A Survey of the Microbial World
Chapter 10- Classification of
Microorganisms
Siti Sarah Jumali
Room 14 Level 3 (ext 2123)
www.slideshare.net/sarah_jumali
The prokaryotes kingdom
• The prokaryotes kingdom
– Bacteria and Archaea
– Classification and identification
– Bergey’s manual and bacteria taxonomy
– Biochemical tests
Evolution
• Similarities among organisms such as having
plasma membrane, the use of ATP, and
possessing DNA are the result of evolutiondescent from common ancestor
• Darwin (1859) says natural selection was
responsible for similarities and difference
among organisms.
Evolution cont’d
Phylogenetic relationship
Evolution can be deduced from phylogeny.
• Taxa (singular: taxon)- a group of one or more
organisms
• Taxonomy- put organisms into categories
(taxa) to show degrees of similarities between
organisms
• Phylogeny or systematics- study of
evolutionary history of organisms
The Domain of Life
(The 3 Domains)
• Comparing cells through ribosomes
– Ribosomes are different in every cells
– Ribosomes are present in all cells
– Comparing the sequences in ribosomal RNA
(rRNA) gives 3 distinct groups:
• Eukaryotes
• Prokaryotes-bacteria and archaea (2 different types or
prokaryotes)
• Differ in membrane lipid structure, transfer RNA
molecules (tRNA) and sensitivity to antibiotics
Eukarya
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Animals
Fungi
Plants
Protists
Eukarya
Prokayotes and Archaea
• Prokaryotes
– pathogenic and non-pathogenic
– Found in soil and water
• Archaea
– includes prokaryotes that do not have peptidoglycan in their
cell walls
– Live in extreme environments and carry out unusual
metabolic processes
– Includes
• Methanogens ( strict anaerobes that produce CH4 from CO2 and H2
• extreme halophiles
• hyperthermophiles
The Domain of Life (The three Domains)
Origin of mitochondria
Origin of choroplast
DNA passed from
ancestors are called
conserved
Nucleoplasm grows larger
Endosymbionts
• Endosymbiotic theory
– Eukaryotic cells evolved from prokaryotic cells
– Eukaryotic cells and prokaryotic cells live in one
another (mitochondria and chloroplast)
The 3 Domains
And..only bacteria is sensitive to antibiotics
Classification of microorganisms
• Scientific nomenclature
– Genus
– Specific epithet (species)
Binomial nomenclature
– Eg. Rhizopus stolonifer
–rhizo –rootlike structure of fungus,
- stolo- long hyphae
– Enables identification of fungus which tells us the
right treatment that can be used
– Follows the trend
• Genus, Family, Order, Class, Phylum, Kingdom,
Domain
Classification of Prokaryotes
• Found in Bergey’s manual of systematic
bacteriology
• Prokayotes are divided into 2 domains- abcteria
and archaea
• Domain divided into phyla
• Based on rRNA sequence similarities
• Class Order  Family  Genera  Species
Classification of Prokaryotes cont’d
• Eukaryotes- a group of closely related organisms
that can interbreed
• Prokaryotes- cell division is indirectly tied to
sexual conjugation, infrequent and not necessarily
species-specific
– Therefore termed as population of cells with similar
characteristics
– Bacteria grown in media at a given time are culture
– Pure culture is often a clone
– But in some cases, the same species are dissimilar in
all ways, therefore called a strain
Classification of Eukaryotes
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Animals
Fungi
Plants
Protists
Eukaryotic Cells
Classification of Viruses
• Not part of either domains
• Not composed of cells
• Use anabolic machinery within host cell to
multiply
• Viral genome can direct biosynthesis inside a cell
• Some can be incorporated into the host’s genome
• Virus is more closely related to its host than to
other virus
• Viral species- morphology, genes, enzymes
• Obligatory intracellular parasites
Viruses
• Hypotheses on the origin of viruses
1) Arose independently replicating strands of
nucleic acids such as plasmids
2) They developed from degenerative cells that
through many generations they gradually lost the
ability to survive independently but could survive
when associated with another cell
Virus
Methods of Classifying and Identifying
organisms
• Classification
– Identification is for practical purposes
• E.g to determine appropriate treatment of infection
– Can be identified microscopically
• Morphology
– Bergey’s manual of Determinative Bacteriology
– Based on criteria
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Cell wall composition,
morphology,
differential staining,
oxygen requirements and;
biochemical test
Methods of Classifying and Identifying
organisms cont’d
• Source and habitat of isolate are a part of
identification
• In clinical microbiology,
• Information returned will allow further treatment
• uses transport media (from swab)
– Not nutritive
– Transport media prolongs viability of fastidious organisms
Identification of microorganisms
• Morphological Characteristics
– Cocci, rod, spirilla
– Tells us little about phylogenetic relationship
– Differences in structures such as endospores and
flagella
• Differential staining
– Gram stain and acid-fast stain
– Based on chemical composition of cell wall
– Not useful for identification of wall-less and archaea
with unusual cell wall
Identification of microorganisms
Biochemical tests
• Ability to ferment certain type of carbohydrate
• Gram identification
– All members of the family Enterobacteriacaea are
oxidase-negative
• Genera Escherichia, Enterobacter, Shigella, Citrobacter and
Salmonella
• All of these ferment lactose to produce acid and gas except
for Shigella and Salmonella
• Selective media
• Differential media
• Rapid identification
Biochemical tests
Biochemical tests
Rapid Identification Method
• Manufactured for medically important group
such as enterics
• Perform biochemical tests simultaneously
• Identify bacteria within 4-24 hours
• Numerical identification- result is assigned
with number
– eg positive = 1, negative = 0
– Results are compared to a database of unknown
organisms
Rapid Identification Method cont’d
Rapid Identification of
bacteria using Becton
Dickinson
Serology
• Study of serum and immune responses
• Microorganisms are antigenic, they stimulate antibodies
• Eg inject a rabbit with killed typhoid bacteria and the
rabbit will produce antibody agaisnt typhoid bacteria
• Solution of antibody-Antiserum
• Slide agglutination test– put sample on slide and add different known antiserum
– Bacteria will agglutinate when mixed with antibodies in
response to species or strain of bacterium
– Positive test is observed in the presence of agglutination
Serology cont’d
• Serological testing
– Can differentiate not only among microbial species
but also strains within species
– Also include ELISA and Western Blotting
• Strains with different antigens are called
serotypes, serovars or biovars
– E.g Different antigens in the cell walls of various
serotypes of streptococci stimulate different
antibodies
Serology cont’d
• But because closely related bacteria also produce
some similar antigens,
– serological testing can be used to screen
bacteriological isolates for possible similarities
• ELISA (Enzyme linked Immunosorbent Assay)
– Used to detect AIDS
– Fast and can be read by computer scanner
– Known antibodies are placed in microplate wells, and
bacteria are added into it
– Reaction produced allows identification of bacteria
Serology cont’d
Western blot
Western blot
ELISA
ELISA cont’d
Other techniques for identification
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Phage typing
Fatty acids profile
Flow cytometry
DNA base composition
DNA fingerprinting
Polymerase Chained Reaction (PCR)
Nucleic Acid Hybridization
Other techniques for identification
• Phage typing
– Looks for similarities among bacteria
– Useful to trace the origin and the cause of outbreak
– determines which phage the bacterium is
susceptible to
• Fatty acids profile
– Fatty Acids methyl esther (FAME)
– Separate cellular fatty acids and compare to fatty
acids profile of known organisms
Flow cytometry
– Identify bacteria without culturing
– Detect difference in electrical conductivity
between cells and the surrounding medium
– Provide information on the size, shape, density and
– Can detect fluorescent cells such as Pseudomonas
or fluorescent tagged cells
Flow cytometer
Other techniques for identification
• DNA base composition
– Percentage of guanine and cytosine (G + C), indirectly tells
the composition of (A + T)
– Similar organisms may have about the same GC percentage
• DNA fingerprinting
– RFLP is used to break DNA fragments (Restriction
enzymes)
– Determine source of hospital-acquired infection
• Polymerase Chained Reaction (PCR)
– Increase amount of DNA
– Detects presence of microorganisms on gel electrophoresis
– Taq polymerase
Nucleic acid Hybridization
• Southern Blotting
– The use of probe
• DNA chips
– The use of probe
– Fluorescent dye
• Ribotyping and rRNA sequencing
– All cells contain RNA
– RNA underwent lots of changes over time
– Does not require cells to be cultured in the laboratory
• FISH (Fluorescent In Situ Hybridization)
– Fluorescent-dye labeled
– Can be used to detect bacteria in drinking water or in patient less
than 24 hr
Nucleic acid Hybridization
FISH- Ikan
Putting Classification Methods Together
• Dichotomous keys
– Identification based on successive questions: Yes/
No, Positive/ Negative
• Cladograms
– Branches
– Using computer
Questions???