Iligan Medical Center College

COLLEGE OF MEDICAL
TECHNOLOGY San Miguel Village, Pala-
o, Iligan City Tel No. (063) 221–4661 local
1119

TOPIC 1: THE WORLD OF THE MICROORGANISMS

Bailey and Scott’s Diagnostic Microbiology Chapter 1 (16th Edition)

Microbiology is the study of microorganisms.

A microorganism is simply a very, very small organism that you cannot see with your naked
eye, but you sure feel its effect whenever your eyes fill with water and mucus flows like an
open faucet from your nose.

Microorganisms are a key component of biological warfare along with chemicals that disrupt
homeostasis. The anthrax attack that followed the 9/11 terrorist attacks clearly illustrated how a
dusting of anthrax in an envelope can be lethal to people in an office building. A_______ is a
disease caused by the microorganism Bacillus anthracis, a bacterium that forms endospores
and infiltrates the body by ingestion, skin contact, and inhalation. An e______ is a bacterium in
a dormant state that forms within a cell.

What is a Microorganism?

Microorganisms are the subject of microbiology, which is the branch of science that studies
microorganisms. A microorganism can be one cell or a cluster of cells that can be seen only
by using a microscope.

Microorganisms are organized into six fields of study: bacteriology, virology, mitology,
protozoology, p_______________, and parasitology.

BACTERIOLOGY
Bacteriology is the study of bacteria. Bacteria are pathogenic organisms. A prokaryotic
organism is a one-celled organism that does not have a true n______.

Many bacteria absorb nutrients from their environment and some make their own nutrients by
p_________ or other synthetic processes. Some bacteria can move freely in their
environment while others are s__________. Bacteria occupy space on land and can live in
an aquatic environment and in decaying matter.
They can even cause disease. Bacillus anthracis is a good example. It is the bacterium
that causes anthrax.

Types of Microorganisms

A. Unfriendly Microorganisms

1|Preparedby:CherryLouN.Celeste,RMT
 Iligan Medical Center College
COLLEGE OF MEDICAL
TECHNOLOGY San Miguel Village, Pala-
o, Iligan City Tel No. (063) 221–4661 local
1119

An i_____ is caused by the infiltration of a disease-causing microorganism known as a

p_______ microorganism. Some pathogenic microorganisms infect humans, but not other
animals and plants. Some pathogenic microorganisms that infect animals or plants also
infect humans.

B. Friendly Microorganisms

Not all microorganisms are pathogens. In fact many microorganisms help to maintain
homeostasis in our bodies and are used in the production of food and other commercial
products. For example, flora are microorganisms found in our intestines that assist in the
digestion of food and play a critical role in the formation of vitamins such as vitamin B and
vitamin K. They help by breaking down large molecules into smaller ones.

Microbial Taxonomy: What’s in a Name?

Taxonomy is the science of naming, describing and classifying organisms and includes all
plants, animals and microorganisms of the world.

Taxonomy is composed of 3 highly interrelated disciplines:

1. Classification
2. Nomenclature (naming)
3. Identification
.

Polyphasic Taxonomy
- Combination of traditional genotypic, phenotypic, and phylogenetic or
evolutionary relationships into a general purpose of classification system.
- Utilizes ribosomal ribonucleic acid (rRNA) sequences, whole genome sequences, and
e______ (variations not caused by nucleic acid sequence similarities or differences)
factors at the molecular level.
Chemotaxonomic_ Methods
- More frequently being applied to the identification and classification of
microorganisms. - Methods include:
o Protein studies
o Fatty acid analysis
o Cell wall composition

Matrix Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry

(MALDI-TOF MS)
- use the separation and analysis of high-abundance peptides for the
classification and identification of bacterial isolates

Surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-

TOF) - uses a protein array chip that captures proteins directly without the loss of
sample and decreased sensitivity

Biosensor Technology
 2|Preparedby:CherryLouN.Celeste,RMT
Iligan Medical Center College
COLLEGE OF MEDICAL
TECHNOLOGY San Miguel Village, Pala-
o, Iligan City Tel No. (063) 221–4661 local
1119

- uses a multiplex pool of polymerase chain reaction (PCR) primers that target the
conserved sequences in bacterial genomes coupled with high-precision electrospray
ionization mass spectrometry to identify and group organisms.

In diagnostic microbiology, classification, nomenclature, and identification of microorganisms

play a central role in providing an accurate and timely diagnosis of infectious

I. Classification
- a method for organizing microorganisms into groups or taxa based on similar
morphologic, physiologic and genetic traits.
- The hierarchical classification system consists of the following taxa
designations: o Domains (Bacteria, Archaea, and Eukarya)
o Kingdom (contains similar divisions or phyla; most inclusive taxa)
o Phylum (contains similar classes; equivalent to the Division taxa in botany)
o Class (contains similar orders)
o Order (contains similar family
o Family (contains similar genus)
o Genus (contains similar species)
o Species (specific epithet; lowercase Latin adjective or noun; most exclusive taxa)

A. Family
- Encompasses a group of organisms that may contain multiple genera and consists of
organisms with a common attribute.
- The name of a family is formed by adding the suffix –aceae to the root name of one of
the group’s genera, called the t ____genus.
- Example:
o Streptococcaceae family from type genus is Streptococcus
- Family exempted from the rule in microbiology:
o Enterobacteriaceae- named after the “enteric” group of bacteria rather than the
type species Escherichia coli.
B. Genus_
- contains different species that have several important features in common. -
Placement of a species within a particular genus is based on various genetic and
phenotypic characteristics shared among the species.

C. Species_
- Abbreviated as sp., singular or spp., plural
- The most basic of the taxonomic group
- Collection of bacterial strains that share common physiologic and genetic features
and differ notably from other microbial species.
- Sub species - taxonomic subgroups within a species; do not display significant enough
divergence to be classified as a biotype or a new species
- Biotype– microorganisms with same or nearly same genotype
- Serotype_/serovar - a distinct variation within a species of bacteria classified together
based on their cell surface antigens
 3|Preparedby:CherryLouN.Celeste,RMT
Iligan Medical Center College
COLLEGE OF MEDICAL
TECHNOLOGY San Miguel Village, Pala-
o, Iligan City Tel No. (063) 221–4661 local
1119

- Genotype – genetic make-up

II. Nomenclature

Nomenclature is the naming of microorganisms according to established rules and guidelines

set forth in the International Code of Nomenclature of Bacteria (ICNB)

Carl Linnaeus
- Developed the system for naming organisms in 1735.
- This system is referred to as binomial nomenclature_.

Rules in Binomial Nomenclature:

1. Each organism is assigned two latinal names because Latin or Greek was the
traditional language used by scholars.
2. The first name is called the genus_. The first letter of the genus should always be
CAPITALIZED. 3. The second name is called the species epithet, which is the name of the
species, and is not capitalized.
4. The genus and the epithet appear underlined or in scriped_.
5. The genus can be abbreviated by:
a. Writing the first letter in CAPITAL followed by a period. Ex.: S. aureus
b. Writing the first syllable, with the first letter always in capital, followed by a period.
Ex.: Staph. aureus

In the diagnostic laboratory, changes in nomenclature are phased in gradually so that

physicians and laboratorians have ample opportunity to recognize that a familiar pathogen has
been given a new name.

III. Identification
- Process by which a microorganism’s key features are defined.
- Once those features have been established, the profile is compared with those of
other previously characterized microorganisms.
- The organism can then be assigned to the most appropriate taxa (classification) and can
be given appropriate genus and species names (nomenclature); both are essential
aspects of the role of taxonomy in diagnostic microbiology and the management of
infectious disease

Identification Methods

Two General Categories:

1. Genotypic characteristics
a. relate to an organism’s _____ makeup, including the nature of the organism’s
genes and constituent nucleic acids.
2. _Phenotypic characteristics
a. based on features beyond the genetic level, including both readily o______
characteristics and features that may require extensive analytic
 procedures to be detected.

4|Preparedby:CherryLouN.Celeste,RMT
Iligan Medical Center College
COLLEGE OF MEDICAL TECHNOLOGY
San Miguel Village, Pala-o, Iligan City
Tel No. (063) 221–4661 local 1119

Table 1-1 Identification Criteria and Characteristics for Microbial Classfication

Criteria Characteristics

Phenotypic

Macroscopic The microbial growth patterns on a___ m_____ as observed when

morphology inspected with the unaided eye.
Examples include the s____, t_____, and p_______ of bacterial
colonies.

Microscopic The size, shape, i______i_______, c______ a________, and

morphology a_______ of cells when observed with the aid of
m_______magnification.

Staining The ability of an organism to reproducibly stain a particular color with

characteristics the application of specific dyes and reagents. Staining is used in
conjunction with microscopic morphology for bacterial identification.
For example, the_____ stain for bacteria is a critical criterion for
differential identification.

Environmental The ability of an organism to grow at various temperatures, in the

requirements presence of oxygen and other gases, at various ___ levels, or in the
presence of other ions and salts, such as NaCl.

Nutritional The ability of an organism to utilize various c____ and n_____

requirements sources as nutritional substrates when grown under specific
environmental conditions.

Resistance The exhibition of a characteristic inherent resistance to specific

profiles a_____, h____ metals, or t____.

Antigenic The profiles of microorganisms established by various s____

properties and i_____ methods to determine relatedness among various
microbial groups.

Subcellular Molecular constituents of the cell that are typical of a particular

properties taxon, or organism group, as established by various analytic
methods. Some examples include c___ w____ components,
components of the c___ m_____, and e______ content of the
microbial cell.

Chemotaxonomic The c_______ constituents of the cell, such as the structure of

 properties t_____ acids, f_____ a____ analysis, and p_____ profiles, as
determined by analytical methods

Genotypic

Deoxyribonucleic DNA comprises four bases (g_____, c______, a______, and t_____).
acid The extent to which the DNA from two organisms is made up of
(DNA) base cytosine and guanine (i.e., G 1 C content) relative to their total base
composition content can be used as an indicator of relatedness or lack thereof.
ratio For example, an organism with a G 1 C content of 50% is not closely
related to an organism with a G 1 C content of 25%.

Nucleic acid (DNA The order of bases along a strand of DNA or RNA is known as the
and ribonucleic b_____ sequence. The extent to which sequences are h_____
acid (similar) between two microorganisms can be determined directly or
indirectly by various molecular

5|Preparedby:CherryLouN.Celeste,RMT
Iligan Medical Center College
COLLEGE OF MEDICAL TECHNOLOGY
San Miguel Village, Pala-o, Iligan City
Tel No. (063) 221–4661 local 1119
[RNA]) base methods. The degree of similarity in the sequences may be a
sequence measure of the degree of organism relatedness, specifically, the
characteristics, ribosomal RNA (rRNA) sequences that remain stable in comparison
including to the genome as a whole.
those
determined by
hybridization
assays

6|Preparedby:CherryLouN.Celeste,RMT