Different methods of classification (1).pptx

Different methods of classification of microbes  Taxonomy (Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern) is defined as the science of biological classification. In a broader sense it consists of three separate but interrelated parts:...

Different methods of classification of microbes  Taxonomy (Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern) is defined as the science of biological classification. In a broader sense it consists of three separate but interrelated parts: classification, nomenclature, and identification. Once a classification scheme is selected, it is used to arrange organisms into groups called taxa (s., taxon) based on mutual similarity Nomenclature is the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules Identification is the practical side of taxonomy, the process of determining if a particular isolate belongs to a recognized taxon  One of the oldest classification systems, called a natural classification, arranges organisms into groups whose members share many characteristics and reflects as much as possible the biological nature of organisms. The Swedish botanist Carl von Linné, or Carolus Linnaeus as he often is called, developed the first natural classification, based largely on anatomical characteristics, in the middle of the eighteenth century. It was a great improvement over previously employed artificial systems because knowledge of an organism’s position in the scheme provided information about many of its properties For example, classification of humans as mammals  However, the taxonomic assignment of microbes is not necessarily rooted in evolutionary relatedness. For instance, bacterial pathogens and microbes of industrial importance were historically given names that described the diseases they cause or the processes they perform (i.e., Vibrio cholerae, Clostridium tetani, and Lactococcus lactis). Although these labels are of practical use, they do little to guide the taxonomist concerned with the vast majority of microbes that are neither pathogenic nor of industrial consequence In practice, determination of the genus and species of a newly discovered procaryote is based on polyphasic taxonomy, includes phenotypic, phylogenetic, and genotypic features  Characterization, Classification & Identification are major objectives in all branches of the biological sciences Classification is a means of bringing order to the bewildering variety of organisms in nature Once we learn the characteristics of an organism - compare it with other organisms to discover similarities and differences Not only prerequisite for classification but essential roles in nature Hierarchical Arrangement in Taxonomy  Numerical taxonomy Development of computers has made possible the quantitative approach Peter H. A. Sneath and Robert Sokal - defined numerical taxonomy as “grouping by numerical methods of taxonomic units into taxa on the basis of their character states”  A scientist may determine many characteristics (usually 100 to 200) for each strain giving equal weightage Using computer calculates the % similarity (%S) of each strain to every other strain NS – number of same characteristics ND – number of different  Those strains having a high %S to each other are placed into groups The degree of similarity needed to rank a group as a species, genus, or other taxon is a matter of judgment on the part of the taxonomist This method of classification has great practical usefulness as well as being relatively unbiased in its approach; it also yields classifications that have a high degree of stability and predictability  The results of numerical taxonomic analysis are often summarized with a treelike diagram called a dendrogram Numerical taxonomic methods also can be used to compare sequences of macromolecules such as RNA and proteins Clustering and Dendrograms in Numerical Taxonomy  Genetic Relatedness Microbial genomes can be directly compared, and taxonomic similarity can be estimated in many ways 1. Determination of DNA base composition 2. DNA homology experiments 3. Ribosomal RNA homology experiments and ribosomal RNA oligonucleotide cataloging  G + C content Percent of G C in DNA, reflects the base sequence and varies with sequence changes as follows  G+C content can be ascertained after hydrolysis of DNA and analysis of its bases with high-performance liquid chromatography (HPLC) Physical method – Melting of temperature (Tm) Greater G+C content : greater melting point A DNA Melting Curve  Two organisms of the same or similar species that are very closely related will have very similar mol% G + C values Two organisms having quite different mol% C + C values are not very closely related Organisms that are completely unrelated may have similar mol% G + C values  G+C content data are valuable in at least two ways Confirm a taxonomic scheme developed using other data - If organisms in the same taxon are too dissimilar in G+C content, the taxon probably should be divided  Characterizing prokaryotic genera because the variation within a genus is usually less than 10% even though the content may vary greatly between genera For example, Staphylococcus has a G+C content of 30 to 38%, whereas Micrococcus DNA has 64 to 75% G+C; yet these two genera of gram-positive cocci have many other features in common  Nucleic Acid Hybridization – DNA homology The double-stranded DNA molecules from two organisms are heated to convert them to single strands The single strands from one organism are then mixed with those from the other organism and allowed to cool If the two organisms are closely relate heteroduplexes will form otherwise not DNA-DNA, RNA-RNA, DNA-RNA  16S rRNA sequence rRNAs from small ribosomal subunits (16S and 18S rRNAs from procaryotes and eucaryotes, respectively) Ideal for studies of microbial evolution and relatedness 1. play the same role in all microorganisms 2. genes encoding SSU rRNAs cannot tolerate large mutations 3. change very slowly with time 4. do not appear to be subject to horizontal gene transfer  The ability to amplify regions of rRNA genes (rDNA) by the polymerase chain reaction (PCR) and sequence the DNA using automated sequencing technology has greatly increased the efficiency by which SSU rRNA sequences can be obtained In this means that PCR primers are readily available or can be generated to amplify rDNA from both cultured and uncultured microbes Ribosome Database Project has sequences from over 200,000 microbes  Multilocus Sequence Typing (MLST) The use of DNA sequences to determine species and strain identity requires the analysis of genes that evolve more quickly than those that encode rRNA Often five to seven conserved housekeeping genes are sequenced and compared  Multiple genes are usually examined to avoid misleading results that can arise through lateral gene transfer MLST is helpful for differentiating isolates at the strain and species levels, the data become too difficult to interpret at higher taxonomic levels  Genomic Fingerprinting Pattern of DNA fragments generated by endonuclease cleavage (called restriction fragments) is a direct representation of nucleotide sequence The comparison of restriction fragments between species and strains is the basis of Restriction Fragment Length Polymorphism (RFLP) analysis Relative Taxonomic Resolution of Various Molecular Techniques