MICROBIOLOGY CHAPTER 10 – CLASSIFICATION OF MICROORGANISMS

Taxonomy – science of the classification of organisms.

Its goal; provides a means of identifying organisms.
THE THREE DOMAINS
THE STUDY OF PHYLOGENETIC RELATIONSHIPS Living organisms are currently classified into three
domains. A domain can be divided into kingdoms.
Charles Darwin
- English naturalist; proposed natural selection was Ribosomes (rRNA) differ in all three cell types.
responsible for the similarities and differences of 1. Eukarya (plants, animals, fungi)
organisms 2. Bacteria (with peptidoglycan)
- Organisms with traits best suited to an environment 3. Archaea (with unusual cell walls)
have higher survival rate
Carl R. Woese
Taxa (sing. taxon) - proposed Domain above the Kingdom level
- categories of organisms showing degrees of - Archaea and bacteria should have separate
similarities due to relatedness through evolution domains on the evolutionary tree

Systematics (Phylogeny) *Each domain shares genes with other domains through
- study of evolutionary history of organisms horizontal gene transfer, which occurred within the
community of early cells.
- The taxonomic hierarchy shows evolutionary, or *DNA passed on from ancestors are described as
phylogenetic, relationships among organisms.
conserved.

Carolus Linnaeus
DOMAIN ARCHAEA
- introduced a formal system of classification with two 1. Methanogens
(2) kingdoms: - strict anaerobes that produce methane (CH 4)
1. Plantae
from carbon dioxide and hydrogen
2. Animalia
2. Extreme Halophiles

Carl von Nageli

- require high concentrations of salt for survival
3. Hyperthermophiles
- proposed that bacteria and fungi belong to plant
kingdom (followed and believed for 100 years)
- normally grow in extremely hot environments

Ernst Haeckel *True nucleus is produced with the infolding of the

plasma membrane surrounding the nuclear region.
- proposed Kingdom Protista to include bacteria,
Evidence: Gemmata Bacteria
protozoa, algae, and fungi
*Endosymbiotic Theory – nucleus was separated; allows
development of organelles
Robert G.E. Murray
- proposed Kingdom Prokaryotae/Monera A PHYLOGENETIC TREE
- Bacteria were separated into the Kingdom - grouping organisms according to common
Prokaryotae in 1968. properties implies that a group of organisms
evolved from a common ancestor
Robert H. Whittaker
- some information for eukaryotic phylogenetic
- Living organisms were divided into five kingdoms in relationships is obtained from fossil records
1969 (1 for Prokaryotes, 4 for Eukaryotes)
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- some fossilized microorganisms include: CLASSIFICATION OF PROKARYOTES
o White Cliffs of Dover, England - standard reference is Bergey’s Manual of
o Stromatolites – filamentous bacteria Systematic Bacteriology; classification according to
phylogenetic relationships
o Cyanobacteria-like microbes (oldest fossil)
- oldest known fossils from 3.5 billion years ago
- Classification does not include Kingdom (Domain,
*Fossil evidence isn’t available for most prokaryotes, Phylum, Class, Order, Family, Genus, Species)
except for isolated living prokaryotes that existed for
(25-40 million years) Prokaryotic Species
 Raul Cano – American microbiologist; grown - population of cells with similar characteristics
Bacillus sphaericus and other microbes
- not directly tied to sexual conjugation
embedded in fossilized plant resin called amber

Culture
*If fossil evidence isn’t available, similarities in genomes
are used to group organisms into taxa. - bacteria grown in media
 Fossil records agree with rRNA sequencing and - often a clone (a population of identical cells
DNA hybridization. derived from a single parent cell)
- sometimes a strain (A group of bacteria derived
Molecular clock from a single cell)
- describe the relationship between evolutionary rate o Closely related strains constitute a bacterial
and time, assuming that the rate of molecular species.
evolution is constant across species
- used to track path of Zika virus CLASSIFICATION OF EUKARYOTES

CLASSIFICATION OF ORGANISMS 1. Protists

- unicellular eukaryotes
Binomial Nomenclature - diverse; where all organisms that didn’t fit to other
- genus name + species epithet kingdoms can be found
- Latin words or latinized by adding: - now divided into Clades (classified protists
- ales (order), aceae (family according to phylogenetic evolution)
- currently being assigned to kingdoms
Eukaryotes Species
- with nucleus; group of closely related organisms that 2. Kingdom Fungi
interbreed only among themselves - unicellular yeasts, multicellular molds,
macroscopic mushrooms
Genus – species that differ from each other but are - possesses hyphae (thin tubes composed of joined
related by descent fungus cells)
Family – related genera
- absorptive chemoheterotrophs that develop from
Order – similar families
spores or fragments of hyphae
Class – similar orders
Phylum – related classes
3. Kingdom Plantae
Kingdom – related phyla
Domain – related kingdoms - multicellular photoautotrophs
- obtains energy through photosynthesis
 MICROBIOLOGY CHAPTER 10 – CLASSIFICATION OF MICROORGANISMS
- includes mosses, ferns, conifers, flowering plants Medical Microbiology
- branch of microbiology that deals with human
4. Kingdom Animalia pathogens (only 5% or less of 11,500 total species
- multicellular ingestive heterotrophs listed in the Approved Lists of Bacterial names)

- obtains nutrients and energy from ingested organic

Transport Media
matter through a mouth
- not nutritive; used to prolong viability of fastidious
- includes sponges, worms, insects, vertebrates
pathogens
- tube of transport medium; where the swab of a
patient’s pus or tissue surface is inserted

VIRUSES
- not composed of cells and do not have ribosomes
- use host’s anabolic machinery to multiply Morphological Characteristics
- more closely related to its hosts than to other - useful in identifying organisms, especially when
viruses aided by differential staining techniques
- according to International Committee on
Taxonomy of Viruses Differential Staining
o Viral Species - based on the chemical composition of cell walls
 it is a population of viruses with similar - not useful in organisms that lack cell walls
characteristics that occupies a particular
- 2 types of differential staining
ecological niche
1. Gram Stain (Gram-positive; Gram-negative)
 obligatory intracellular parasites
2. Acid Fast Stain
- 3 hypothesis of its origin
- for a more limited group of microbes
1. They arose from independently replicating
strands of nucleic acids (i.e. plasmids)
Biochemical Tests
2. They developed from degenerative cells
3. They coevolved with host cells - use of enzymes to differentiate bacteria and yeasts
- can differentiate among the genera
METHODS OF CLASSIFYING - use of selective and differential media can reduce
AND IDENTIFYING MICROORGANISMS time for organism identification
- Limitations of biochemical testing:
Classification Scheme
o mutations and plasmid acquisition can result
- provides a list of characteristics and a means for
in strains with different characteristics
comparison to aid in the identification of an
o large number of biochemical tests needed for
organism
a correct identification
- Bergey’s Manual of Determinative Bacteriology –
standard reference for laboratory identification of
Rapid Identification Methods
bacteria
*Only 1% of bacteria and archaea have been
- designed to perform several biochemical tests
simultaneously
discovered.
- can identify bacteria within 4-24 hours
 MICROBIOLOGY CHAPTER 10 – CLASSIFICATION OF MICROORGANISMS
- manufactured for enterics
 Enzyme-linked Immunosorbent Assay (ELISA)
- sometimes called Numerical Identification
 results of each test are assigned a number - widely used; fast and can be read by a computer
(1 for positive, 0 for negative) scanner

- Automated Rapid Identification - used to detect AIDS through the presence of HIV
 lysis of cells  known antibodies are placed and adhered to
 extraction of proteins through acetonitrile the wells of a microplate
 measurement of molecular mass through  unknown bacterium is added to each well
mass spectrophotometer  its reaction identifies the bacteria

Serology  Western Blotting

- science that studies serum and immune responses - used to identify antibodies in a patient’s serum
in serum - confirms infection of HIV and Lyme Disease
- Microorganims (carries or serves as antigens) that - proteins (antigens) are separated by
enter the human body stimulate it to produce electrophoresis and can be detected by their
antibodies (binds with antigen) reactions with antibodies

Antiserum
- solution of antibodies used in the identification of
microorganisms
Phages/Bacteriophages
- known antisera can be used to identify unknown
bacteria - bacterial viruses that usually cause lysis of the
bacterial cells they infect
1. Slide Agglutination Test  when infected, there is an appearance of
 unknown bacterium is placed in a drop of saline clearings in bacterial growth called plaques
on each of several slides - highly specialized; infect only members of a
 different known antiserum is added particular species or strains within a species
to each sample
 bacteria agglutinate (clump) when mixed with Phage Typing
antibodies produced in response to antigens - identification of bacterial species and strains by
determining their susceptibility to various phages
2. Serological Testing
- trace food-associated infections
- useful in determining the identity of strains and
species, as well as relationships among organisms Fatty Acid Profiles
- includes ELISA and Western Blotting - can be used to identify some organisms
 Serotypes/Serovars/Biovars  Fatty acids
- strains with different antigens - synthesized by bacteria
- same species, different strains - constant for a particular species
 Rebecca Lancefield
 Fatty Acid Methyl Ester (FAME)
- classified streptococcal serotypes by studying - used in clinical and public health laboratories
serological reactions
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- separation of cellular fatty acids to compare - produced when restriction fragments cut a
them to fatty acid profiles of known organisms molecule of DNA wherever a specific base
sequence occurs
Flow Cytometry
- identifies bacteria in a sample by measuring Nucleic Acid Hybridization
physical and chemical characteristics of cells - determines the extent of similarity between base
without culturing it sequences of two organisms
 Flow Cytometer - Single strands of DNA, or of DNA and RNA, from
- detects the presence of bacteria by detecting related organisms will hydrogen-bond to form a
the difference in electrical conductivity between double-stranded molecule
cells and surrounding medium - measures the ability of DNA strands from one
 a moving fluid is forced through a small organism to hybridize (bind through
opening complementary base pairing) with DNA strands of
 the fluid can be dyed by fluorescent another organism
 the fluid is illuminated by a laser
- hybridization level of 70% or above indicates that 2
 scattering of light provides info regarding cell
organisms belong to the same species
size, shape, density, surface through analysis
of a computer
- PCR, Southern blotting, DNA chips, and FISH are
examples of nucleic acid hybridization technique
DNA Sequencing
DNA base composition 1. Nucleic Acid Amplification Tests (NAATs)

- can draw conclusions about organisms’ relatedness - used to amplify a small amount of microbial
DNA to levels that can be tested by gel
- expressed as the % of Guanine-Cytosine base pairs;
electrophoresis
can be used in the classification of organisms
- presence or identification of organism is
- requires great amount of time
indicated by amplified DNA

DNA Fingerprinting
- use of PCR, reverse-transcription PCR, real-
time PCR
- detects genetic similarities and differences through
comparing patterns of two DNA fingerprints
- George Whipple used PCR to determine
causative agent of Whipple’s disease
- used to determine the source of hospital-acquired
infections
2. Southern Blotting
- aims to produce DNA bar code - identify unknown microorganisms
DNA fingerprint
- use of DNA probes in rapid identification
methods
- produced when restriction fragments are
separated by electrophoresis
- detection of specific DNA
- patterns (numbers and sizes of DNA fragments or
3. DNA Chips/Microarray
DNA fingerprints produced by restriction enzymes)
are compared to detect genetic similarities and
- detects a pathogen in a host/environment by
identifying a unique gene to the pathogen
differences
- composed of DNA probes
Restriction fragments - use of fluorescent dye as DNA label of the
organism
 MICROBIOLOGY CHAPTER 10 – CLASSIFICATION OF MICROORGANISMS
- hybridization of DNA probe and DNA sample is
detected by fluorescence

 Ribotyping and Ribosomal RNA Sequencing

- used to classify organisms and determine
phylogenetic relationships
- detects bacteria without culturing it
- used to classify newly discovered organisms

 Fluorescent In Situ Hybridization (FISH)

- uses fluorescent dye-labeled DNA or RNA
probes to stain microorganisms in situ
- determines identity, abundance, relative
activity of microorganisms
- detects bacteria without culturing it

PUTTING CLASSIFICATION METHODS TOGETHER

Dichotomous Keys
- identification of organisms is based on successive
questions with 2 possible answers until organism is
identified

Cladograms
- maps that show phylogenetic relationships among
organisms
 2 rRNA sequences are aligned
 % of similarity between sequences is identified
 horizontal branches are drawn with length
proportional to % of similarity
 species under one node (branch point) arose
from the same ancestor