Microbial Taxonomy PDF

REAN STAR PAULINE C. CORTINA, RMT Taxonomy area of biologic science comprising three distinct but highly interrelated disciplines: üClassification üNomenclature (naming) üIdentification of organisms  orderly classification and grouping of organisms into taxa (categories) based on simila...

REAN STAR PAULINE C. CORTINA, RMT Taxonomy area of biologic science comprising three distinct but highly interrelated disciplines: üClassification üNomenclature (naming) üIdentification of organisms  orderly classification and grouping of organisms into taxa (categories) based on similarities and differences in genotype and phenotype Carl von Linne: laid down the basic rules for taxonomic categories CLASSIFICATION  method for organizing microorganisms into groups or taxa based on similar morphologic, physiologic, and genetic traits Hierarchical classification system consists of the following taxa designations: a. Domain: Bacteria and Archaebacteria b. Kingdom: contains similar divisions or phyla c. Phylum: contains similar classes; equivalent to the Division taxa d. Class: contains similar orders e. Order: contains similar families f. Family: contains similar genera group of organisms that may contain multiple genera and consists of organisms with a common attribute Example:Enterobacteriaceae, Streptococcaceae g. Genus: contains similar species based on various genetic and phenotypic characteristics shared among the species h. Species: most basic of the taxonomic groups and can be defined as a collection of bacterial strains that share common physiologic and genetic features and differ notably from other microbial species  i. Subspecies: taxonomic subgroups within a species  species subdivided based on phenotypic the following differences: a. Biotype considered the same species with the same characteristic genetic makeup that displays differential physiologic characteristics based on biochemical test result differences b. Serotype based on serologic differences Phage typing (based on susceptibility to specific bacterial phages) has also been used for this purpose Note!!! ØDiagnostic microbiologists traditionally emphasize placement and naming of bacterial species into three categories: üthe family üa genus üa species ØSpecies definitions are distinguished using DNA profiling, including a nearly complete 16S rRNA sequence in combination with phenotypic traits NOMENCLATURE  naming of microorganisms according to established rules and guidelines set forth in the International Code of Nomenclature of Bacteria (ICNB) or the Bacteriological Code (BC) Genus designation first letter is always capitalized Species designation first letter is always lower case ØTwo components are used simultaneously and are printed in italics or underlined in script Example: Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus bovis üWhen bacteria are referred to as a group, their names are neither capitalized nor underlined (e.g., staphylococci) IDENTIFICATION process by which a microorganism’s key features are delineated Process of discovering and recording the traits of organisms so that they may be placed in an overall taxonomic scheme organism can then be assigned to the most appropriate taxa (classification) and can be given appropriate genus and species names (nomenclature) IDENTIFICATION METHODS Genotypic Characteristics relate to an organism’s genetic makeup, including the nature of the organism’s genes and constituent nucleic acids Examples: base sequencing of DNA or RNA and DNA base composition ratio to measure the degree of relatedness of two organisms Phenotypic characteristics based on features beyond the genetic level and include both readily observable characteristics and characteristics that may require extensive analytic procedures to be detected Examples: macroscopic (colony morphology on media) and microscopic (size, shape, arrangement into groups or chains of organisms) morphology, staining characteristics (gram-positive or gram-negative), nutritional requirements, physiologic and biochemical characteristics, and susceptibility or resistance to antibiotics or chemicals Major Characteristics Used in Taxonomy Classical Characteristics Useful in routine identification of phylogenetic information Example: morphology, physiology and metabolism, ecology and genetic analysis  Phylogenetic and phyletic classification is based on evolutionary relationships instead of general resemblance Molecular characteristics  Based on the study of nucleic acid composition and proteins  Classification by Cellular Type: Prokaryotes, Eukaryotes, and Archaeobacteria ØOrganisms fall into three distinct groups based on type of cell organization and function: prokaryotes, eukaryotes, and archaeobacteria ØTaxonomists have placed all organisms into three domains that have replaced some kingdoms: Bacteria, Archaea, and Eukarya ØEach of these domains is divided into kingdoms based on the similarities of RNA, DNA, and protein sequences Prokaryotes: Archaea and Bacteria (Eubacteria) Eukaryotes: fungi, algae, protozoa, animals, and plants Archaea (Archaeobacteria) closely related to eukaryotic cells than to prokaryotic cells found in microorganisms that grow under extreme environmental conditions cell walls lack peptidoglycan but they mostly contain a protein or glycoprotein wall structure—”S-layer” can stain gram-positive and gram-negative C e l l u l a r s t r u c t u r e i n c l u d e t h e c e l l w a l l , p l a s m a membrane, ribosomes and flagella Do not contain a nucleus and membrane-bound orhganelles Produce through binary fission, fragmentation or budding Examples: Methanospirillum, Halobacterium, Sulfolobus