Chapter 1.

MICROBIAL IDENTIFICATION AND

CLASSIFICATION
1. Naming a strain
2. Identification and classification based on morphology
3. Identification and classification based on genetic markers (genetics)
4. Identification and classification based on biochemical activities (specifically
metabolic reactions)
5. Identification and classification based on nutrition and energy (metabolic
system).
Identification : How they are differentiated from
the others?
•Morphology: cells, colonies, spores
• Mobility
• Cellular structure specifications
•Biochemical reactions in metabolism: sugar
utilizations, type of respiratory, fermentation,
production of enzymes, pigments, acids, - Is it known or un- known?
polysaccharides, lipids and so on. - Are they relatives?

Classification: what their position in a If it is un-known where its

system? Tree of live: Kingdom Phylum position in the tree of life?
Order…. …genus species
Taxonomy: science of classifying organisms with goal of showing relationships
among organisms.
• Taxonomic categories: Taxon / Taxa
• Provides universal names for organisms and a means of identifying them.
Phylogeny (or systematic): evolutionary history of group of organisms.
• Taxonomic hierarchy shows phylogenetic (evolutionary), relationships among
organisms.
• 1969: Living organisms divided into five kingdoms.
• 1978: Two types of prokaryotic cells found. Prokaryotic relationships
determined by rRNA sequence.
 8. Members of the Microbial World?

Prokayotes

Archaea

Eukayotes

Universal Phylogenetic Tree of Three Domains of Life. These evolutionary relationships are based on
rRNA sequence comparisons. Man (Homo) is highlighted in red.
Microorganisms in Kingdoms
yeasts, molds
Protista (microalgae,
protozoa, slime molds
slime molds, protozoa
water molds) water molds
Fungi (yeasts, molds)
microalgae

Bacteria
Archaea

Microorganisms are diverse, and their classification has always been a challenge for microbial taxonomists
 9. How prokaryotic and eukaryotic cells are different?
Prokaryotic cells: organisms with a Eukaryotic cells : have a membrane enclosed
primordial nucleus, have a much simpler nucleus; they are more complex morphologically
morphology than eukaryotic cells and lack a and are usually larger than prokaryotes
true membrane delimited nucleus
microalgae, protozoa, slime molds, water molds,
Bacteria, Archaea yeasts, molds

DNA

If E.coli is the size of a human, then yeast is about the

E.coli 0.2 mm in diameter and 4-8 mm in size of an elephant.
length
S. serevisae (baker yeast) cell is about 5 mm in diameter
 Virus and phages are not classified in a kingdom because they do not live
independently, they need a host

They are particles made by proteins and DNA or RNA

Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species: depending on the host name

Viruses infect eukaryotic cells

Bacteriophages infect bacterial cells
 Scientific classification
7. Scientific name
Kingdom (giới) Bacteria
Phylum (ngành) Actinobacteria
Class (lớp) Actinobacteria
Order (bộ) Actinomycetales
Suborder: Corynebacterineae
Family (họ) Mycobacteriaceae
Genus (chi) Mycobacterium
Mycobacterium tuberculosis is a pathogenic Species (loài) M. tuberculosis
bacterial species in the family Mycobacteriaceae and Binomial name
the causative agent of most cases of tuberculosis. Mycobacterium tuberculosis
First discovered in 1882 by Robert Koch

Strain (an example) •Isolation profile

•Identification
Mycobacterium tuberculosis H37Rv •biochemistry markers
•genetic markers etc.
 Scientific Nomenclature
Scientific Binomial Source of Genus Name Source of
Specific Epithet

Klebsiella pneumoniae Honors Edwin Klebs The disease

Pfiesteria piscicida Honors Lois Pfiester Disease in fish

Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in mice

(muri-)

Streptococcus pyogenes Chains of cells (strepto-) Forms pus (pyo-)

Saccharomyces cerevisiae Fungus (-myces) that uses Makes beer (cerevisiae)

sugar (saccharose)

Trypanosoma cruzi Corkscrew-like (trypano-, Honors Oswaldo Cruz

borer; soma-, body)
7. Identify a microbe based on its morphology?

1.Bacteria
2. Archaea
3. Fungi
4.Slim molds
5.Protozoa
6. Microalgae
7.Virus/phages

spiral-shaped
motile bacteria
Based on size of the cell
Based on cellular structure
 Bacteria
• Prokaryotes
• Peptidoglycan cell walls
• Binary fission
• For energy: use organic chemicals,
inorganic chemicals, or
photosynthesis
Desulfovibrio vulgaris is the best-studied
sulfate-reducing bacteria species; the bar in
the upper right is 0.5 mm long.

That can obtain energy by oxidizing organic compounds or molecular hydrogen

(H2) while reducing sulfate (SO42- ) to hydrogen sulfide (H2S). In a sense, these
organisms "breath" sulfate rather than oxygen in a form of anaerobic respiration
Based on the Shapes of Bacterial Cells
 Bacterial classification : Proteobacteria and Non-proteobacteria
Phylum Proteo-bacteria Nonproteo-bacteria
Contribution to Very divers
diversity > 32%
Gram staining negative negative and positive
Structure lipopolysaccharide
outer membrane
Mobility Flagella, Non mobility or gliding moving
rare non mobility or gliding
Energy and acultatively or obligately anaerobic, Photrophic and
metabolism chemoautotrophic and heterotrophic Chemotrophic

Representative genus Pathogenic (E.coli, Salmonella, Cycanobacteria

Helicobacter,
 Based on Bacterial Colony Morphology

Examples of commonly Colony morphology can vary dramatically with the

observed colony medium on which the bacteria are growing. These
morphologies beautiful snowflake -like colonies were formed by
Bacillus subtilis growing on nutrient-poor medium
 Bacterial Colony Morphology
Variations in bacterial colony morphology seen with the naked eye

looking down at the top

of the colony

viewed from the

side (vertically)
as the plate is
held at eye level
 Actinobacteria
• Well-defined clade of high GC bacteria,
most are Gram positive
• Habitats: soil, rhizosphere, marine and
freshwater systems.
• Several are important human and animal
pathogens, a limited number being
pathogenic to plants.
• The vast majority of Actinobacteria are
important saprophytes capable of breaking
down a wide range of plant and animal
debris in the process of decomposition.

Some genera such as Streptomyces and Micromonospora produce a diverse range of

bioactive metabolites, including antibiotics, enzymes, enzyme inhibitors, signaling molecules,
and immune-modulators.
 Actinobacteria (xạ khuẩn)

Phan Cảnh Trình 2021: finding-antimicrobial-strains-of-soil-borne-actinobacteria-in-vietnam

 Archaea (cổ khuẩn)
• Prokaryotic
• Lack peptidoglycan
• Live in extreme environments, include:
Methanogens- anaerobes that produce large amounts of methane gas (CH4)
important in the carbon cycle: - strict anaerobes - they are poisoned by
oxygen- often used in sewage treatment plants
Extreme halophiles- "salt-loving" Archaea found in such extremely saline locales
such as the Dead Sea and the Great Salt Lake mostly heterotrophs, but can
switch to photosynthesis because of a unique pigment called
bacteriorhodopsin
Extreme thermophiles- "heat-loving" Archaea found in hot springs, acidic soils,
near volcano vents, etc. They use H2S to generate ATP.
 Typical Shapes of methanogenes cells

Methanothermus
fervidus, a short rod
form without flagella

Methanosarcina barkeri, a
Methanococcus lobed coccus form lacking
janaschii, a coccus form flagella
with numerous flagella
attached to one side

Methanobacterium
thermoautotrophicum,
an elongate rod form.
 Bergey’s Manual:
Classifying and Identifying Prokaryotes

Bergey’s Manual of Determinative Morphology, differential

Bacteriology: staining, biochemical tests
Is standard reference for laboratory to test for presence of
identification of bacteria. various enzymes.

Bergey’s Manual of Systematic

Bacteriology
Based on rRNA sequence
Provides phylogenetic information on
bacteria and archaea
 Microbial fungi
1. Fungi are widely distributed and are found wherever moisture is present. They are of great
importance to humans in both beneficial and harmful ways.
2. Cell wall present, composed of cellulose and/or chitin. Eukaryotes - true nucleus and other
organelles present. Food storage - generally in the form of lipids and glycogen.
3. All fungi require water and oxygen (no obligate anaerobes).
4. Fungi exist primarily as filamentous hyphae. A mass of hyphae is called a mycelium.
5. Like some bacteria and protists, fungi digest insoluble organic matter by secreting exoenzymes,
then absorbing the solubilized nutrients.
6. Two reproductive structures occur in fungi:(1) sporangia form asexual spores, and (2) gametangia
form sexual gametes.
7. Like the study of protists,fungal systematics is an area of active research. Recently, 6 fungal
subdivisions are presented, including the Chytridiomycetes, Zygomycota, Ascomycota,
Glomeromycota, and Microsporidia.
 Microbial fungi
yeasts, Aspergilus sp., Penicilium sp.,
Trichoderma.sp. etc

dikaryotic stage

no sexual stage
no sexual stage

Human pathogens

flagellated fungi
(water ecology) Mucor sp.
 Microbial fungi
1. Chytridiomycetes are a group of terrestrial and aquatic fungi that reproduce by motile
zoospores with single, posterior, whiplash flagella.
2. The Zygomycota are characterized by resting structures called zygospores—cells in which
zygotes are formed.
3. The Ascomycota form zygotes within a characteristic saclike structure, the ascus. The ascus
contains two or more ascospores.
4. Yeasts are unicellular fungi—most are ascomycetes.
5. Basidiomycetes possess dikaryotic hyphae, one of each mating type. The hyphae divide
uniquely, forming basidiocarps within which club-shaped basidia can be found. The basidia
bear two or more basidiospores.
6. Ustilaginomycetes and Urediniomycetes include important plant pathogens, whereas the
Glomeromycota form important associations with vascular plants and enhance plant
nutrient uptake.
7. Some members of Microsporidia are considered emerging pathogens of humans.
A spore germinates and hypae grows into mycelium forming a fungal colony

germination

Growth

VIDEO CLIPS: Mold Time Lapse

https://www.youtube.com/watch?v=JsQHWj2RfXg
 Asexual Reproduction in the Fungi and
Some Representative Spores

(b) (c)
(a) Transverse fission. (b) Hyphal fragmentation resulting
in arthroconidia (arthrospores) and (c) chlamydospores.
 Asexual Reproduction in the Fungi and
Some Representative Spores.

(d) Sporangiospores in a sporangium. (e) Conidiospores arranged in chains at the end of a

conidiophore. (f) Blastospores are formed from buds off of the parent cell
Thermomucor pusillus (previously called
Mucor pusillus), a thermophilic species
Trichoderma harzianum
common in composts
(white areas do not
contain spores, green
densed masses of
spores (conidia)
This genus is important
for solid wastes
treatment and
Aspergillus spp. are important preventing plant
fungi in food industry pathogens
 Yeasts
• Single celled fungi
• Reproduction by
“budding”
• Adapted to liquids
– Plant saps
– Water films
– Moist animal
tissues

Saccharomyces
sp. used in wines Candida spp. , some are human
and alcohols pathogens and some are organic
production pollutants degraders
Protists- "the kingdom of primitive forms"

• Animal-like Microfungi
• Fungi-like
• Plant-like
Water, Soil, Sediment and
Activated Sludge
microorganisms
Extremely
environments
 Animal-like protists - protozoa

• Eukaryotes
• Absorb or ingest organic
chemicals
• May be motile via
pseudopods, cilia, or flagella
• Most free some parasites

Amoeba Helizoans
VIDEO CLIPS: Diversity_of_Protists
https://www.youtube.com/watch?v=Ln69k7LyTsU
Animal-like protists - protozoa
Mastigophora (flagellated) - these
are frequently parasitic

Cilliaphora (cilliates) - cilliated protists

Fungi-like protists - heterotrophs

• Slime molds
– have two stages in life cycle
• free living (amoeboid) stage
• plasmodial ("slug") stage
– are often brightly colored
• probably most closely related to sarcodina

Figure 1.1b
Water molds

• Water molds - closely related to true

fungi
– important marine decomposers
– Phytophthora infestans caused Irish
potato famine
• a fish-gill infestation is also caused by a
water mold

Figure 1.1b
 Plant-like protists - photosynthetic
1. Green Algae
• Eukaryotes
• Cellulose cell walls
• Use photosynthesis for
energy (primary
producers)
• Produce molecular
oxygen and organic
compounds
• Metabolically diverse Chlorophytes (green algae)
mostly fresh water species
possess same pigments identical to land
plants - they are their closest relative

Figure 1.1d
2. Chrysophytes - diatoms and their
relatives
prominent photosynthetic pigment :
fucoxanthin
Diatom anatomy
3. Euglenoids - flagellated,
have photoreceptors,
photosynthetic, autotrophic
Dinoflagelates - two flagella and a silicon test, that cause red tides
 CILIA AND FLAGELLA
Whiplash and Tinsel Flagella.
Transmission electron
micrograph of a shadowed
whiplash flagellum, WF, and a
tinsel flagellum, TF, with
mastigonemes.
Coordination of Ciliary Activity.
A scanning electron micrograph of
Paramecium showing cilia (X1,500).The
ciliary beat is coordinated and moves in
waves across the protozoan’s surface,
as can be seen in the photograph
 Viruses
• A cellular
• Consist of DNA or RNA core
• Core is surrounded by a protein coat
• Coat may be enclosed in a lipid envelope
• Viruses are replicated only when they are
in a living host cell
Classification is based on:
– 1) not the host
Enveloped Structure of HIV
– 2) virus’s nucleic acid genome
– 3) the shared physical properties of the infectious agent
(e.g capsid symmetry, dimensions, lipid envelope)
DNA virus RNA virus
8. Identification/classification of
microbe based on physiological
and metabolic characteristics
9. Identification/classification of a microbe based on genetic
characteristics
 16S rRNA genes

S = subunit
r : ribosome
 low conserved regions
16S rRNA genes  species High conserved region genus
E.coli
Mycobacterium spp