Chapter 17 Microbial Taxonomy. Microbial Classification and Taxonomy Taxonomy? Refer Pg 389; 17.2...
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Transcript of Chapter 17 Microbial Taxonomy. Microbial Classification and Taxonomy Taxonomy? Refer Pg 389; 17.2...
Chapter 17
Microbial Taxonomy
Microbial Classification and Taxonomy
Taxonomy? Refer Pg 389; 17.2Science of biological classificationConsists of three separate but interrelated
partsclassification – arrangement of
organisms into groups (taxa, sing.taxon)nomenclature – assignment of names to
taxaidentification – determination of taxon to
which an isolate belongs
Natural Classification
Natural Classification arranges organisms into groups whose members share many characteristics
First such classification in 18th century developed by Linnaeus based on anatomical characteristics
this approach to classification does not necessarily provide information on evolutionary relatedness in microbes
E.g classification of humans as mammals –milk producing, hair, self regulating temp. etc.
Polyphasic Taxonomy
Polyphasic Taxonomy is used to determine the genus and species of a newly discovered procaryote
incorporates information from phenetic (phenotypic) and phylogenetic analysis
Phenetic Classification
groups organisms together based on mutual similarity of phenotypes
can reveal evolutionary relationships, but not dependent on phylogenetic analysis
E.g because motility and flagella are always associated in particular organisms, it is reasonable to suppose that flagella is involved in some types of motility
Phylogenetic Classification
Phylogenetic, also called phyletic classification systems
Phylogeny is based on evolutionary development of a species
usually based on direct comparison of genetic material and gene products this approach is widely accepted large databases exist for rRNA sequences
Taxonomic Ranks and Names
microbiologists often use informal names that don’t necessarily have taxonomic significance e.g., purple bacteria,
spirochetes, methane-oxidizing bacteria
Table 17.2 shows the levels of taxonomic names
Defining Procaryotic SpeciesThe basic taxonomic group in microbial
taxonomy is the species. Cannot use definition based on
interbreeding because procaryotes are asexual.
A prokaryotic species is collection of strains that share many stable properties and differ significantly from other groups of strains.
Also suggested as a definition of species as a collection of organisms that share the same sequences in their core housekeeping genes (genes required to code for products needed by cells)-bases on sequence data.
Figure 17.6 Hiearchical arrangement in Taxonomy
Strains
Descended from a single, pure microbial culture
Strains vary from each other in many waysBiovars – differ biochemically and
physiologicallyMorphovars – differ morphologicallySerovars – differ in antigenic
properties
Type Strain
Usually one of first strains of a species studied
Often most fully characterizedNot necessarily most representative
member of species
Genus
Genus- well-defined group of one or more strains
Clearly separate from other genera Often disagreement among
taxonomists about the assignment of a specific species to a genus
Binomial System of Nomenclature
Binomial system was devised by Carolus Linnaeus Each organism has two names
genus name – italicized and capitalized (e.g., Escherichia)
species epithet – italicized but not capitalized (e.g., coli) can be abbreviated after first use (e.g., E. coli) a new procaryotic species cannot be recognized
until it has been published in the International Journal of Systematic and Evolutionary Microbiology
Techniques for Determining Microbial Taxonomy and
PhylogenyClassical characteristics morphological physiological metabolic ecological genetic
Molecular characteristics nucleic acid base composition nucleic acid hybridization nucleic acid sequencing genomic fingerprinting amino acid sequencing
Ecological Characteristics
Life-cycle patternsSymbiotic relationshipsAbility to cause diseaseHabitat preferencesGrowth requirements
Genetic Analysis Genetic Analysis Study of chromosomal gene exchange by
transformation and conjugation plasmids can be used for the analysis of
phenotypic traits
Nucleic Acid Base Composition Determine the G + C content
Where G=Guanine, C=Cytosine, A=adenine and T=Thymine ( nucleotide are the DNA base)
The G+ C content is often estimated by determining the melting temperature (Tm) of the DNA
Higher G + C gives a higher melting temperature
100%TACG
CGC)(GMol%
Nucleic Acid Hybridization
Nucleic Acid Hybridization measure of sequence homology ( molecular relatedness) common procedure for hybridisation:
bind nonradioactive DNA to nitrocellulose filter incubate filter with radioactive single-stranded
DNAThe quantity of radioactivity bound to the filter
reflects the amount of hybridisation between the 2 DNA and thus similarity of the 2 sequences.
…Nucleic Acid Hybridization
measure amount of radioactive DNA attached to filter.
The degree of similarity is expressed as the % of experimental DNA radioactivity retained on the filter as compared to other sps. of the same genus under the same conditions.
Usually less than 5 % difference in melting point ( T m ) is considered as members of same sps.
Nucleic Acid Sequencing
Nucleic Acid Sequencingmost powerful and direct method for
comparing genomessequences of 16S (procaryotes) and
18S (eucaryotes) ribosomal RNA (rRNA) are used most often in phylogenetic studies
complete chromosomes can now be sequenced and compared
…Nucleic Acid Sequencing
Comparative Analysis of 16S rRNA Sequences: Oligonucleotide signature sequences are short
conserved sequences specific for a phylogenetically defined group of organisms
either complete or, more often, specific rRNA fragments can be compared
when comparing rRNA sequences between 2 organisms, their relatedness is represented by an association coefficient or Sab value
the higher the Sab value, the more closely related the organisms
Use of DNA Sequences to Determine Species Identity
DNA sequences can also be used to determine species strains in addition to genus
It requires analysis of genes that evolve more quickly than rRNA encoding genes
Multilocus sequence typing (MLST), the sequencing and comparison of 5 to 7 housekeeping genes instead of single gene is done.
This is to prevent misleading results from analysis of one gene.
Genomic Fingerprinting
Genomic Finger Printing also used for microbial classification and determination of phylogenetic relationships
Genomic Finger Printing does not involve nucleotide sequencing
Can be used because of multicopies of highly conserved and repetitive DNA sequences present in most gram-negative and some gram-positive bacteria
Multicopies can be obtained by Polymerase chain reaction using restriction enzymes
…Genomic Fingerprinting
uses restriction enzymes (endonucleases) that recognize specific nucleotide sequences
Restriction Enzyme cuts DNA at specific sites
Restriction fragments are compared by Gel Electrophoresis.
…Genomic Fingerprinting
Repetitive sequences amplified by the polymerase chain reaction
amplified fragments run on agarose gel, with each lane of gel corresponding to one microbial isolate
pattern of bands analyzed by Gel Document system comparison of bands is called restriction fragment length
polymorphism (RFLP) It allows for identification to species, subspecies
and often allows strain level identification PCR has a widespread application
Figure 17.9 Genomic Finger Printing
Amino Acid Sequencing
the amino acid sequence of a protein is a reflection of the mRNA sequence and therefore of the gene which encodes that protein
amino acid sequencing of proteins such as cytochromes, histones and heat-shock proteins has provided relevant taxonomic and phylogenetic information
cannot be used for all proteins compare protein mass spectra
Assessing Microbial Phylogeny
evolutionary relationships represented using phylogenetic trees
A phylogentic tree is a graph which connects nodes and branches
Phylogenetic Trees
Figure 17.11
a. Unrooted tree –b. Rooted treehas node thatserves ascommonancestor
The Major Divisions of Life
Currently held that there are three domains of life Domain BacteriaDomain ArchaeaDomain Eucarya
scientists do not all agree how these domains should be arranged in the “Tree of Life”
Figure 17.12
Impact of Horizontal Transfer
extensive horizontal gene transfer has occurred within and between domains
pattern of microbial evolution is not as linear and treelike as once thought
Universal Phylogenetic Tree with Lateral Gene Transfer
Figure 17.13
Domain Eucarya
The domain Eucarya is divided into four kingdoms by most biologists:
The domain Eucarya is divided into four kingdoms by most biologists:Kingdom Protista, including the protozoa
and algaeKingdom Fungi, the fungi (molds, yeast, and
fleshy fungi)Kingdom Animalia, the multicellular animalsKingdom Plantae, the multicellular plants
Domain Archaea
Phylogeny of domain ArchaeaBased primarily on rRNA sequence data,
domain Archaea is divided into two phyla
Phylum CrenarchaeotaPhylum Euryarchaeota
Domain Bacteria
Phylogeny of domain Bacteria
Bergey’s Manual of Systematic Bacteriology
In 1923, David Bergey, bacteriologist, Univ of Pennsylvania and 4 other colleagues published a classification of bacterial sps.
It is an accepted system of procaryotic taxonomy
Detailed work containing descriptions of all procaryotic species currently identified
The First Edition of Bergey’s Manual of Systematic Bacteriology
The first edition, published in 1984 and is currently in its ninth edition
It contained descriptions of all known procaryotic species then identified, mostly based on phenotypic characters i.e phenetic
The Second Edition of Bergey’s Manual of Systematic Bacteriology
largely phylogenetic rather than phenetic ; 5 volumes.
procaryotes are divided between two domains and 25 phyla
BibliographyBibliography
Lecture PowerPoints Prescott’s Lecture PowerPoints Prescott’s Principles of Microbiology-Mc Graw Principles of Microbiology-Mc Graw Hill Co.Hill Co.
http://en.wikipedia.org/wiki/http://en.wikipedia.org/wiki/Scientific_methodScientific_method
https://files.kennesaw.edu/faculty/https://files.kennesaw.edu/faculty/jhendrix/bio3340/home.htmljhendrix/bio3340/home.html
http://www.uic.edu/classes/bios/http://www.uic.edu/classes/bios/bios100/lecturesf04am/lect12.htmbios100/lecturesf04am/lect12.htm
http://www.uic.edu/classes/bios/http://www.uic.edu/classes/bios/bios100/summer2003/krebsfull.htmbios100/summer2003/krebsfull.htm
http://www.niles-hs.k12.il.us/jacnau/http://www.niles-hs.k12.il.us/jacnau/chpt9.html#Krebs%20Cyclechpt9.html#Krebs%20Cycle