identification of an organism Phylogeny or Systematics Shows evolutionary relationships and history among organisms Some obtained from fossil record Most bacteria use rRNA sequencing or some other sequence information A goal is to identify all organisms by 2025  The 5 Kingdoms based on nutrient procurement Plantae Multicellular photoautotrophs Animalia ingestive Fungi absorptive Protozoa Mostly singe celled Prokaryotes Phage Typing Determining a strains susceptibility to certain phage or bacterial viruses  Genetics DNA base composition Guanine + cytosine moles% (GC) DNA fingerprinting Electrophoresis of restriction enzyme digests rRNA sequencing Polymerase Chain Reaction (PCR) DNA Hybridization  The 3 domains Eukarya Plants, animals fungi and protists Bacteria (with peptidoglycan) Archaea With unusual cell walls and membranes The Three-Domain System Phylogenetic Relationships of Prokaryotes Differentiate between classification and identification