Naming, Classifying, and Identifying Microorganisms

In a nomenclature system designed by Carolus Linnaeus (1735), each living organism

is assigned two names. The two names consist of a genus – is the first name and
always capitalized and a specific epithet - species, both of which must be
underlined and italicized.

 In the five-kingdom system, all organisms are classified into Prokaryotae (or
monera), Protista, Fungi, Plantae, and Animalia.

 
TAXONOMIC RANKS

FORMAL RANKS EXAMPLE

Kingdom Prokaryotae

Division Gracilicutes

Class Scotobacteria

Order Eubacteriales

Family Enterobacteriaceae

Genus Escherichia

Species coli

 Ernst Heinrich Haeckel (1866) – a German zoologist, proposed a classification

system with 3 kingdoms: Animalia, Plantae, and Protista. The Protista consisted of
single-celled microorganisms such as bacteria, fungi, algae, and protozoans.

 Robert Whittaker (1969) – devises a five-kingdom classification system that is

based on cellular organization and nutritional patterns of organisms.

 Prokaryote or Monera (eubacteria and archaebacteria)

 Protista (slime molds, protozoans, algae)
 Fungi (yeast, molds, mushrooms)
 Plantae (ferns, conifers, flowering plants)
 Animalia (sponges, worms, insects, and vertebrates)

 Carl Woese (1977) – believed that prokaryotes and eukaryotes evolved completely
in different pathways. He proposed the 3 primary kingdoms or 3 super kingdoms:
eubacteria, archaebacteria, eukarya.
METHODS OF IDENTIFYING MICROORGANISMS
 Morphology and Staining of Microorganism

Two general ways of observing microorganisms under a microscope:

 Living state
*wet mount – Ex.a drop of bacteria suspension in glass slides, shape and
arrangement of organism is observe
*hanging drop method – best observe for motility; depression
Different ways to observe motility
1. Hanging drop method
2. SIM (Sulfide Indole Motility Medium) – semisolid test tube with depth of 5cm
3. Staining the flagella by simple staining – used Leiffson stain
4. Serological test- observe the flagellar antibody and flagellar antigen
5. Fluorescent antibody test
6. Swarming phenomenon
 Fixed state – fixed slide;ready to focus

 Classification of Bacteria:

1. Morphology / Fundamental Shapes of Bacteria

 Cocci (coccus) – round; spherical organisms

 Bacilli (bacillus) – rod-shaped
 Spirilli (spirillum) – spiral ex.
Vibrio - straight rod or with single rigid curve)
Spirillum – rigid helical rod
Spirochetes – flexus helical rod
 Pleomorphic organisms – vary in size and shape of bacteria

2. Arrangement
 Grapelike cluster – ex. staphylococcus
 Chain – ex. Streptococci; streptobacilli
 Diploarrangement – in pairs – ex. Pneumococci; n. gonorrhea
 Tetrads -group of 4- ex. Micrococcus, gaffkya, peptococcus
 Cubical – packets of 8 – ex. sarcinae
 Palisade – it tends to place themselves side by side- like a pack of cigarette
 Chinese character – snapping -

 3. Size (measure in terms of micrometer) 1 micrometer=1/25,000 of an inch

Average size of bacteria 0.5- 2 micrometer
Smallest bacillus – size:0.2 X 0.5 um – called HAEMOPHILUS
Largest pathogenic bacillus – size: 1x3-10 um – called BACILLUS ANTHRACIS

Staining – process of artificially coloring microorganism using dyes

Purpose of staining:
1. To observe and appreciate the appearance of microorganism
2. To differentiate an organism from another organism
3. It helps to identify the microorganism and give some special structures
 Kinds of Stains Utilized in the Study of Bacteria:

1. Simple stain – only use 1 particular dye to stain a particular organism

*Safranin - red or pink

2. Differential stain – use 2 or more dye to stain organism and differentiate

4 solution usually involved:

1. Crystal violet (primary staining)

2. Iodine (mordant) – substance to enhance an affinity of the stain
3. Acid alcohol (decolorizer)
4. Safranin (secondary stain)

STEPS:

1. PUT CRYSTAL VIOLET

 Called VIAS
Ex:     * Gram stain

          * Acid Fast stain

 Methods of Acid-Fast Staining:

 Ziehl-Neelsen Methods
 Kinyouns Methods
 Pappenheim's Methods
 Baumgartens Methods

    3. Special stain

Ex:

 Cell Wall Stain – dyar method

 Capsular Stain – the capsules appear as faint blue halos or zones around the
purple colored microorganism
Example of capsule stain: Gins mtd, Anthonys mtd, Welch Capsular stain mtd,
tylers mtd, muirs mtd
 Metachromatic Stain – ex. LAMBS(Loefllers Alkaline Methyline Blue Stain),
Neissers Stain, Alberts Stain, Ljubinsky stain
 Spores Stain – Ex. Heat and acetic acid stain, wirtz and Conklin stain and
schaeffers stain
 Flagellar Stain – ex. Grays mtd, Leiffson mtd, fisher and conn mtd

5. Indirect, Relief or (-) Staining Method

Microorganisms appear as colorless object
2 rapid non stain system
1. LANA (L- alanaine; 4-nitroanilide) it turns yellow when touch to gram (-)
bacteria)
2. 3% KOH
 Cultural Methods
Classification of Culture Media:

 According to Consistency/Physical State

 According to Composition
 According to How the Medium is Dispensed or Distributed
 According to Use
           * simple medium

          * enrichment medium

          * enriched medium

          * differential medium

          * selective medium

          * Special / specific culture medium 

The technique of Inoculation:

 Liquid Culture Medium

 Slant Medium
 Butt Medium
 Butt/Slant Medium
 Plated Medium

 Types of Colonies:

 Smooth
 Mucoid
 Rough
Physiological Characteristics
Growth Requirements:

 Nutritional Requirements
 Oxygen Requirements
 Temperature Requirements

 Classification of Bacteria as To Temperature Requirements:

 Psychrophilic, Cryophilic, Cold Loving Bacteria

 Mesophilic Bacteria
 Thermophilic, Heat Loving Bacteria
 Extreme thermophiles

 Bacterial Growth Curve:

 Lag Phase / Phase of Rejuvenescent / Physiologic Youth

 Exponential / Logarithmic Phase
 Maximum Stationary Phase
 Death Phase / Decline Phase