PMB 213.BACTERIAL TAXONOMY.docx

**GENERAL PHARMACEUTICAL MICROBIOLOGY** **BACTERIAL TAXONOMY** BRIEF HISTORY Today, microorganism names originate from Four different sources: - Descriptive -- For example Staphylococcus aureus (grape-like cluster of spheres, golden in colour), Streptococcus viridans (chains of spheres...

**GENERAL PHARMACEUTICAL MICROBIOLOGY** **BACTERIAL TAXONOMY** BRIEF HISTORY Today, microorganism names originate from Four different sources: - Descriptive -- For example Staphylococcus aureus (grape-like cluster of spheres, golden in colour), Streptococcus viridans (chains of spheres, \--green in colony color), Proteus vulgaris (first and common), Helicobacter pylori (spiral shaped rod at the entrance to the duodenum) - \- Scientist's names -- e.g., Escherichia coli (Theodor Esherich), Erlichia (Paul Erlich), Nessieria (Albert Neisser), Listeria (Joseph Lister), P-asturella (Louis Pasteur), Yersinia (Alexandre Yersin), Bartonella (Alberto Barton), Morganella (H. de R. Morgan), Edwardsiella (P. R\-\--Edwards) - Geographic places -- e.g., Legionella longbeachiae (Long Beach, \--California), Pasturella tularensis (Tulare County, California), P-seudomonas fairmontensis (Fairmount Park, Pennsylvania), -Mycobacterium genavense (Geneva, Switzerland), Blastomyces -brasiliensis (Brazil), Providencia spp. (Brown University, Providence, RI) - Organizations -- e.g., Legionella (American Legion), Afipia felis (Air -Force Institute of Pathology), Cedecea spp. (Centers for Disease Control), Bilophila wadsworthia (VA Wadsworth Medical Center in Los -Angeles) **INTRODUCTION** A significant period for taxonomy was that of Linnaeus. Carolus Linnaeus (1707-1778), a Swedish naturalist, often referred to as the Father of Taxonomy. He Published *SystemaNaturae.* He also introduced a system of nomenclature of plant and animals known as the Binomial Nomenclature which is also applicable to microorganisms (microbial taxonomy) Living organisms are fascinating by its diversity whether it is plants, animals or microbes. They play important essential roles in nature. So if we arrange these microbes in order or hierarchy based on its similarity or differences in any charac-teristics, we can easily get to know and easily access all the microbes for specific- information. So it is desirable to determine the classification. Greek Philosopher Aristotle who is the one classified the living things as plants and animals -around 2000 years ago. Taxonom-ic Hierarchies: Seven obligate categories - Domain, - Kin-gdom: collection of two or more phyla - Phylum (Divisions): grouping together of classes - Clas-s (ending with -ia and idae for sub class): the arranging together of order - Order (ending with *--ales and -ineae)*: the collection of families with identical characteristic features - *Family* (ending with *--aceae and --oideae for sub family):* the collection of genera - Genus: clubbing together of two or more species. Genus essentially includes a cluster of species all of which predominantly possess subst-antial resemblance to one another to be considered intimately related and, therefore, may be distinguished very conveniently from the respective bonafide members of the other genera. Importantly, the boundaries of certain genera are defined explicitly and sharply; whereas, the boundaries of species are relatively difficult and cumbersome to define precisely - Species ( or specific epithet): the fundamental rank in the classification system. a collection of strains with almost similar characteristic features. Interestingly, one may critically observe that the various strains strategically present very much within species may differ slightly from one another in three prominent manners, namely: a. -Biovars: These are variant bacterial strains and are duly characterized by biochemical or physiological characteristics. b. -Morphovars: These are variants within a species defined by -v-ariation in morphological characteristics. c. \--Serovars: These are variants within a species defined by variation i-n serological reactions \- -Memory Keys: Keep pots clean or family gets sick or kindly pay cash or furn-ish good security **-Bacterial Taxonomy** T\-\--he branch of science that deals with the study of principles and specific procedures of biological classification is called taxonomy (*taxis*-arrangement, *nomos*-law coined by A.P. de candolle1813.Taxonomy enfold three fundamental elements: classification, nomenclature and identification.Therefore bacterial taxonomy is the ordering of -bacteria into groups which is also applicable to other microorganisms (Microbial Taxonomy) **Classificatio-n** This is the arr-angement of organisms into groups on the basis of their affinities or relationships or is the arrangement of organisms into groups or taxa (s., taxon) based on mutual similarity or evolutionary relatedness. It involves the placing of a k-ind of organisms or a group of different kinds of organisms in particular categories depending upon the system of classificaton but in conformity with nomenclature system. It is bringing order to the diverse variety of organisms present in nature. So there are two general ways the classification can be constructed. First one is based on the morphological characters (phenetic classification) and second is based on evolutionary relationship (phylogenetic classification). - [Phenetic -classification]- Grouping organisms together based on the mutual si\--milarity of their phenotypic characteristics. Phenotypic classification-n systems is based on 1. Gram staining and bacterial morphology; 2. Bioche-mical: Many commercial systems have been developed for microbial identification API -- biochemical test profiling -- often carbon \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\--ctivities and other attributes Enterotube -- biochemical test profiling Biolog -- tests usage of 95 different carbon sources and compares results to a database of characterized bacteria 3. physiological data: based on bacterial growth requirements 4. serologic system; 5. Fatty acid analysis: FAME -- fatty acid methyl ester -- this techniques determines the cellular fatty acid profile and compares it to a database of characterized bacteria( a commercial system) the patterns of polar lipids present in the membrane; 6. Composition of cell wall 7. Antibiotic sensitivity; 8. pigment formation; 9. Respiratory quinines; 10. phage typing and environmental reservoir - [Phylogenetic classification]- These are systems based on evolutionary relationships rather than external appearance. Refers to the evolutionary development of a species. It is based on the direct comparison of genetic materials and/or gene product.Genotypic systems include 1. Molecular subtyping; 2. DNA-DNA Hybridization: genomic DNA from one organism is labelled and hybridized with the genomic DNA from another organism. This technique measures the similarity between the two DNAs. Does not work well for comparing distantly related microorganisms. DNA chip technology has made it possible to "print" many different species specific probes (\> 10,000) onto a glass slide (i.e., the "chip"). Genomic DNA is extracted from an unknown organism and labelled with a fluorochrome. The labelled genomic DNA is hybridized with the probes on the chip. Hybridization reactions fluoresce and can be identified by reading the DNA chip with an instrument known as a DNA chip reader 3. The guanine (G)+ cytosine (C) content (% GC): G + C content = the percent of G + C in the DNA. Can be determined by hydrolysis of DNA and HPLC analysis of the resulting bases or by melting temperature (Tm) determination. Organisms that differ in their G + C content by more than 10% are likely to have quite different base sequences. 4. Multilocus Sequence Typing (MLST) ; This technique involves the \--sequencing fragments from 6 to 7 genes (often housekeeping genes) from an organism and comparing these with the same gene set from different strains of the same organism Can distinguish between closely related strains While rRNA gene sequence analysis is capable of identifying organisms to the genus level, MLST is useful for identifying organisms to the species level and below. MLST is not useful above the species level because is it too sensitive This technique has been used in epidemiological studies to track virulent strains of bacteria as well as differentiating strains of a particular pathogen 5. D-NA profiling; 6. 16S rRNA and 18S rRNA gene sequence analysis: Ribosomal RNA sequence analysis -- rRNA genes (i.e., rDNA) from an unknown is isolated, sequenced and compared to database entries. The rDNA can easily be isolated by using rDNA specific primers and PCR. The amplified rDNA gene fragments are sequenced and compared to database entries (e.g., GenBank or Ribosomal Database project) 7. Mu\--lti-gene sequence analysis and 8. Whole-genome sequence analysis 9. Ribotyping \_a technique used for bacterial identification. Genomic DNA is digested with restriction enzymes and then probed with an rRNA probe Banding pattern is compared to a database This technique is also known as molecular fingerprinting because a unique banding pattern appears for virtually any organism. **Nomenclature** Latin,*nomen:* name and *calare*: call.it is the science of providing distinct and proper names to organisms as per the established universal practices and rules so that they can be easily recongnized and differentiated from others.The system developed by Linnaeus is known as Binomial Nomenclature.This is the system of scientific naming using genus as the first part and species as the second part. A species is designated by two Latin names, the first of which denotes the genus, both together characterizing the species. Some rules of Binomial Nomenclature - A scientific name consists of two words, first genus and second species. - The generic name is always written first, which is like a noun having its first letter in capital or upper case form and followed by the species in lower case (the second word is a particular epithet (i.e., a descriptive word) which\--h is not capitalized at all). Species name is never abbreviated - The scientific name is always printed in italics whereas it is underlined while handwritten.This is done to make the scientific name distinct from the text- - Names of all taxa (kingdoms, phyla, classes, orders, families, genera, species, and subspecies) are printed in italics to denote they are Latin words. and should be underlined if handwritten; strain designations and numbers are not. If all the surrounding text is italic, then the binary name would be non-italic (Roman typeface) or underlined - The two-word name are generally followed by the name of the discoverer or author.the author name can be written in full or abbreviated( called the Authority)Take note the authors name is not written in italics - When a species is transferred or revised, the name of the original author is retained but in parenthesis - In case an organism has been given more than one name,the earlier legitimate one is recongnised to be valid (principle of priority) - Names of categories at or above the genus level may be used alone, but species and subspecies names (species names) may not. - Generic name is written out in full the first time it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital letter (e.g., E. coli), provided there can be no confusion with other genera used in the paper. - Vernacular (common) names should be in lowercase roman type, nonitalic - use "sp." for a particular species, "spp." for several species ("spp" stands for "species plural"). These abbreviations are not italicized. In writing, the abbreviation "sp." following the genus indicates a single unidentified species and "spp." indicates multiple species. - subspecies names must be denoted with 'ssp.' when following a species name. Names are italicized or underlined, while ssp. is not italicized or underlined - Plural of genus is genera Plural of specie (sp.) is species (spp.) Plural of medium is media (never say "this culture media") Plural of fungus is fungi Plural of streptococcus is streptococci (staphylococcus - staphylococci; enterococcus - enterococci, etc) Plural of bacillus is bacilli Plural of bacterium is bacteria Plural of alga is algae Plural of protozoan is protozoa **Identification** This is the practical determination of the correct place in a system of classification and finding out the correct name of an organism. it is done with the help of keys. This is carried out for an organism determining its similarity with an already known organism: application of classification & nomenclature to assign proper name to unknown organism and place it in its proper position within classification system: is the practical side of taxonomy, the process of determining that a particular isolate belongs to a recognized taxon. (So in short Identify-Naming them and classify them) New species or strains are deposited in an approved culture collection for future reference - type culture - ATCC - American Type Culture Collection - DSMZ - *Deutsche Sammlung von Mikrooganismen und Zellkulturen* - NCTC- National Collections of Type Cultures and Pathogenic Fungi - NCIMB- National Collections of Industrial and Marine Bacteria - EGSC- *E. coli* Genetic Stock Centre - BGSC- Bacillus Genetic Stock Centre - FGSC- Fungal Genetic Stock Centre **Taxonomical Hierarchies of some bacteria of Pharmaceutical and Medical importance.** +-------------+-------------+-------------+-------------+-------------+ | **Taxonomic | A | B | C | | | Hierarchies | | | | | | ** | | | | | +=============+=============+=============+=============+=============+ | Domain | *Bacteria* | *Bacteria* | *Bacteria* | | | | | | | | | Kingdom | *Bacteria* | *Bacteria* | *Bacteria* | | | | | | | | | Phylum | *Firmicutes | *Proteobact | *Firmicutes | | | | * | eria* | * | | | Class | | | | | | | *Cocci* | *GammaProte | *Bacilli* | | | Order | | obacteria* | | | | | *Bacillales | | *Bacillales | | | Family | * | *Enterobact | * | | | | | eriales* | | | | Genus | *Staphyloco | | *Bacillacea | | | | ccaceae* | *Enterbacte | e* | | | Species | | riaceae* | | | | | *Staphyloco | | *Bacillus* | | | Binomial | ccus* | *Escherichi | | | | name | | a* | *Bacillus | | | | *Staphyloco | | subtilis* | | | | ccus | *Escherichi | | | | | aureus* | a | *Bacillus | | | | | coli* | subtilis* | | | | *Staphyloco | | | | | | ccus | *Escherichi | | | | | aureus* | a | | | | | | coli* | | | +-------------+-------------+-------------+-------------+-------------+ **Taxonomical Hierarchies of some bacteria of Pharmaceutical and Medical importance.** +-----------------+-----------------+-----------------+-----------------+ | **Taxonomic | A | B | C | | Hierarchies** | | | | +=================+=================+=================+=================+ | Domain | *Bacteria* | *Bacteria* | *Bacteria* | | | | | | | Kingdom | *Bacteria* | *Bacteria* | *Bacteria* | | | | | | | Phylum | *Firmicutes* | *Proteobacteria | *Firmicutes* | | | | * | | | Class | *Cocci* | | *Bacilli* | | | | *GammaProteobac | | | Order | *Bacillales* | teria* | *Bacillales* | | | | | | | Family | *Staphylococcac | *Enterobacteria | *Bacillaceae* | | | eae* | les* | | | Genus | | | *Bacillus* | | | *Staphylococcus | *Enterbacteriac | | | Species | * | eae* | *Bacillus | | | | | subtilis* | | Binomial name | *Staphylococcus | *Escherichia* | | | | aureus* | | *Bacillus | | | | *Escherichia | subtilis* | | | *Staphylococcus | coli* | | | | aureus* | | | | | | *Escherichia | | | | | coli* | | +-----------------+-----------------+-----------------+-----------------+