CHAPTER 4

VIRUSES & PROKARYOTIC MICROBES

BACTERIA & OTHER PROKARYOTIC MICROBES
DOMAIN BACTERIA
• There are 5,000 species named
• 1% only are identified
• Contains organism divided into three
phenotypic categories: Gram positive, negative
and those who lack cell wall
• Microbiologists established numerical BACTERIAL CELL MOTILITY
taxonomy • Motile if able to “swim”
• Characteristics provide data for identification • Motility is associated with the presence of
and classification flagella or axial filaments
• Includes shape and morphologic arrangement, • Bacteria never possess cilia
etc. • Most spiral-shaped and half of bacilli are motile
BACTERIAL CELL MORPHOLOGY • Cocci are generally non-motile
• Vary in size from spheres measuring 0.2 μm in • Flagella can be stained to demonstrate the
diameter to 10.0 μm long spiral-shaped bacteria presence, number and location to describe
to even longer filamentous bacteria bacterial cell
• Three basic shapes: round or spherical, BACTERIAL CELL MOTILITY
rectangular or rod-shaped and curved and • Can be demonstrated by stabbing the bacteria
spiral-shaped into a semisolid agar or hanging-drop technique
• Divides via binary fission • Growth in agar produces turbidity
• Nonmotile will grow only along the stab line
• Motile will spread
• Hanging-drop will be examined with microscope
BACTERIA COLONY MORPHOLOGY
• Cannot be seen in solid medium unless it
produces colony
• Contains millions of organisms
• Varies from one species to another
• Includes size, color, overall shape, elevation and
appearance of the edge of colony – important
in identification
• Size is determined via generation time
• Also includes enzymatic activity on various
culture media
BACTERIAL ATMOSPHERIC REQUIREMENTS • Able to grow in environment without oxygen
• Classification according its relationship to • Clostridium, Veillonella and Fusobacterium are
oxygen or carbon dioxide examples
• Isolate can be classified into major groups: AEROTOLERANT ANAEROBE
obligate aerobes, microaerophilic aerobes, • Does not require oxygen
facultative anaerobes, aerotolerant anaerobes • Grows better in the absence of oxygen
and obligate anaerobes • Can survive in atmospheres containing
• In liquid medium, the region which organism molecular oxygen
grows depends on the oxygen needs of • Tolerance to oxygen concentration varies from
particular species one species to another
FACULTATIVE ANAEROBES
• Capable of surviving in either the presence or
absence of oxygen
• Anywhere from 0% to 21% oxygen
• Many bacteria are facultative anaerobes
• E.g. members of family Enterobacteriaceae,
most streptococci and staphylococci
CAPNOPHILES
• Also known as capnophilic organisms
• Grow better in vitro in increase concentration
of carbon dioxide
• Some Bacteroides and Fusobacterium are
capnophiles

MAJOR CLASSIFICATIONS
(Aerobic Organism) TEMPERATURE REQUIREMENTS
OBLIGATE AEROBES • Bacteria are capable of growth in wide range of
• Require an atmosphere containing molecular temperatures
oxygen in concentrations comparable to that • Some can grow slowly in freezing temperatures
found in room air • Others can grow at extremely high
• 20%-21% Oxygen needed temperatures
• Mycobacteria and fungi are examples of • Pathogenic bacteria are somewhat limited in
obligate aerobes their optimal growth range because they are
MICROAEROPHILIC AEROBES adopted to human body temperature
• Also known as Microaerophiles • Some organisms prefer as low as 30 C or as high
• Require oxygen for multiplication but in lower as 42 C
in concentrations found in room air NUTRITIONAL REQUIREMENTS
• Neisseria gonorrheae and Campylobacter spp. • All bacteria need elements such as carbon,
Are examples hydrogen, oxygen, sulfur, phosphorus and
• Prefer 5% oxygen nitrogen for growth
MAJOR CLASSIFICATIONS • Special elements such as potassium, calcium,
(Anaerobic Organism) iron, manganese, magnesium, cobalt, copper,
OBLIGATE ANAEROBES zinc and uranium are required by some bacteria
• Can grow only in anaerobic environment
 • Some have specific vitamin requirements and • Methanogens produce methane
organic secretions by other living organism • Cell walls does not contain peptidoglycan
• Some are fastidious or being “fussy” • 16S rRNA sequences but closely related to
BICHEMICAL & METABOLIC ACTIVITIES eukaryotes than bacteria
• Bacteria produce waste products and secretions
• Some are enzymes that enable them to invade
host cell and cause disease (staphylococci &
streptococci)
• They can produce gases such as carbondioxide,
hydrogen sulfide, oxygen or methane
PATHOGENICITY
• Will be discussed in details in Chapter 14
• Able to cause disease
• They possess capsules, fimbrae or endotoxins,
enterotoxins and exoenzymes that damage cells
and tissues
• Pathogenicity is tested by injecting the
VIRUSES
organism into mice or cell cultures
• Virions – Complete virus particles
UNIQUE BACTERIA
• 10 to 300 nm
• Rickettsias, chlamydias and mycoplasmas that
• The smallest about the size of RBC
do not possess all attributes of typical bacterial
• 1930s – Electron microscopes
cells
• 1940 – Photographs of viruses
• Small and difficult to isolate
• 1959 – Negative staining was developed
• Formerly thought to be viruses
• No organism is safe from viral infection
CHLAMYDIAS
• Causes many human diseases
• Referred to as energy parasites • Oncoviruses – Causes cancers, such as
• Can produce ATP but prefer to use ATP of host lymphomas, carcinomas, and some leukemia
cells • Typical virion consists of either DNA or RNA
• Are obligate intracellular pathogens • Surrounded by capsid (protein coat)
• Transmitted through inhalation or aerosols • Capsid is composed of small units of
• C. pneumonia causes pneumonia capsomeres
MYCLOPLASMAS • Nucleic acid and capsid are called nucleocapsid
• Are the smallest of the cellular microbes • Some has enveloped composed of lipids &
• Lack cell walls polysaccharides
• Assumes shapes from coccoid to filamentous • Bacterial viruses (bacteriophage) do not have
• Appears pleomorphic an envelope (naked viruses)
• Cannot be grown inartificial media • May also have tail, sheath or tail fibers
• Formerly known as PPLOs isolated from cattle • No ribosomes for protein synthesis
with lung infection • No sites for energy production
• Causes primary atypical pneumonia and
genitourinary infections
• Resistant to antibiotics that inhibits cell wall
synthesis
DOMAIN ARCHAEA
• Discovered in 1977
• Formerly known as archaebacterua
• Archae means “ancient”
• More closely related to eukaryotes
• Bacteria and archaea diverged from common
ancestor
• Shaped as cocci, bacilli or long filaments
• Most are extremophiles
 SHAPES & SYMMETRY
POLYHEDRAL
• 20 sides or facets
• Geometrical
• Referred to as icosahedral
• Each facets consist of several capsomeres
• Size is determined by the size of each facet and
the number of capsomeres
HELICAL
• Nucleic acid coils into a helical shape
• Appears circular in electron microscope
• Capsomeres coils around the nucleic acid
SPECIFIC PROPERTIES OF VIRUSES
NUCLEIC ACID
Possess either DNA or RNA
METABOLISM
They lack the genes and enzymes necessary for energy
production
REPRODUCTION
Unable to replicate on their own and uses the host cell
DNA & ribosome to reproduce itself COMPLEX
G&D • Asymmetrical
They depend on ribosomes, enzymes and metabolites • Possesses protein tails
of host cell fro protein and necleic acid production • Complex outer wall
CLASSIFICATIONS • Most bacteria viruses or bacteriophage (phage)
• Type of genetic material • Uses tail to attache to a bacteria
• Single or double stranded nucleic acid
• Positive or negative-sense nucleic acid
• Shape of capsid
• Number of capsomeres
• Size of capsid
• Presence or absence of an envelope
• Type of host that it infects
• Type of disease it produces
• Target cell
• Immunologic or antigenic properties
GENOME TYPE
• Double-stranded DNA
• Single-stranded RNA
• Circular molecules
• Linear (having two ends)

HISTORY OF VIRUSES
Viruses existed for as long as bacteria and archaea have
existed. It has been debated for many years. There are
major theory that emerged regarding its origin
THREE MAJOR THEORY PENETRATION OF NONENVELOPED VIRUS VIA
COEVOLUTION ENDOCYTOSIS
Viruses originated from primordial soup and coevolved
with bacteria and archaea. This theory has fe supporters
RETROGRADE EVOLUTION
Viruses evolved from free-living prokaryotes that
invaded other living organisms and gradually lost
functions that were provided by hosts cell. This theory
has little support
ESCAPED GENE
Viruses are pieces of host cell RNA or DNA that have
LATENT VIRAL INFECTIONS
escaped from living cells and re no longer under cellular
control. Of the three, this is currently the most widely
• Infected individual always harbor the virus with
accepted explanation
minimal to asymptomatic
• Stress, fever or over exposure to sunlight
ANIMAL VIRUSES
produces more virus
• Viruses that infect humans and animals
• Is limited by the immune system
• Contains either DNA or RNA
• When immune system becomes weaker,
• May only have nucleic acid and capsid or nay be
disease will appear
complex
• May be enveloped
• May contain enzymes for viral multiplication
STEPS IN VIRAL MULTIPLICATION
1. Attachment (adsorption)
• Attaches to the host’s cell wall
• Only attaches to cells with appropriate
protein or polysaccharide receptors
2. Penetration
• Entire virion enters the host cell or ONCOGENIC VIRUSES
phagocytized or fused with the cell • Viruses that cause cancer
3. Uncoating • Also called oncoviruses
• Viral nucleic acid escapes from the • First found in chickens experiments
capsid • E.g. Epstein-Barr virus, human herpesvirus 8,
• Enables transcription and replication Hepa B & C viruses, HPV & HTLV-1
4. Biosynthesis
• Dictated the host cell
• Viral nucleic acid and proteins are
produced
• Some do not initiate this step but rather
remain latent
5. Assembly
Fitting the virus pieces together to produce virions
6. Release
• Virions escape from host cell either
through lysis or budding.
• Budding makes the virus enveloped
• Remnants or inclusion bodies of the cell HUMAN IMMUNODEFICIENCY VIRUS
are used as diagnostic tool to identify • Causes AIDS
the disease • Is an enveloped, single-stranded RNA virus
• Is a lentivirus and family of retroviruses
• Posses an enzyme that allows RNA to provirus
DNA form
 • Attach and recognizes CD4 cells ZIKA VIRUS
• Causes serious birth defects
• Causes microcephaly and other congenital
malformations
• Transmitted through mosquitos
• Spread to America from Micronesia
• Enveloped, spherical, single-stranded RNA,
positive-sense

PROVIRUS
• Causes latent infection
• Able to inject itself to cell host cell DNA
• Replicated during host cell division
• Later, can exit the host cell and undergo viral
replication
• Est. 8% of human genome may exist in the form
of endogenous retroviruses

BACTERIOPHAGES
• Infects bacteria
• Obligate intracellular pathogens
• Can be single-stranded DNA or RNA phages
(vice versa)
• Three categories according to shapes
• Categorized according to events that occur after
invasion
BACTERIOPHAGES SHAPES
ICOSAHEDRON
• Almost spherical shape
• 20 triangular facets
• Smallest about 25 nm in diameter
EBOLA VIRUS FILAMENTOUS
• Causes high mortality in recent years • Long tubes formed by capsid proteins
(Hemorrhagic fever) with 11,000 deaths • Assembled into a helical structure
• Thread-shaped virus • Can be up to 900 nm long
• Cross infection from bats to humans COMPLEX
• Outbreak in W. Africa in 2014-15 • Icosahedral heads attached to helical tails
• May cause worldwide pandemic • May also possess base plates and tail fibers
CATEGORIES OF BACTERIOPHAGE ACCORDING TO • Discovered in 2003
AFTER INVASION EVENTS • Extremely large double-stranded DNA virus
VIRULENT • Named as Mimivirus
• Causes lytic cycle • 7nm thick capsid and 750 nm in diameter
• Ends in destruction of the cell • An array of 80 to 125 nm closely packed fibers
• Takes less than 1 hour from attachment to lysis • Capsid is surrounded by 4 nm thick lipid
• Replicative cycle is similar to animal virus except membrane
entering the host cell • Possesses 1,000 genes
• Contains RNA molecules
• Causes Pneumonia

TEMPERATE PLANT VIRUS

• Also known as lysogenic phages • More than 1,000 different viruses
• Do not initiate lytic cycle • Citrus, cocoa, rice, barley, tobacco, turnips,
• DNA integration into the bacterial cell cauliflower, trees and grains
chromosome • Resulted in huge economic loss at an est, $70
• Similar to provirus, bacteriophage genome is billion per year worldwide
referred to as prophage • Transmitted via insects (aphids, leaf hoppers
and whiteflies), mites and nematodes, infected
seeds, and contaminated tools
• Condition referred to as transmissible
spongiform encephalopathies

VIROIDS
• Less complex infectious agent
• Short, naked fragments
COMPARISON BETWEEN BACTERIOPHAGE & ANIMAL • Single-stranded RNA
VIRUS MULTIPLICATION • About 300-400 nucleotides in length
• Attack and sometimes kill plants
• Transmitted to the plants the same way as
viruses
• No animal diseases have been discovered that
are caused by viroids

GIANT AMEBAE VIRUSES

 • Investigated for use as drug delivery of
PRIONS medicine
• Small infectious proteins • Potential for nanotechnology
• Causes fatal neurologic diseases in animals & DINOFLAGELLATES
humans • Unicellular, flagellated, photosynthetic
• Brain becomes riddled with holes • Phytoplanktons
• Transmitted through consumption of • Produces oxygen
contaminated food • Responsible for “red tides”
• All diseases are untreatable and fatal • Can be found in ponds and are called green
• Mechanism to cause disease remains a mystery algae
• Most resistant to destruction DESMIDS
• Division of green algae
• Land plants emerged from
• Highly symmetrical, attractive and diverse in
forms
• Found mostly in fresh water
• Unicellular and form chains of cell called
filaments
• Pyrenoids stores CHO
• Reproduce through asexual fission
MULTICELLULAR ALGAES
• Large seaweeds such as brown kelp – found in
ocean shores
• Green scum – Floating in ponds and on wet
rocks (slippery material)

CHAPTER 5
EUKARYOTIC MICROBES
ALGAE
CHARACTERISTICS
• Are photosynthetic, eukaryotic organisms
• Kingdom of Protista
• Phycology – Study of algae
ALGAE
• Consist of cytoplasm, cell wall, cell membrane,
IMPORTANCE
nucleus, plastids, ribosomes, mitochondria, and
• Source of food
Golgi bodies
• Iodine and other minerals
• Some have pellicle, stigma and flagella
• Fertilizers
• More like plantlike than protozoa
• Emulsifiers for pudding
• Sizes ranges from unicellular to multicellular
• Stabilizers for ice cream
• Arrange in colonies or strands
• Gelling agent for jams
• Produce energy through photosynthesis
• Nutrient media for bacterial growth
• Most contains cellulose
• Being studied for biofuels
• Depending on pigments they appear in different
• Causes damage to water systems
colors
MEDICAL SIGNIFICANCE
CLASSIFICATION
PROTOTHEA
DIATOMS
• Causes very rare human infections
• Usually unicellular
(protothecosis)
• Found in freshwater and seawater
• Lives in soil and enters wounds
• Phytoplankton
• Causes small subcutaneous lesion that progress
• 200 genera are known
to wat-looking lesion
• E.g. diamotamaceous earth
• Debilitating and fatal in lymphatic system
 • Releases phycotoxins that are poisonous to • Some are parasites and are pathogenic
humans and animals • Coexist through mutualistic symbiotic
relationship
CLASSIFICATION & MEDICAL SIGNIFICANCE
• Divided into groups according to locomotion
AMEBAE
• Move by pseudopodia – ameboid movement
• Surrounds and fuse with food particle
• Lysosomes release digestive enzymes
• Fluids are ingested in a process known as
pinocytosis
• Entamoeba histolytica causes amebic dysentery

CILIATES
• Move by hairlike cilia
• Exhibit an oarlike motion
• Most complex of all protozoa
PROTOZOA • Transmitted to humans from drinking water
CHARACTERISTICS contaminated with swine feces (Balantidium
• Eukaryotic organisms coli).
• Kingdom of Protista • Mostly asymptomatic but some experience
• Protozoology – the study of protozoa persistent diarrhea, abd. Pain and perforated
• Most are unicellular colon
• Ranging from 3 to 2,000 micrometers in length FLAGELLATES
• Free-living found in soil and water • Move by whiplike flagella
• Animal-like cells • Kinetosome anchors flagella within cytoplasm
• Consist of various eukaryotic structures and • Exhibit a wave like motion
organelles • Trypanosoma brucei – transmitted through
• Possess pellicles, cytosomes, contractile tsetse fly, causes African sleeping sickness
vacuoles, pseudopodia, cilia and flagella • Trichomonas vaginalis – trichomoniasis (STD)
• No Chlorophyll • Giardia intestinalis & lambdia – causes
• Ingest algae, yeasts, bacteria and smaller persistent diarrheal disease
protozoans
• Others live on dead & decaying organic matter
• Do not have cell walls
• Two stages of life cycle: Trophozoite & Cyst
stage
o Trophozoite stage
▪ Motile
▪ Feeding
▪ Dividing
o Cyst stage
▪ Non-motile
▪ Dormant NONMOTILE PROTOZOA
▪ Survival (like bacterial spores) • Lacking pseudopodia, flagella or cilia
 • Classified as sporozoa like Plasmodium spp. – • Reproduce by budding, hyphal extension or
causes malaria formation of spores (sexual and asexual spores)
• Transmitted by Anopheles mosquitoes • Sexual spores – produced by fusion of 2
• Carried by vectors who took up blood from gametes (e.g., ascospores, basidiospores and
infected individual with malaria zygospores)
• Classified taxonomically by type of sexual spore
they produce or the structure which the spores
are produced
• Asexual spores are produced in sac-like
structure called sporangium (sporangiospore) or
NONMOTILE PROTOZOA from fungal component called conidiophore
• Cryptosporidium parvum – causes severe (conidia) which are carried by wind and
diarrheal disease (cryptosporidiosis) in patients resistant to elements which causes allergies to
with AIDS humans
• Oocysts in drinking water resulted in 400,000
cases
• Babesia spp. (babesiosis), Cyclospora
cayetanensis (cyclosporiasis), Toxoplasma
gondii (toxoplasmosis)

FUNGI
CHARACTERISTICS
• Diverse and classified across 3 kingdoms
• Fungi pathogenic to humans are placed in the
kingdom of Fungi (Eumycota)
• Mycology – the study of fungi
• Found almost everywhere on Earth
• Some are harmful or beneficial
• Causes deterioration of unlikely materials
• Include yeasts, moulds and mushrooms
• Saprophytes – “Garbage disposers” or original
“recyclers”
• Fungal cell wall contains chitin CLASSIFICATION
• Usually are unicellular, others grow as filaments • Classified according to their mode of sexual
called hyphae that forms mycelium or thallus reproduction.
• Some are septate or aseptate hypae PHYLA – LOWER FUNGI
Zygomycotina
• Common bread moulds
• Other fungi that cause food spoilage

Chytridiomycotina
REPRODUCTION • Not considered as true fungi
 • Lives in water and soil • Referred to as blastospores or blastoconidia
• Absortive mode of eating • Observed through microscope
• Cell wall made of chitin • Reproduce through budding
• Forms pseudohypha
• Some produce thick-walled, sporelike structures
called chlamydospores
• Found in soil, water, skins of fruits and
vegetables
Yeasts
• Causes fermentation
• Saccharomyces cerevisiae – common yeast
known as “baker’s yeast” ferments sugar to
PHYLA – HIGHER FUNGI alcohol under anaerobic condition; breaks down
Ascomycotina sugars into carbon dioxide and water in aerobic
• Sac fungi or ascomycetes condition
• Includes yeasts like Candida species • Leavening agent in bread production
• Aspergillus, penicillium and plant pathogens • Good source of nutrients
• Produces colonies similar to bacteria in
appearance
• Larger than bacteria
Moulds
• Often seen in water, soil and food
• Grows cytoplasmic filaments or hyphae that
makes up the mycelium
\ • Extends above the surface (aerial or
PHYLA – HIGHER FUNGI reproductive hyphae)
Basidiomycotina • Some are beneath the surface (vegetative
• Include yeasts like Cryptococcus, some skin and hyphae)
plant pathogens • Reproduction is through spore formation
• Large and “fleshy fungi” • Sexually or asexually
• Lives in the woods • Does not include Microsporidia
• E.g., mushrooms, toadstools, bracket fungi and • Chytridiomycotina are not pathogenic
puffballs Moulds
• Great commercial importance
• Ascomycotina are found in antibiotic-producing
moulds
• Produce large quantities of enzymes (e.g.
amylase), citric acid and other organic acids
Dimorphic Fungi
• Can live as yeast or moulds (dimorphism)
• Includes some human pathogens
• Unicellular at 37 C
• Moulds (mycelia) at 25 C
• Histoplasma capsulatum, Sporothrix shenckii,
PHYLA – Deuteromycotina coccidioides immitis & Coccidioides posadii, and
Deuteromycota Blastomyces dermatitidis
• Fungi Imperfecti Microsporidia
• Contains undiscovered sexual form • New in Eumycota
• Lost their ability to reproduce • Obligate intracellular parasitic fungi
• Includes Candida albicans – causes yeast • Classified as protozoa before
infection • Possess polar filament
Yeasts • Coiled around microsporidial spore
• Unicellular that lacks mycelia • Extrudes filament to penetrate the recipient cell
 • Produces spores in the cell • Tinea capitis – Scalp
• Causes eye or GIT infections • Tinea barbae – Face & neck
• Tinea corporis – trunk of the body
• Tinea crusis – groin area

Superficial & Cutaneous Mycoses

• Candida albicans causes infections due to
reduction in microflora
• C. albicans are opportunistic yeasts but lives
harmlessly
Fleshy Fungi
• Causes oral thrush, skin thrush and vaginitis
• Large fungi in the forests
(candidiasis)
• Mushrooms, toadstools, puffballs & bracket
• Local infection may become focal site for
fungi
systemic infection
• Class of true fungi – mycelium
• Grows in soil or rotting log and fruiting body
• Forms & release spores
• Delicious to eat
• Some resemble as edible fungi are extremely
toxic and causes permanent liver and brain
damage or death
Medical Significance
• Variety of fungi are significant due to disease Subcutaneous & Systemic Mycoses
they cause • Severe types of mycoses
• Produce mycotoxins • Subcutaneous are infections of the dermis &
• Moulds & yeasts are called mycoses underlying tissues
• Mycoses – superficial, cutaneous, subcutaneous • Arise from traumatic implantation into the
or systemic subcutaneous tissue
• Some cases, infection progresses through all the • Grotesque in appearance (e.g. Madura foot)
stages that contains fungus bumps
Superficial & Cutaneous Mycoses
• Superficial mycoses are outermost area
infections
• Cutaneous mycoses affects the dermis
• Dermatophytes causes tinea infections
(ringworm)
• Are named according to the part that is infected
• tinea pedis - athlete’s foot)

Superficial & Cutaneous Mycoses Subcutaneous & Systemic Mycoses

• Tinea unguium – Fingernails & toenails • Systemic are infections of internal organs and
(onychomycosis) sometimes two or more different organ system
 • E.g., simultaneous respiratory and bloodstream • When isolated, yeasts are identified by
infections inoculating to a series of biochemical tests but
• Conidia of pathogenic fungi may be inhaled with rarely used
dust from soil or dried bird or bat feces or • Subtrates can be determine
through wounds of hands & feet • Miniaturized biochemical test are commercially
available
• Macro & microscopically observed & the speed
they grow
LICHENS
CHARACTERISTICS
• Found usually in the woods
• Colored, circular patches on tree trunks & rocks
• Thought to be a combination of algae and
fungus
• Recent evidence – includes yeast embedded in
the cortex
Subcutaneous & Systemic Mycoses • Classified as Protists
• If inhaled, they germinate and causes • Relations are referred to as symbiotic
respiratory infection similar to tuberculosis relationships
• E.g., blastomycosis, coccidiodomycosis, • Represents mutualism
cryptococcosis & histoplasmosis • Not associated with human disease
• May invade further especially in • Have antibacterial properties
immunocompromised SLIME MOULDS
• Bread mould such as Rhizopus and Mucor spp. CHARACTERISTICS
Cause disease or death in immunocompromised • Found in soil an on rotting logs
called zygomycosis or mucormycosis • Have fungal and protozoal characteristics
• Transferred to the Kingdom of Protozoa
• They are not moulds
• Possess complex life cycles
• Starts as ameba to multicellular organism
• Not know to cause human disease

Laboratory Diagnosis
• Clinical specimens are submitted to mycology
section