MC 3: MICROBIOLOGY AND PARASITOLOGY

MODULE 4: MICROBIOAL DIVERSITY pt1

2ND SEMESTER I S.Y 2021-2022TRANSCRIBED BY: LERHIZA JOY P. AGLERON

LECTURER:

CATEGORIES OF MICROBES VIRUSES ARE CLASSIFIED BY;

 Microbes can be divided into those that are truly cellular  Type of genetic material (either DNA or RNA)
(bacteria, archaea, algae, protozoa, and fungi) and those  Shape and size of capsid
that are acellular (viruses, viroids, and prions).  Number of capsomeres
 Cellular microbes (microorganisms) can be divided into  Presence or absence of an envelope
those that are prokaryotic (bacteria and archaea) and those  Type of host it infects
that are eukaryotic (algae, protozoa, and fungi).  Disease it produces
 Viruses, viroids, and prions are often referred to as  Target cell(s)
acellular microbes or infectious particles.  Immunologic/antigenic properties
ACELLULAR MICROBES: VIRUS

 Complete virus particles are called virions.

 Very small and simples in structure (10 – 300 nm)
 No type of organism is safe from viral infection
 Some viruses, called oncogenic viruses or oncoviruses,
cause specific types of cancer.
 A typical virion consists of a genome of either DNA or RNA,
surrounded by a capsid (protein coat), which is composed
of protein units called capsomeres.
 Some viruses
(enveloped
viruses) have an
outer envelope
CATEGORIES BASED ON GENOME
composed of
lipids and  Double-stranded DNA viruses
polysaccharides.  Single-stranded RNA viruses
 Viruses have five properties that distinguish them from  Single-stranded DNA viruses
living cells:  Double-stranded RNA viruses
1. They possess either DNA or RNA, whereas living  Most viral genomes are circular molecules, but some are
cells possess both. linear.
2. They are unable to replicate on their own. But by
ORIGIN OF VIRUSES
their hosts
3. Unlike cells, they do not divide by binary fission,  Coevolution theory - coevolved with bacteria and archaea
mitosis, or meiosis. from the primordial soup
4. They lack the genes and enzymes necessary for  Retrograde evolution theory – viruses evolved from free-
energy production. living prokaryotes that invaded other living organisms, and
5. They depend on the ribosomes, enzymes, and gradually lost functions which were provided by the host
metabolites of the host cell for protein and nucleic cell
acid production.  Escaped gene theory – viruses are a piece of host cell RNA
or DNA that have escaped from living cells and are no
longer under cell control -- currently most widely accepted
BACTERIOPHAGES

 Viruses that infect bacteria are known

as bacteriophages or simply phages.
 Categorized based on shape, nucleic
acid, and events that occur after entry
into a host cell
 Shape: icosahedron, filamentous,
complex
 Nucleic acid: ss DNA, ds DNA, ss RNA,
ds RNA
 Events: virulent vs temperate
 MC 3: MICROBIOLOGY AND PARASITOLOGY

MODULE 4: MICROBIOAL DIVERSITY pt1

2ND SEMESTER I S.Y 2021-2022TRANSCRIBED BY: LERHIZA JOY P. AGLERON

LECTURER:

VIRULENT TEMPERATE ANIMAL VIRUSES

BACTERIOPHAGES BACTERIOPHAGES
 Infect animals or humans
Known as lyctic cycle, which Lysogenic phages
 DNA or RNA
ends with the destruction of the
 Simple or complex
bacterial cells.
 Steps in the multiplication of animal viruses are
Lyctic cycle steps: Do not immediately initiae the
o Attachment
lytic cycle
o Penetration
Instead, integrates their DNA
into the bacterial cell o Uncoating
chromosome o Biosynthesis
Phage switched to lytic cycle o Assembly
as a result of environmental o Release
clues
LATENT VIRUS INFECTION
Attachment Uses of bacteriophages  Viral infections in which the virus is able to hide from a
Penetration Destroy bacterial pathogens host’s immune system by entering cells and remaining
Biosynthesis Treat bacterial infection dormant.
Assembly Prevent food contamination  Herpes viral infections are examples.
Release  Once acquired, herpes virus infections (e.g., those that
cause cold sores, genital herpes, and chickenpox/shingles)
never completely go away; for example, chickenpox may
be followed, years later, by shingles- both the result of the
same virus.
ANTIVIRAL AGENTS

 Antibiotics are not effective against viral infection

 Antiviral agents are drugs that are used to treat viral
infection
 These agents interfere with virus-specific enzymes and
virus production by disrupting critical phases in viral
multiplication of inhibiting synthesis of viral DNA, RNA, or
proteins.
ONCOGENIC VIRUSES OR ONCOVIRUSES
 These viruses cause cancer.
 Examples:
o Epstein-Barr virus
o Human papillomaviruses
o Hepatitis B and C
o Human herpesvirus 8
HUMAN IMMUNODEFICIENCY VIRUS (HIV)

 This viruses causes acquired immunodeficiency syndrome

(AIDS).
 It is an enveloped, single-stranded RNA retrovirus
 The primary targets for HIV are CD4+ cells – those having
CD4 receptors on their surfaces.
PLANT VIRUSES

 Cause plant disease

 Result in economic losses in excess of $70 billion per year
worldwide
 Infects cocoa tree, rice, barley, tobacco, turnips,
cauliflower, potatoes, tomatoes, etc.
 MC 3: MICROBIOLOGY AND PARASITOLOGY

MODULE 4: MICROBIOAL DIVERSITY pt1

2ND SEMESTER I S.Y 2021-2022TRANSCRIBED BY: LERHIZA JOY P. AGLERON

LECTURER:

ACELLULAR MICROBES: VIROIDS AND PRIONS
 Viroids and prions are smaller and less complex infectious
particles than viruses
o Viroids
• Viroids are short, naked fragments of
single-stranded RNA, which can
interfere with the metabolism of plant
cells.
• Viroids are transmitted between plants
in the same manner as viruses.
• Examples of plant diseases caused by
viroids are potato spindle tuber and
citrus exocortis.
• Does not cause animal disease
o Prions
• Prions are small infectious proteins that
cause fatal neurologic diseases in
animals and humans
• Scrapie
• mad cow disease
• Kuru
• Creutzfeldt–Jacob disease
• Fatal Familial insomnia
• Of all pathogens, prions are the most
resistant to disinfectants.
• The mechanism by which prions cause
disease remains a mystery.
DOMAIN BACTERIA: CHARACTERISTICS
 Bacteria are divided into three major phenotypic
categories:
o Those that are Gram-negative and have a
cell wall
o Those that are Gram-positive and have a
cell wall
o Those that lack a cell wall (Mycoplasma
spp.)
 Characteristics of bacteria used in classification and
identification include cell morphology, staining
reactions, motility, colony morphology, atmospheric
requirements, nutritional requirements, biochemical
and metabolic activities, enzymes that the organism
produces, pathogenicity, and genetic composition.
DOMAIN BACTERIA: CELL MORPHOLOGY
 There are three basic categories of bacteria based on
shape:
o Cocci (round bacteria)
o Bacilli (rod-shaped bacteria)
o Curved and spiral-shaped bacteria


COCCI
 Cocci may be seen singly or in pairs (diplococci), chains
(streptococci), clusters (staphylococci), packets of 4
(tetrads), or packets of 8 (octads).
 Medically relevant: Enterococcus, Neisseria,
Staphylococcus, Streptococcus
BACILLI
 They are often referred to as rods; they may be short or
long, thick or thin, and pointed or with curved or blunt ends.
 They may occur singly, in pairs (diplobacilli), in chains
(streptobacilli), in long filaments, or branched.
 Extremely short bacilli are called coccobacilli.
 Examples of medically important bacilli:
o Escherichia, Klebsiella, Proteus,
o Pseudomonas, Haemophilus, and Bacillus spp.
CURVE
 Comma shaped
 Medically relevant: vibrio
 Usually occur single, but some may form pairs
SPIRAL SHAPE
 Called spirochetes
 Vary in length, rigidity, size, number and amplitude of their
coils, and tightness of coils
o Preponema pallidum (syphilis), Borrelia (Lyme
disease)
 Shape can be lost due to adverse growth conditions
 Some bacteria can exist in a variety of shapes
(pleomorphic)
DOMAIN BACTERIA: STAINING PROCEDURES
 Most bacteria are colorless, transparent, and difficult to see
 Three major categories of staining procedures
o Simple staining procedures
o Structural staining procedures
 MC 3: MICROBIOLOGY AND PARASITOLOGY

MODULE 4: MICROBIOAL DIVERSITY pt1

2ND SEMESTER I S.Y 2021-2022TRANSCRIBED BY: LERHIZA JOY P. AGLERON

LECTURER:

 Capsule staining
 Spore staining
 Flagella staining
o Differential staining procedures
 Gram and acid fast staining procedures

DOMAIN BACTERIA: MOTILITY

 If a bacterium is able to “swim,” it is said to be motile.

 Bacterial motility is most often associated with flagella and
less often with axial filaments.
 Bacterial smears must be fixed prior to staining.
 Most spiral-shaped bacteria and about 50% of bacilli are
 The fixation process serves to kill organisms, preserve their
motile; cocci are generally nonmotile.
morphology, and anchor the smear to the slide.
 Motility can be demonstrated by stabbing the bacteria into a
 The two most common techniques of fixation:
tube of semisolid medium
o Heat fixation- not a standardized technique;
excess heat will distort bacterial morphology DOMAIN BACTERIA: COLONY MORPHOLOGY
o Methanol fixation- a standardized technique; the
 A bacterial colony contains millions of organisms.
preferred method
 Colony morphology (appearance of the colony) varies from
one species to another.
 Colony morphology includes size, color, overall shape,
elevation, and the appearance of the edge or margin of the
colony.
 Colony morphology can also include the results of
enzymatic activity on various types of media.
 As is true for cell morphology and staining characteristics,
colony morphology is an important “clue” to the
identification (speciation) of bacteria.
DOMAIN BACTERIA: ATMOSPHERIC REQUIREMENTS

 Bacteria can be classified on the basis of their atmospheric

 Some bacteria are neither consistently purple nor pink after requirements, including their relationship to O2 and CO2.
Gram staining; they are known as Gram-variable bacteria,  With respect to O2, bacterial isolates can be classified as
for example, Mycobacterium spp. o Obligate aerobes
 Mycobacterium spp. are often identified using the acid-fast o Microaerophilic aerobes
stain. o Facultative anaerobes
 The acid-fast stain o Aerotolerant anaerobes
o Carbol fuchsin is the red dye that is driven
o Obligate anaerobes
through the bacterial cell wall using heat.
 Capnophilic organisms grow best in the presence of
o Heat is used to soften the waxes in the cell wall.
increased concentrations of CO2 (usually 5%–10%)
o Because mycobacteria are not decolorized by the
acid–alcohol mixture, they are said to be acid-
fast.
 MC 3: MICROBIOLOGY AND PARASITOLOGY
MODULE 4: MICROBIOAL DIVERSITY pt1
2ND SEMESTER I S.Y 2021-2022TRANSCRIBED BY: LERHIZA JOY P. AGLERON
LECTURER:
DOMAIN BACTERIA: NUTRITIONAL REQUIREMENTS
 All bacteria require some form of the elements such as
carbon, hydrogen, oxygen, sulfur, phosphorus, and
nitrogen for growth.
 Some bacteria require special elements (e.g., calcium, iron,
or zinc) or vitamins
 Organisms with especially demanding nutritional
requirements are said to be fastidious (“fussy”).
 The nutritional needs of a particular organism are usually
characteristic for that species and are sometimes important
clues to its identity.
DOMAIN BACTERIA: BIOCHEMICAL AND METABOLIC
ACTIVITIES
 As bacteria grow, they produce many waste products and
secretions
 Pathogenic strains of many bacteria, such as staphylococci
and streptococci, can be tentatively identified by the
enzymes they secrete.
 In particular environments, some bacteria produce gases
such as carbon dioxide or hydrogen sulfide.
 To identify bacteria in the laboratory, they are inoculated
into various substrates (i.e., carbohydrates and amino
acids) to determine whether they possess the enzymes
necessary to break down those substrates.
DOMAIN BACTERIA: PATHOGENICITY
 Many pathogens are able to cause disease because they
possess capsules, pili, or endotoxins, or because they
secrete exotoxins and exoenzymes that damage cells and
tissues.
 Frequently, pathogenicity is tested by injecting the
organism into mice or cell cultures.
 Examples of some common pathogenic bacteria:
o Neisseria meningitidis, Salmonella typhi, Shigella
spp., Vibrio cholerae, Yersina pestis, and
Treponema pallidum
DOMAIN BACTERIA: GENETIC COMPOSITION
 Laboratory identification of bacteria is moving toward
analyzing the organism’s DNA or RNA
 The composition of the genetic material (DNA) of an
organism is unique to each species.
 Through the use of 16S rRNA sequencing, the degree of
relatedness between two different bacteria can be
determined.
DOMAIN BACTERIA: UNIQUES BACTERIA
 Rickettsias, chlamydias, and mycoplasmas are bacteria,
but they do not possess all the attributes of typical bacterial
cells.
 Rickettsias and chlamydias have a Gram-negative type of
cell wall and are obligate intracellular pathogens
 Rickettsias
o Disease transmitted by arthropods
o Cause typhus and spotted fever rickettsiosis
o have “leaky membranes.”
 Chlamydias
o are “energy parasites,” meaning they prefer to
use ATP molecules produced by their host cell.
o Transferred by aerosols or direct contact
o Cause trachoma, inclusion conjunctivitis,
nongonococcal urethritis, pneumonia, and
respiratory disease
 Mycoplasmas
o smallest of the cellular microbes.
o lack a cell wall and therefore assume many
shapes (i.e., pleomorphic)
o May be free living or parasitic
o Pathogenic to many animals and some plants
o In humans, pathogenic mycoplasmas cause
primary atypical pneumonia and genitourinary
infections.
o Because they have no cell wall, they are resistant
to drugs like penicillin that attack cell walls.
 MC 3: MICROBIOLOGY AND PARASITOLOGY

MODULE 4: MICROBIOAL DIVERSITY pt1

2ND SEMESTER I S.Y 2021-2022TRANSCRIBED BY: LERHIZA JOY P. AGLERON

LECTURER:

DOMAIN BACTERIA: PHOTOSYNTHETIC BACTERIA

 Photosynthetic bacteria include purple bacteria, green

bacteria, and cyanobacteria
 they all use light as an energy source (photosynthesis), but
not in the same way.
o Purple and green bacteria do not produce oxygen
(anoxygenic photosynthesis), whereas
cyanobacteria do (oxygenic photosynthesis)
 Cyanobacteria
o Believed to be the first organisms capable of
carrying out oxygenic photosynthesis
o When appropriate conditions exist in a pond or
lake, a water bloom will occur
o Perform nitrogen fixation
o Produce toxins
DOMAIN ARCHAEA

 Archaea (meaning “ancient”)

 they are prokaryotic organisms.
 Genetically, archaea are more closely related to eukaryotes
than they are to bacteria.
 Archaea vary widely in shape; some live in extreme
environments, such as extremely acidic, extremely hot, or
extremely salty environments.
 Archaea possess cell walls, but their cell walls do not
contain peptidoglycan (in contrast, all bacterial cell walls
contain peptidoglycan)