the microbiology and parasitology hand outs.

1. Featuresthat distinguishprotozoal &helminthicinfections:
1.) More important in tropical countries than in countries like the U. S. However,parasitic diseases are
becoming more prevalent in the U. S. as more infected people move here; also because people with
immune deficiencies such as AIDS are more susceptible to certain parasites.
2.) How the immune system responds to these parasites is a mystery. An immune response is activated,
but the immune system is seldom able to rid the body of them.
3.) They have more complex life cycles,with multiple hosts involved.
FUNGI
A. SomeGeneral Characteristics:
eukaryotic cells
nonmotile
heterotrophic (use organic compounds a carbon source; they can’t make their own sugars; no
photosynthesis)
prefer more acidic conditions than bacteria
can tolerate higher osmotic pressure and lower moisture than bacteria
larger than bacteria and have more cellular and morphologic detail
cannot tolerate the high temps. that bacteria can (fungal spores aren’t as resistant as bacterial spores)
most are aerobic;some are facultativeanaerobes (ex. yeasts) & some are anaerobes
important in ecosystems as decomposers (calledsaprophytes -they obtain nutrients by decomposing
dead & decaying matter); some are parasites, causing disease (mycosis;mycosesisplural); some produce
toxins that cause disease (mycotoxicosis;mycotoxicoses isplural).
major cause of plant diseases
the study of fungi is mycology
B. General Morphology:
most, with exception of unicellular species, have a vegetative structure called a mycelium (a
multinucleate mass of cytoplasm enclosed within a system of rigid, branched, tube-like filaments
called hyphae).
hyphaecan be coenocytic(undividednetwork of branching tubes) or have septa (cross walls).
cells walls are composed of cellulose, chitin (contains nitrogen - also found in the exoskeletons of insects,
crayfish,etc.), or a combination of the two.
specific morphology willbe discussed later foreach group of fungi
C. Reproduction-Fungi are classified by how they reproduce (sexually or asexually).
[Functions of spores include dissemination and reproduction]
1. Asexual Reproduction -Occursby elongation of hyphae, budding, or asexual spore production.
Asexual spores arespecialized cells that are dispersed & germinate in a favorable environment to
produce a new fungus; they are products of a typeof cell division called mitosis(one cell divides to
form 2 daughter cells that are identical to one another and to the original parent
cell). Types: sporangiospores,conidiospores.
2. Sexual Reproduction -Occursby producing sexual spores,whichformfollowingsexual fusion of
gametes (similar to sperm & eggs). Types: zygospores,ascospores,&basidiospores.
D. 2 General GroupsofFungi -Yeasts vs. Molds
[These are descriptive terms, not taxonomic! These organisms belong to many groups of fungi.]
1. Yeasts - characteristics:
nonfilamentous, unicellular
reproduce asexually by budding
reproduce sexually by producing various kinds of spores
aerobic or facultativeanaerobes
used to prepare bread, wine, beer, etc. (fermentation of carbohydrates produces ethanol &
carbon dioxide) ex. Saccharomycescerevisiae (cervesameans beer in Spanish)
some are pathogenic; ex. Candidaalbicans (causes yeast infections, thrush; see below)
2. Molds-characteristics:
filamentous, multicellular

2. have a vegetative structure called a mycelium(a multinucleate mass of cytoplasm enclosed
within a system of rigid, branched, tube-like filaments called hyphae).
hyphaecan be coenocytic(undividednetwork of branching tubes) or have septa (cross walls).
also possess reproductivehyphae whichproduce different kinds of spores (discussed above and
below)
see below forexamples.
E. ClassificationofSomeoftheLowerFungi:
1. Zygomycetes:
a. Characteristics: coenocytic hyphae,produce sporangiospores(asexualspores)
& zygospores (sexualspores).
b. Ex. Rhizopusnigricans - blackmold that develops on stale bread; the tiny blackdots on the
mold are the sporangia,whichhold the sporangiospores; sporangia look like tiny mushroom
caps.
c. can be opportunistic; some are pathogenic in the immnocompromised
F. ClassificationofSomeoftheHigherFungi:
1. Ascomycetes(SacFungi)
a. Characteristics: includes molds with septate hyphae and some yeasts; ascospores (sexual
spores) develop within sacs called asci (sing. ascus); also produce conidiospores(asexual
spores).
b. Examples:
1.) Saccharomycescerevisiae -yeast is used to make beer, bread, wine; cervesameans beer
in Spanish.
2.) Trichophyton-causes athlete's foot(tineapedis);ringworm of the feet;other species
infect differentparts of the body (dandruff,nail fungus, jockitch)
3.) Penicillium spp. - conidiospores form long chains on branching conidiophores, creating
a brush-like structure that looks like a broom (penicillus means “brush"); some species
produce the antibiotic penicillin.
4.) Aspergillus spp. - form long chains on a globelike conidiophore; cause aspergillosis,a
pulmonary disease of animals & humans; infection is often secondary to tuberculosis,
immunodeficiency,& steroid therapy.
5.) Histoplasmacapsulatum -causes Mississippi Valleyfever (histoplasmosis);canget
from bird droppings and bat guano; endemic disease in this area; pulmonary disease.
6.) Candidaalbicans - part of our natural flora;opportunistic; becomes a problem when
defenses are weakened or balance of microbes is upset (ex. from antibiotic treatment);
cause of vaginal & intestinal yeast infections & thrush in the mouth ("cottagecheese
patches") - called candidiasis.
2. Basidiomycetes(ClubFungi)
a. Characteristics: many form basidiocarps (mushrooms,puffballs,or shelflike bodies on
trees); some are molds, a few are yeasts; produce conidiospores;also
producebasidiospores (sexualspores); basidiospores formon the "gills" of mushroom
basidiocarps.
b. Examples:
1.) Amanita - poisonous mushroom; toxin causes a mycotoxicosis
2.) Cryptococcus - yeast cells surrounded by a capsule; causes fatal meningitis
(cryptococcosis);transmission – inhalation of contaminated dust; found in 8% of AIDS
patients.
3. Deuteromycetes(ImperfectFungi)
a. Characteristics: called the imperfect fungi because no sexual stage has been observed; we put
them in this group until a sexual stage is observed; these fungi grow as yeasts or molds; identify
on basis of shape & arrangement of their conidiospores (asexual spores); some species are
pathogenic; many of these fungi have recently been placed in other phyla.
G. DimorphicFungi -Some fungi switchbetween a single-celled yeast phase of growth & a mycelial phase
(called dimorphism);discoveredby Pasteur; some species will switchif oxygen supply decreases. Pathogenic
dimorphic fungi are mycelial outside of the host & single-celled inside the host. Withpathogenic species, it is
usually high body temperature that causes the switch. Candidachanges in response to the higher nutrient

3. concentrations found in the body. The problem withdimorphism is that single cells are more readily spread in
bloodstream, leading to systemic infections.
H. Mycoses(Fungal Diseases)
Humans usually acquire fungal disease from nature; they are not highly contagious.
mycotoxicosis vs.opportunisticmycoses:
See above for diseases
Some produce toxins that are hallucinogenic; ex. muscarin-produced by a mushroom
Some produce toxins that are highly poisonous; ex.
1.) Claviceps (ryemold) - produces ergot;causes death to anyone eating bread made from
contaminated rye;LSD is made form fruiting structures (causes hallucinations)
2.) Aspergillus – produces aflatoxin;whichgrows in many plant materials; low levels of toxin can
be carcinogenic.
3.) Amanita - poisonous mushroom
I. Antibiotics: Penicillinsproduced by Penicillium ; Cephalosporins produced by Cephalosporium.
II. PROTOZOA
A. General Characteristics:
Unicellular eukaryotes.
The protistan lineages continue into the kingdoms of plants, fungi, and animals.
Limited to a moist environment because they lack a cell wall
Heterotrophs
Most reproduce asexually by fission (one cell divides to form 2 identical daughter cells & budding; some
(ex. Plasmodiumthat causes malaria) under go schizogony(multiplefission). Sexual reproduction occurs
by conjugation,thefusionof vegetative cells, or by the fusion of specialized gametes called gametocytes.
Some have complex life cycles,requiring multiple hosts and changing their morphology
(ex. Plasmodium uses the mosquito as an intermediate host)
Trophozoite-active,motile, feeding stage of protozoans; parasitic stage that causes the disease in the
host.
Cyst - resistant, inactivestage; how diseases are usually transmitted by the fecal-oralroute; usually
more useful than trophozoites for lab identification.
B. Classification: [basedon mode of locomotionor motility]
1. Mastigophora orZoomastigophora (moveby means of flagella)
a. Trypanosomagambiense -infectsthe blood and tissue fluids; causes African sleeping sickness
(it leads to the loss of consciousness and death when it invades the CNS); can also infectcattle;
vectoris the tsetse fly.
b. Giardialamblia - body has the appearance of a human face (4 “eyes” are nuclei);have 2-6
flagella; form cysts; causes a waterborne dysentery (traveler'sdiarrhea); one of the “don’t drink
the water” diseases; firs sigh is usually an explosive, foul-smelling watery diarrhea followedby
copious amounts of campers are a high-risk group because of asylvaticcycle(parasite is found
in mountain streams contaminated withhuman feces or animal feces, especially beavers).
c. Trichomonasvaginalis -causes vulvovaginitis; numerous flagella
2. Sarcodina(moveby means of pseudopodiaor"falsefeet" - temporary extensions of the cell body
caused by protein filaments of the cytoskeletonpushing on the cell membrane); feed on algae, bacteria,
and other protozoans by phagocytosis.
a. Amoebaproteus -freshwater;not pathogenic
b. Entamoebahistolytica -causes amoebicdysentery;usually acquired by consuming fecally
contaminated water or food;flies and cockroachescan also be mechanical vectors;produce
cysts; first protozoanto be shown to be a pathogen (1875);one of the “don’t drink the water”
diseases; trophozoites may invade the intestinal mucosa where they can cause ulceration and
escape into the blood vessels; they may allow bacteria in fecal material to enter the body cavity
and cause peritonitis.
c. Naegleriafowleri- causes amoebic meningioencephalitis; usually seen in swimmers.
d. Acanthamoebapolyphaga – accumulateson the water surface of contaminated hot tubs when
tubs are covered; cause ulceration of the eyes and skin; can invade the central nervous system
and cause meningioencephalitis.
3. Ciliophora (moveby means of cilia)
a. Parameciumcaudatum - freshwater; not pathogenic

4. b. Balantidiumcoli - only ciliophoran that causes disease; produces cysts;causes diarrhea of
large intestine; rare except in the Philippines; symptoms are similar to those of amoebic
dysentery.
4. ApicomplexaorSporozoaorHaemosporina -Basically nonmotile. All have an infectious, sporelike
stage (sporozoite) thatis oftentransmitted to new hosts by an insect vector. All are parasitic
(obligate parasites - cannot live apart fromthe host). Some have elaborate life cycles,changing body
form (trophozoite,sporozoite,merozoite);lifecycleincludesschizogony(multiple
fission). Examples
a. Plasmodiumvivax - causes malaria;vectoris the mosquito; kills 1-3.5 million people each
year; malaria= bad air; used to infect people with malaria to stop the progression of syphilis
(feverswould kill the bacteria).
b. Toxoplasmagondii -causes toxoplasmosis;humansacquire the disease by consuming cystsin
the meat of infectedanimals or ingesting material contaminated by cat feces containing the
parasite (can get it from cleaning the litter box - doctors warn pregnant women not to do this).
c. Cryptosporidium-formcysts; cause enteritis & diarrhea; can occurin water supplies; can also
be transmitted by fecal-oraltransmission fromkittens/puppies; resistant to chlorine (it can
survive full-strength Chlorox!); threat only AIDS patients and those immunocompromised; no
effectivetreatment found.
d. Pneumocystiscarinii - may be a fungus!!; causes pneumocystispneumonia;spreadin
respiratory droplets; common in AIDS patients.
III. HELMINTHS – Flatworms& Roundworms
General Characteristics:
Animals
Cephalization - concentration of sensory receptors toward the anterior end.
Organ/system level or organization/
Sexual reproduction. Most flatwormsare monoecious (male& female reproductive organs in same animal).
Roundworms are dioceious (separatesexes).
A. Platyhelminthes (Flatworms= Trematodes + Cestodes) - most are free-living; marine and freshwater;
predators, scavengers, or parasitic; some have regenerative capabilities.
1. Trematoda (Flukes) - all parasitic of vertebrates; have complex life cyclesthat include sexual and asexual
phases; they require at least 2 kinds of organisms to complete the cycle - they reach sexual maturity in
a primaryor definitivehost(alwaysa vertebrate), their larval stages develop or become encysted in
an intermediatehost(usually an invertebrate).
a. Clonorchissinensis (Chinese or Human LiverFluke)
Adults live in bile ducts (in the liver) of humans (definitivehost)
Intermediate hosts: snail (first) and fish (second)
Life cycle: a snail ingests the eggs; the eggs hatch & release a larval stage whichgoes through
several transformation before finally forming a tadpole-like cercariae;the cercariae bore
through the flesh of the snail, & escape into the water; they swim until they find the appropriate
species of fish; they encyst in the muscle tissues of the fish (forming metacercariae);theadult
flukes develop in livers of humans who eat raw, infected fish; eggs of the parasite are excreted
in the feces; when human fecesend up in ponds, etc., snails ingest the eggs & the cyclerepeats
itself.]
b. Schistosoma mansoni (Schistosomes or Blood Flukes) - adults live in circulatory system; spiny eggs
break through the blood vessel wall and through the gut wall to be expelled in feces;eggs hatch into
cercaria in water; cercaria then penetrate skin when a person is bathing or swimming; cause spleen
and liver enlargement, dysentery, and cirrhosis of the liver
2. Cestoda(Tapeworms) - intestinal parasites of vertebrates; no digestive system like in trematodes &
nematodes; they absorb nutrients through their tegument!
Morphology: scolex(head)with suckers and/or hooks (forattachment), proglottids (body units- each
one has male and female reproductive organs): immature proglottids (closesttothe scolex),mature
proglottids (nextclosest to the scolex), and gravidproglottids (furthestfromthe scolex - in these
proglottids, the uterus is filled witheggs).

5. General life cycleof tapeworms: the gravid proglottids break off and are passed in the definitive host's
feces; larval forms hatch when the eggs are ingested by the intermediate host; larvae then encyst in the
intermediate host (called a cysticercusorbladderworm);adultworms usually develop in the definitive
host when raw or poorly cookedinfected meat is eaten. Examples:
a. Taeniasolium (pork tapeworm) – reaches a length of 2-7 meters; primary host: humans, etc.;
intermediate host: swine
Humans can be infected withthe adults by consuming rare pork containing cysticerci larvae;
larvae then develop into adults in digestive tract of the human.
Humans can also be infected with larval forms when they accidentally ingest eggs (they get them
from other infected humans who contaminate food, etc.with the eggs when they don’t use proper
hygiene after going to the bathroom). In this case every organ in the body may
harbor cysticerci. When a cysticercusdies, it releases toxins and usually causes a severe allergic
reaction, whichis sometimes fatal.
b. Taeniasaginata (beef tapeworm) – reaches a length of 5-25 meters; primary host: humans, etc.;
intermediate host: cattle, sheep, etc.; life cyclesimilar to that of T. soliumabove;beef riddles with
encysted larvae is called “measly beef.”
c. Echinococcusgranulosus (dogtapeworm); small - only 3 proglottids long; typicallife cycle:
dogs are infected by adults when they eat raw butchered livestockcontaining larvae (ex. raw
bones, etc.)
eggs are passed in feces of dog; livestockeat vegetation with eggs when grazing
larvae hatch and encyst in the muscle tissue of livestock
Humans can get hydatidcysts (larvae) from ingesting the eggs (the eggs are passed in feces of dog, dog
licks himself, then dog licks your face). These cystsdevelop in the liver, lungs, and brain. Eachfluid-
filledcyst,containing many larvae, can reach the size of a grapefruit.
d. Dipylidiumcaninum (dog & cattapeworm) - often seen in children; flea is the intermediate host - it eats
the eggs on an animal; larvae develop in flea; if a dog, cat, or human ingests the flea, the adult will
develop. Note: Larvae are not transmitted through the bite of the flea!!
e. Hymenolepisnana (dwarf tapeworm) - most common tapeworm of humans in the world; intermediate
host is a grain beetle; humans can ingest the eggs in cereals and other foods that contain parts of the
insects; intermediate host is optional (meaning that if youingest the eggs of this worm, youget an adult
infection).
B. Nematoda(Nematodes)
General characteristics:
Nematodes are everywhere!!!! They are freeliving in soil, fresh & salt water, & are parasitic in plants
and animals.
Dioecious (separate sexes).
Possess a nonliving cuticle,whichis secreted by the epidermis and is resistant to the digestive
enzymes of the hosts.
More highly developed than flatworms.
Adults do not latch onto the host like the tapeworms.
1. Ascarislumbricoides (intestinal roundworm of pigs, horses, humans)
largest intestinal nematode in humans.
disease is called ascariasis
Eggs can remain viable even in preservative!
Females are longer; males are shorter & have a hooked posterior end.
2. Enterobiusvermicularis (pinworm)
parasitizes large intestine of humans (especially children)
at night the females migrate to the perianal region to lay eggs
their presence there causes itching
hosts become infected by accidentally ingesting the eggs.
3. Ancylostomacaninum&Necatoramericanus (hookworms)
larvae can penetrate the skin of a barefoot person
once inside, the larvae travels through the bloodstream to the lungs, moves up the trachea, is coughed
up & swallowed;it matures in the small intestine.
Ancyclostoma has “fangs”;Necator has cutting plates.

6. 4. Trichinellaspiralis (porkroundworm)
humans usually become infectedby eating insufficiently cooked pork
larvae are encysted in the muscle tissues of the pig
causes trichinosis;larvalmigration can cause death.
5. Wucheriabancrofti
adults live in lymph nodes where obstruction of lymph vessels leads to grotesque enlargement of
these nodes & to a condition called elephantiasis
a mosquito is the intermediate host.
6. Dirofilariaimmitis - causes heartwormdiseaseindogs; a few cases in humans & cats; mosquito is
intermediate host.
7. Trichuristrichiura - (whipworm) - adults partially embed in the mucosa of the large intestine; each adult
produces 1,000-7,000 eggs/day!
The Viruses
General Characteristics:
virus means poison; someone once called them "a piece of bad news wrapped in a protein;"
obligateintracellularparasites (canreproduce/replicate only inside a host cell)
not cells; debate over whether or not they are considered “alive” (see below)
consist of nucleic acids (DNA or RNA) in a protein coat, called a capsid (no cell membrane)
they insert themselves into a host cell & direct the host cell's metabolic machinery to make more virus; the
virus supplies information (the plan) in the form of its nucleic acid - raw materials and driving force(ATP &
reducing power)are supplied by the host cell.
all cellular organisms can be attacked by viruses; however,viruses are very specific for the organisms & cells
they infect.
AreVirusesAlive?
Characteristics of living things: reproduction, metabolism, organized as cells, contain all organic molecules
(lipids, enzymes, nucleic acids, carbs), evolution & adaptation to changing environments.
Viruses have some of these char's: they can evolve,they contain some macromolecules, they direct their own
reproduction; However,they are not cells - they do not have cytoplasm, a cellmembrane, organelles,
ribosomes, or a nucleus. They have DNA or RNA, unlike prokaryotic and eukaryotic cells, whichhave both. In
addition, they lacka metabolism of their own(they cannot produce ATP,etc.) - raw materials and driving force
(ATP & reducing power)are supplied by the host cell.
I. HOW ARE THEYCLASSIFIED? (4ways:size, structure, host range, life cycles)
A. Size- range from about 1/10th to 1/3rd the size of a small bacterial cell.
B. Structure- basic structure of a virus is a nucleic acid surrounded by a protein capsid; a membrane
envelope may also be present outside of the capsid, but this is acquired fromhost cell. A complete viral
particle (= capsid + nucleic acid + envelope if it is present) is called a virion.
1. NucleicAcid- Viruses can store their genetic info.in different types of nucleic acid (each virus
has only type). Viruses can have DNA or RNA. Their nucleic acid can be double stranded (ds) or
single stranded (ss);they can even have double stranded RNA! RNA viruses can have a (-)
sense strand or a (+)sense strand of RNA.
(+) sense RNA acts like mRNA and can be translated into proteins by the host cell’s
ribosomes. (-) sense RNA does not make sense to the host cell’s ribosomes. After the virus
containing this type of RNA enters the host cell, a complementary (+) sense strand is made from
its (-)sense strand. Only (+) sense strand RNA can be read by the host cell’s ribosomes!
2. Capsids-protein coat that surrounds the nucleic acid;the constituent protein molecules
making up the capsids are called capsomeres;there are 3 basic shapes based on how the
capsomeres are arranged. See diagrams of these shapes!!
a. helical - proteins fit together as a spiral to form a rod-shaped structure.
b. polyhedral -proteins are arranged in equilateral triangles that fit together to form a
geodesic dome-shaped structure; some appear almost spherical; you may have seen
architectural structures that have this shape.

7. c. complex -combination viruses with a helical portion (tail) attached to a polyhedral
portion (head); ex. many bacteriophages; may also have a tail sheath (participates in
injecting the viral nucleic acid into the host cell), plate, pins,& tail fibers (help virus
attach to host cell).
3. Viral Envelopes -piecesof the host cell'scell membrane that the virus acquires as it emerges
from its host cell;the virus pushes out of the cell membrane, forming a bud that encloses the
virus - then the bud pinches off behind, resealing the cell - as a result the host cell is not
lysed. Glycoproteinspikes fromthe host cell’s glycocalyxmay stick out of the envelope. Viruses
that lack envelopes are called naked viruses. Because envelopes are acquired from host’s cell
membranes, viruses may be hidden from attach by the host’s immune system. Envelopes also
help viruses infect new cells by fusion of the envelope with the host’s cell membrane. On the
other hand, enveloped viruses are damaged easily by physical and chemical antimicrobial
agents.
C. HostRange- defined as the spectrum of organisms a virus attacks; viruses exhibit considerable
specificity forhosts and even cells within that host; viral specificity is determined by whether or not a
virus can attach to a cell. Attachment depends on the presence specific receptorsites on the surface of
host cell and on specific attachment structures on the viralcapsid or envelope. Examples of receptor
sites are proteins, LPS’s, glycolipids, or glycoproteins.
D. LifeCyclesofBacteriophages (virusesthatinfectbacteria – means“bacteriaeating”)
1. Replication [= Lytic Cycle] Seediagram Events:
a. Adsorption-the virion attaches itself to a specific receptor site on the surface of the host
cell.
b. Penetration- the viral nucleic acid penetrates the host cell
c. Uncoating - removing the capsid & envelope; basically 2 waysit can happen:
1.) during penetration, the virion disassembles so that only the viral nucleic acid
enters host cell
2.) the entire virion enters the host cell & uncoating occurslater
d. Viral Synthesis (LatentPeriod)(also called biosynthesis) - more viral components
(nucleic acids & proteins forcapsids) are synthesized by the host cell.
d. Maturation(Assembly)-components are assembled into new viruses
f. Release(BurstPeriod)- hundreds of intact virions exit host cell;2 ways:
1.) If the virus is of the naked type, an encoded protein, lysozyme,dissolves the cell
membrane &/or cell wallof the host cell,causing the cell to lyse & releasing the
hundreds of viruses inside it.
2.) If the virus is to be an enveloped virus, it pushes out the cell membrane, forming a bud
that encloses the virus - then the bud pinches off behind, resealing the host cell; as a
result the host cellis not lysed.
2. LysogenicCycle(LysogenyorTemperance)-Temperenceinvolvesthe capacity of certain
viruses to set up long-term relationships with their host cells - the virus remains latent formany
cellular generations by becoming integrated into a host cell's chromosome (the integrated viral
DNA is called a prophage). Inthis case no new viral components are synthesized & the host cell is
not harmed. The virus may remain latent forlong periods of time before initiating a lytic cycle. The
problem withthis type of cycleis that the viral nucleic acid that becomes integrated into the host
cell's chromosome gets replicated along with the host cell's chromosome and is passed to daughter
cells during cell division. In the prophage state, some viral genes are expressed, which may slightly
change the host cell's phenotype (ex. only lysogenic strains of Corynebacteriumdiphtheriae cause
the disease diphtheria because the disease-causing toxin is encoded in the prophage of the infecting
virus). Something (ex. temperature change) may trigger prophages to go into the lytic
cycle. Released virions cannot infectcells that are carrying the same prophage - it makes the cell
immune to attack by a virion of the same phage.
II. TAXONOMY
Family names all end in viridae; family names are oftenconverted into English (ex. Retroviridae are called
retroviruses). Genus names end in virus - species names are English words.
Ex. Retroviridae, Lentivirus, Human Immunodeficiency Virus (HIV)
Groupings reflect only common characteristics and are not intended to represent evolutionary relationships.
III. ANIMALVIRUSES

8. A. CultivatingAnimal Viruses&DiagnosingViral Illnesses
At one time animal viruses had to be cultivated & counted by infecting animals.
In the 1930's it was discovered that embryonatedchickeneggs couldbe used to culture
animal viruses; embryonated eggs are inoculated with dilutions of a virus sample to determine
the highest dilution that kills the embryo; this procedure was more economical& efficient than
using adult animals.
In the 1950's cell culture& tissueculturemethods were developed. This solved the
problem of viral specificity. Ex. Before cell cultures it was impossible to culture viruses in mice
or chickeneggs that only infected humans (ex. HIV); continuouscell lines are usually derived
from cancerous tissue & grow indefinitely in culture; regular cell lines grow increasingly slowly
after 20-30 subcultures & eventually lose their ability to support viral replication; the most
famous c.c.l.is the HeLacell line (named after Helen Lack,the donor - from cervicalcancer).
Important Note: Physicians rely on symptoms to diagnose most viral illnesses. Culturing
viruses takes too long & antibodies in the blood can usually be detected only after patient has
recovered.
Viral infectionssometimes affecthuman cells in ways that can be seen under the
microscope. For ex. the measles virus causes the membranes of neighboring cells to fuse,
creating giant, multinucleated cells. Some virus-infected cells can be id. because they
contain inclusionbodies,collectionsof viral components such as capsids and nucleic acid,
waiting to be assembled into new viral particles. For example, the rabies virus produces
inclusion bodies called negribodies ininfected nerve cells (this is what welook forin
suspected cases of rabid animals - have to look fornegribodies in brain - animals have to be
euthanized).
B. ReplicationofAnimal Viruses (Lyticcycle)-proceeds through similar stages as bacteriophage
replication.
1. Adsorption-Proteins in cell membrane actas receptor sites for a virus; remember, no cell
walls in animal cells; adsorption is largely responsible fortissue specificity of animal viruses -
only cells witha complementary receptor are attacked by a particular virus.
2. Penetrationcan occurin 3 ways:
a. viral envelope fuses withcell membrane, emptying the rest of the virion inside the cell.
b. other enveloped viruses enter by being phagocytized by a host cell
c. most naked animal viruses enter as most bacteriophages do - the capsid adsorbs to cell
surface & only the viral nucleic acid enters cell.
3. Uncoating - Envelopes/capsids are often removed in the penetration process; viruses that
enter the cell partially or completely intact are uncoated inside the cell by the host cell'sown
hydrolytic enzymes, sometimes those in its lysosomes.
4. Viral Synthesis -The specifics of this process depend on whichof the 5 types of nucleic acids is
present in the virus.
5. Maturation- Assembly not really understood
6. Release- Enzymescause lysis of the host cell or viruses "bud." Viruses that kill the host cellby
causing lysis are called cytocidal. Viruses that damage the host cell but do not kill it are
called cytopathic. Persistent viral infections can last foryears, producing new virus particles
by budding withoutkilling the infected cell.
C. Latency (similar to temperance or lysogeny) - Sometimes the viral nucleic acid is integrated in the
host cell's DNA (called a provirus),allowingthe infected animal cells to function normally foryears
(just as a lysogenic bacteriophage or prophage does).
Ex. Typicalof DNA viruses belonging to Herpesvirus family - herpes simplex 1 (causes fever
blisters) causes a symptomless latent infectionof nerve cells of mouth & lips - infection can be
reactivated by a fever,a cold,too much sun, or stress.
Ex. Varicella Zoster (another Herpsevirus) causes chickenpoxas the primary infection &
shingles as the reactivation.
Ex. HIV (Human Immunodefiency Virus) – belongs to the Retrovirus family; causes AIDS
(Acquired Immune Deficiency Syndrome).
D. SomeAnimal RNAViruses
Retroviruses (Retroviridae)
large group of RNA viruses; includes HIV (Human Immunodeficiency Virus) which causes
AIDS (acquired immune deficiency syndrome); infects T cells (type of white blood cell).
capsid contains 2 copies of the same (+) sense RNA molecule (called a diploidvirus);capsid
also contains the enzyme reversetranscriptase.

9. Retro means "backward." This virus uses the enzyme reversetranscriptase tomake DNA
from its RNA. This DNA can be integrated into the host cell'schromosome. The proviral DNA
can now be transcribed into mRNA and translated into viral proteins to assemble new viruses
for release; As with prophages, the provirus can stay in a latent stage in which it is replicated
along withhost cell DNA, causing the host cell no damage.
AZT (azidothymidine),which is used against HIV,helps stop reverse transcription by
targeting the enzyme reverse transcriptase.
Flaviviridae
enveloped; polyhedral capsid; (+) sense RNA
includes Yellow Fever (hemorrhagic fever)
Togaviridae
enveloped; polyhedral capsid; (+) sense RNA
includes Rubella virus (Rubella or German measles)
Picornaviridae
naked; polyhedral capsid
includes Enterovirus (causes polio);Rhinovirus (commoncold);Hepatovirus (Hepatitis A)
Orthomyxoviridae-InfluenzaViruses
Flu viruses; 3 types (A, B, C); A is the most common, infecting many species of animals,
including humans; A is responsible for many pandemics (worldwideepidemics); B & C only
infect humans & do not cause pandemics; Outbreaks of B occurevery 2-3 years; C causes mild
cold-likeillnesses.
enveloped RNA viruses; protein spikes in envelope; its (-) sense RNA is divided into 8 separate
pieces, each one packaged in a helical capsid
This virus exhibits antigenic shift- sudden changes in properties that id. the virus as a foreign
invader to the defenses of the human immune system; occurs from genetic changes that can
occurwhen 2 differentflu viruses infectthe same cell; when this happens it is likely that the
RNA molecules of the 2 infecting virions recombine in various ways among the new virions,
producing a virus that is significantly different from either of the original infecting strains. This
is why youcan get the flu over and over again!
Rhabdoviridae
enveloped; helical capsid; (-) sense RNA
includes Rabies virus
Paramyxoviridae
enveloped; helical capsid; (-) sense RNA
includes viruses that cause Mumps, Measles, Viral pneumonia, Bronchitis
Bunyaviridae
enveloped; segmented RNA; (-) sense RNA
includes Hantavirus (“4 corners disease”)
Filoviridae
enveloped; filamentous capsid; (-) sense RNA
includes Ebolavirus
Reoviridae
naked; polyhedral capsid; ds RNA
includes Rotavirus (most common cause of diarrhea in infants and young children under the
age of 2)
E. SomeAnimal DNAViruses
Adenoviridae
naked; polyhedral capsid; ds DNA
mainly responsible forhuman respiratory diseases; also causes diarrhea in babies and young
children
Herpesviridae -enveloped;polyhedral capsid; dsDNA

10. Simplexvirus – Herpes simplex 1 (oral) and 2 (genital & neonatal)
Varicellovirus – Varicellazoster – chicken pox and shingles
Roseolovirus – Roseolainfantum – roseola in infants (rash and fever)
Lymphocryptovirus – EpsteinBarr virus – causes infectious mononucleosis and Burkitt’s
lymphoma; also linked to Hodgkin’s disease.
Poxviridae
enveloped; brick shaped capsid; ds DNA; largest of all viruses
includes Orthopoxvirus – small pox & cow pox
Papovaviridae
naked; polyhedral capsid; ds DNA; replicate in nuclei of host’s cells.
Includes Papillomavirus – warts(some associated with cervicalcancer)
Hepadnaviridae
enveloped; mostly ds DNA; hepa = liver
Hepatitis B virus
Parvoviridae
naked; ssDNA; uses a helper virus to supply necessary component to produce more viruses.
Includes Canine parvovirus– causes severe and sometimes fatal gastroenteritis in dogs.
Also includes Erythrovirus(B19) – causes 5th disease (erythema infectiosum) – deep red rash
on children’s cheeks and ears and both a rash and arthritis in adults; can cross placenta and
damage fetus.
F. VirusesandCancer
1. Tumors- uncontrolled growthof tissue (cells are dividing out of control);most
are benign(non-lifethreatening); some are malignant(they spread or metastasize to
surrounding tissues).
2. Cancer– malignant tumors that metastasize to surrounding tissues.
3. Cause– Most human cancers arise form genetic mutations or cellular damage caused by
environmental factors(chemicals - nicotine, pesticides; radiation - UV, X-rays,etc.; diet). About
15% are attributed to viral infections.
4. Examples:
a. Human T-cellleukemia (blood cancer),
b. Epstein-Barr virus causes Burkitt's lymphoma
c. Hepatitis B virus causes hepatocellular carcinoma (livercancer)
d. human papillomavirus causes skin & cervicalcancers.
e. Kaposi’s sarcoma – thought to be associated with Herpesvirus
5. How? Some tumor viruses are retroviruses; they converta normal cell to a tumor cell by
introducing an oncogeneintoit (oncogenicprovirus). Someresearchers believe even normal
retroviruses might cause tumors - merely inserting a normal provirus into the host
chromosome near a normal gene might alter its expression and convertit to an oncogene.
G. VirusesandTeratogenesis
Teratogenesis – theinduction of defects during embryonic development. A teratogen is a drug or
other agent that induces such defects. Viruses are teratogens that can be transmitted across the
placenta and infect the fetus. Cytomegalovirus (CMV),Herpes Simplex virus (HSV), and Rubella
accountfor a large number of teratogenic effects. TORCH series is a series of blood tests used to detect
antibodies to these viruses.
IV. VIROIDS
Defined - a circular molecule of ssRNA without a capsid; don’t produce proteins
Cause several economically important plant diseases; none known to infectanimals
1/10 the size of the smallest plant virus
How it causes disease is a mystery; one theory is that it interacts in some way with the host genome,
changing the expression of the host genes to cause disease.

11. V. PRIONS
Defined: infectious agent composed only of protein
Affectthe central nervous system.
Ex. scrapie of sheep, Creutzfeldt-Jakobdisease (CJD) of humans, mad cow disease.
Not known exactly how it causes disease.
Microbial Growth
The term microbial growth refersto the growth of a population (or an increase in the number of cells), not to an
increase in the size of the individual cell. Cell division leads to the growth of cells in the population.
Two TypesofAsexual ReproductioninMicrobes:
1.) BinaryFission-Bacterial reproduction occursthrough fission,aprimitive formof cell division that does not
employ a spindlefiberapparatus.[A spindle fiber apparatus made of protein filaments is responsible for
moving the chromosomes around during cell division (mitosis & meiosis) in most eukaryotic cells. Bacteria do
not have these structures.] The bacterial cell doubles in size and replicates its chromosome. FollowingDNA
replication, the twochromosomes attach to separate sites on the plasma membrane, and the cellwall is laid
down between them, producing two daughtercells.
2.) Budding - A few bacteria and some eukaryotes (including yeasts) may also replicate by budding,forminga
bubble-like growth that enlarges and separates from the parent cell.
I. MicrobialGrowth
A. PhasesofGrowth - A microbial lab culture typically passes through 4 distinct, sequential phases of
growth that form the standard bacterial growthcurve:(Notall growth phases occurin all
cultures). See graph;beableto draw & label.
1. Lag Phase- In the lag phase, the number of cells doesn't increase. However,considerable
metabolic activity is occurring as the cells prepare to grow. (This phase may not occur, if the cells
used to inoculate a new culture are in the log phase & provided conditions are the same).
2. LogPhase(logarithmic or exponential phase) - cell numbers increase exponentially; during each
generation time, the number of cells in the population increases by a factorof two). The number
of microbes in an exponentially increasing population increases slowly at first, then extremely
rapidly. Organisms in a tube of culture medium can maintain log growthfor only a limited time, as
nutrients are used up, metabolic wastes accumulate, microobes suffer from oxygen depletion.
3. StationaryPhase - The number of cells doesn't increase, but changes in cells occur:cell become
smaller and synthesize components to help them survive longer periods without growing (some
may even produce endospores); the signal to enter this phase may have to do with overcrowding
(accumulation of metabolic byproducts, depletion of nutrients, etc.).
4. DeathPhase - In this phase, cells begin to die out. Death occurs exponentially, but at a low
rate. Death occurs because cell have depleted intracellular ATP reserves. Not all cells necessarily
die during this phase!
B. ContinuousCultureofMicrobes
In the lab, cultures usually pass through all growth phases - not in nature. In nature, nutrients
continuously enter the cell'senvironment at low concentrations, and populations grow continually at a
low but steady rate. The growth rate is set by the concentration of the scarcest or limiting nutrient,
not by the accumulation of metabolic byproducts- in nature there is always some other microbe that
can use these metabolic byproducts fortheir ownmetabolism. In the lab, wehave tocontinually
replace the media.
II. MeasuringNumbers ofMicrobes
A. IndirectMeasurements (measure a property of the mass of cells and then ESTIMATE the number of
microbes)
1. Turbidity – Can hold tube up to the light and lookfor cloudiness as evidence of growth (difficultto
detect slight growth). A spectrophotometer can measure how much light a solution of microbial

12. cell transmits; the greater the mass of cells in the culture, the greater its turbidity (cloudiness) and
the less light that will be transmitted. Disadvantages: Not sensitive in terms of numbers of bacterial
cells & not useful fordetecting minor contamination.
2. MetabolicActivity -3 ways:
a. The rate of formation of metabolic products, such as gases or acids, that a culture produces.
b. The rate of utilization of a substrate, such as oxygen or glucose.
c. The rate of reduction of certain dyes. Ex. methylene blue becomes colorless when reduced.
B. DirectMeasurements -Give more accuratemeasurements of numbers of microbes.
1. DirectCounts - Coulter Counter - electronic counter; rapid & accurate only if bacterial cells are the
only particles present in the solution. [gives a total count - live & dead cells].
3. Plate Count– Bacterial colonies are viewed through the magnifying glass against a colony-counting
grid; called a Quebec colony counter (wehave this in the lab). [gives a viable count]
4. Filtration- A known volume of liquid or air is drawn through a membrane filterby vacuum. The
pores in the filter are too small formicrobial cells to pass through. Then the filteris placed on an
appropriate solid medium and incubated. The number of colonies that develop is the number of
viable microbial cell in the volume of liquid that was filtered. This technique is great for
concentrating a sample, ex. a swimming pool, where small populations may go undetected using
some other methods. [gives a viable count]
III. GrowthFactors - Microbes can exist in a great many environments because they are small, easily dispersed,
need only small quantities of nutrients, are diverse in their nutritional requirements.
A. Physical Factors
1. pH – bacteria can classified as:
a. acidophiles (acid-loving) – grow best at a pH of 1 to 5.4; Ex. Lactobacilllus (ferments milk)
b. neutrophiles – existfrom pH to 5.4 to 8.5; most bacteria that cause human disease are in this
category.
c. alkaliphiles (baseloving) – exist from pH to 7.0 to 11.5; ex. Vibrio cholerae (causes cholera)
2. Temperature– bacteria can be classified as:
a. psychrophiles (cold-loving) 15oCto 20oC; some can grow at 0oC.
b. mesophiles -grow best between 25oC and 40 C; human body temp is 37oC.
c. thermophiles (heat-loving) – 50oC to 60oC; found in compost heaps and in boiling hot springs.
3. Moisture– only the spores of sport-forming bacteria can exist in a dormant state in a dry
environment.
4. Hydrostaticpressure – pressure exerted by standing water (ex. lakes, oceans, etc.);some bacteria
can only survivein high hydrostatic pressure environments (ex. ocean valleysin excess of 7000
meters); the high pressure is necessary to keep their enzymes in the proper 3-D shape; without it,
the enzymes lose their shape and denature and the cell dies.
5. Tonicity(hypotonic,hypertonic,isotonic) – The use of salt as a preservative in curing meats and
the use of sugar in making jellies is based on the fact that a hypertonic environment kills or inhibits
microbial growth. Halophiles (saltlovers) inhabit the oceans.
6. Radiation– UV rays and gamma rays can cause mutations in DNA and even kill
microorganisms. Some bacteria have enzyme systems that can repair some mutations.
B. OxygenRequirements
1. strict orobligateanaerobes – oxygenkills the bacteria; ex. Clostridiumtetani
2. strict orobligateaerobes – lackof oxygen kills the bacteria; ex. Pserdomonas
3. facultativeanaerobes – can shift their metabolism (anaerobic if oxygen is absent or aerobic if
oxygen is present); ex. E. coli, Staphylococcus
4. aerotolerant– the bacteria don’t use oxygen, but oxygen doesn’t harm them; ex. Lactobacillus
5. microaerophiles – likelow oxygen concentrations and higher carbon dioxide concentrations;
ex. Campylobacter
C. Nutritional (Biochemical)Factors – Nutrients needed by microorganisms include:
Carbon– carbon containing compounds are needed as an energy source (ex. glucose)and for
building blocks.
Nitrogen- needed for amino acids and nucleotides; some can synthesize all 20 amino acids;
others have to have some provided in their medium.
Sulfur– needed for amino acids, coenzymes,

13. Phosphorus – needed for ATP,phospholipids, and nucleotides
Vitamins– a vitamin is an organic substance that an organism requires in small amounts and that
is typically used as a coenzyme; many bacteria make their own, but some are required in the
medium; microbes living in the human intestine manufacture vitamin K, needed for blood clotting,
and some of the B vitamins, thus benefiting their host.
Certaintrace elements – ex. copper, iron, zinc,sodium, chloride, potassium, calcium, etc.; often
serve as cofactorsin enzymatic reactions.
III. CULTURING BACTERIA
A. Methods ofObtainingPureCultures (aculture that contains only 1 species of organism)
1. TheStreakPlate Method – Bacteria are picked up on a sterile wire loop, and the wire is moved
lightly along the agar surface, depositing streaks of bacteria on the surface. The loop is flamed and
a few bacteria are pickedup from the region already deposited and streaked onto a new
region. Fewer and fewerbacteria are deposited as the streaking continues, and the loop is flamed
after each streaking. Individual organisms (individual cells) are deposited in the region streaked
last. After the plate is incubated at a suitable growth temperature for the organism, small colonies
(each derived from a single bacterial cell) appear. The loop is used to pick up a portion of an
isolated colony and transfer it to another medium for study. The use of aseptic technique assures
that the new medium will contain organisms of a single species. We’ll do this in lab.
IV. CULTURE MEDIA
A. TypesofMedia
1. Syntheticmedium – prepared in the lab from materials of precise or reasonably well-defined
composition.
2. Complexmedium– contains certain reasonably familiar materials but varies slightly in chemical
composition from batch to batch (contains extracts from beef, yeasts, blood); ex. nutrient agar,
nutrient broth
B. Selective& Differential Media (wewilllearn about these in detail in lab!)
1. Selective– one that encourages the growth of some bacteria but suppresses the growth of others.
2. Differential – has an ingredient that causes an observable change in the medium when a particular
biochemical reaction occurs(ex. a coloror pH change).
C. ControllingOxygenContentofMedia
1. Candlejars – the inoculated tube or plate is placed in a jar; a candle is lit before the jar is sealed;
the burning candle uses the oxygen in the jar and adds carbon dioxide to it; when the carbon
dioxide extinguishes the flame, condition are optimum forthe growthof microorganisms that
require small amounts of carbon dioxide (ex. Neisseriagonorrhoeae)
2. Thioglycollatemedium– oxygen-binding agent added to the medium to prevent oxygen from
exerting toxic effectson anaerobes; media is usually dispensed in sealed screw-captubes.
3. AnaerobicChamber(Brewer Jar)– A catalystis added to a reservoir in the lid of the jar. Water is
added to the gas-pak. Water is converted into hydrogen gas and carbon dioxide. The hydrogen gas
can then bind with any oxygen in the jar toform water. A methylene blue test strip is included in
the jar to ensure that anaerobic conditions are reached. When oxidized (oxygen is present) the
strip is blue; when reduced (no oxygen), the strip is clear.
H2O -----------> CO2 + H2
H2 + O2 -----------> H2O
Intro. To Taxonomy & The Classification of the Bacteria
I. Principles of Biological Classification
Organisms are classified into any particular group because they have certain common
characteristics. Classification of organisms
1.) establishes the criteria for identifying organisms;

14. 2.) it arranges related organisms into groups based on shared characteristics; and
3.) it provides important information on how organisms evolved.
A classification system based on collectingindividuals into groups and groups into progressively more
inclusive and broader groups is called a hierarchical scheme of classification. A basic principle of taxonomy is
that members of higher-level groups share fewercharacteristics than those in lower-levelgroups. For
example, humans have backbones like all other vertebrates, but they share fewer characteristics withfish and
birds than withother mammals. Likewise, nearly all bacteria have a cellwall, but in some the wall is G(+) and
in others it is G (-).
Taxonomyisthe science of classifying organisms.
A Swedish biologist names CarolusLinnaeus deviseda taxonomic scheme that was both practicaland
adaptable to expanding information. The Linnaeanschemeremains the basis forbiological classification
today in 2 regards: 1.) we continue to group organisms hierarchically,& 2.) weuse his nomenclature (see
below).
Speciesdefined: groups of actually or potentially interbreeding natural populations whichare reproductively
isolated from other such groups. Bacteria, withtheir variety of forms of genetic exchange, do not fit this
definition neatly. Microbiologists use the term “species,” more as a category of convenience (bacteria are
grouped based on similarities), existing more in the human mind than in the natural world.
The Linnaean scheme uses the followinghierarchical classification scheme:
Kingdom
Phylum(division)
Class
Order
Family
Genus
Specific epithet
Example: Humans Example: Treponemapallidum (causes syphilis)
Kingdom – Animalia Kingdom Monera (Prokaryotae)
Phylum– Chordata PhylumGracilicutes
[Subphylum - Vertebrata]
Class – Mammalia Class Scotobacteria
Order – Primates Order Spirochaetales
Family – Hominidae Family Spriochaetaceae
Genus – Homo Genus Treponema
Species - Homo sapiens Species – Treponemapallidum
II. Binomial Nomenclature
Linnaeus introduced a binomial nomenclature (each organism is designated by 2 names). Thefirst nameis
the organism’sgenusdesignation&thesecondisits specificepithet.Together,the 2 constitute
the speciesname. The species name is always latinized and underlined or italicized. The genus
designation is capitalized, but the specific epithet is not. Thus, the proper designation forhumans is Homo
sapiens (or Homo sapiens ). By convention,the genus designation can be replaced with an initial if the
complete genus name has been used recently enough to avoid possible confusion. For example, the
bacterium Staphylococcusaureus becomes S. aureus . All eukaryotes & prokaryotes are named this
way. Viruses are not!
III. Artificial &Natural Systemsof Classification
1. Artificial -the Linnaean scheme; he grouped organisms on the basis of visible similarities, but does not
indicate how closely organisms are related.
2. Natural - based on evolutionary (phylogenetic) relatedness.

15. IV. Usinga TaxonomicKey
Biologists often use a taxonomic key to id. organisms according to their characteristics. The most common
kind of key is a dichotomous key, whichhas paired statements describing characteristics or
organisms. Paired statements present an “either –or” choice,such that only one statement is true. Each
statement is followedby directions to go to another pair of statements until the name of the organism
finally appears. See example given in class.
V. TheFive KingdomClassificationSystem
No singleclassificationsystemiscompletelyacceptedby all biologists,butoneofthe mostwidelyacceptedis
the five-kingdomsystem.
KingdomMonera – prokaryotic;unicellular;mosthavea cell wall;reproduction
usuallybybinary fission;photosynthetic,somechemosynthetic;acquirenutrientsfrom
environmentbyabsorption.
KingdomProtista – eukaryotes; most are unicellular (some are organized
into colonies); cell wallpresent in some, absent in others; reproduction mostly asexual,
sometimes sexual; some are photosynthetic;acquire nutrients fromenvironment by
absorption and ingestion; this group includes the algae (resemble plants), the protozoa
(resemble animals), and the euglenoids (resemble both plants and animals).
KingdomFungi – eukaryotic;unicellular or multicellular; cell wall present;
sexual and asexual reproduction; acquire nutrients by absorption of organic matter from
dead organisms.
KingdomPlantae – eukaryotic;multicellular; cell wall present; sexual and
asexual reproduction; photosynthetic;acquirenutrientsfromenvironmentby
absorption.
KingdomAnimalia -eukaryotic;multicellular; no cell wall; primarily sexual
reproduction; acquire nutrients fromenvironment by ingestion (some parasites by
absorption).
VI. TheThree-DomainClassificationSystem
After the discovery of the archaeobacteria in the 1970’s, scientists suggested that these organisms
represented a third cell typeand they proposed another scheme for the evolution of living things froma
universal common ancestor. This common ancestor gave rise to the archaeobacteria, the urkaryotes, and
the eubacteria (true bacteria). They hypothesized a group of urkaryotes that gave rise to the eukaryotes
directly rather than by way of the prokaryotes. See figure 9.11 on p. 232. In 1990 Woesesuggested a new
taxonomic category,the domain,to be erected abovethe level of kingdom. The three domains Woese
proposes are shown in Figure 9.13 on p. 234. The domain Eukaryacontains all those kingdoms of
eukaryotic organism (animals, plants, fungi, and protists). The traditional kingdom Monera has been
divided into 2 domains: the domain Bacteria(true bacteria ) and the domain Archaea. The Archaea
exhibit many differences fromthe Bacteria:
Different cellmembrane structure
Cell wallpresent, but not composed of peptidoglycan
First amino acid in proteins not methionine like in other bacteria and eukaryotes
DNA Contains histone-like proteins similar to eukaryotes (true bacteria have no histone
proteins)
Live in only extreme environments (groups include extreme halophiles, extreme
thermoacidophiles, and methanogens)
VII. ClassificationofBacteria
The artificial scheme of classification in Bergey's ManualofSystematicBacteriology is widely used. Bergey’s
Manualdisregards evolutionary relationships because they often group bacteria into assemblages that
cannot be easily identified by standard laboratory procedures. Instead, the manual takes a strictly practical
approach so that it can be used as a comprehensive & quickreference when accuracy & speed are
important, as is often the case in diagnostic labs. Bergey’s Manual divides bacteria into 4 divisions on the
basis of their cell wall [G(+)or G(-)], their lack of a cell wall(mycoplasmas), & walls lacking peptidoglycan
(archaeobacteria). Bacteria species in each division are assigned to one or twosections; sections have no
taxonomic standing; they are simply groups of bacteria, whichshare certain easily identifiable properties.
Howdo we identifybacteria?
1.) We begin withmorphological characteristics (shape, arrangement, etc.),

16. 2.) Rely primarily on physiological characteristics (ability to grow on a selective medium, metabolic end
products, etc.).
3.) Knowing the source of the bacterium is also important.
4.) Can also use DNA probes.
THE FOLLOWING IS A LIST OF THE MEDICALLYIMPORTANT MEMBERS OFSELECTED SECTIONS DEFINED
IN BERGEY’S MANUALOF SYSTEMATICBACTERIOLOGY.
I. GRAM-NEGATIVE BACTERIA (eubacteria) - have an outer membrane, a periplasmic space, & a thin
peptidoglycan cell wall.
A. Section1 - Spirochetes -Distinguished by their corkscrew shape; possess axial filaments (bundled
flagella contained within the periplasm) that enable them to move through viscousenvironments (mud,
mucous). Some live harmlessly in our mouths. Ex. of pathogenic species:
Treponemapallidum – syphilis, Borreliaburgdorferi -lyme disease (carried by
ticks)
Leptospira -leptospirosis
B. Section2 - Aerobic/Microaerophilic,Motile,Helical/VibrioidBacteria-Helicalmembers are
corkscrew shaped, but flagella are ordinary; vibrioid members are comma-shaped. Ex. of species:
Campylobacterjejuni- major cause of diarrhea [hint: the jejunum is part
of the small intestine]
Helicobacterpylori- cause gastric ulcers in humans
C. Section4 - AerobicRods&Cocci -large & diverse group. Ex. of species:
Bordetellapertussis - pertussis (whooping cough)
Neisseriameningitidis -meningococcalmeningitis (infection of meninges or
coverings of the brain/spinal cord)
Neisseriagonorrhoeae -gonorrhea
Pseudomonasaeruginosa - important opportunistic pathogen; common cause of
infection in weakened hosts, such as burn victims;another species has been used to clean
up oil spills.
Brucella– brucellosis
Legionella -pneumonia and other respiratory infections.
Francisella-tularemia
D. Section5 - FacultativelyAnaerobicRods -Grouped into 3 Families; many can be distinguished by
their characteristic fermentation reactions; includes the enterics; Examples:
Salmonellatyphi- typhoidfever; other species cause food poisoning
Shigella spp. - shigellosis, a form of dysentery
Yerseniapestis - bubonic plague
Vibrio cholerae - cholera
Escherichiacoli- some species cause diarrhea & dysentery; uti’s
Enterobactercloacae – opportunistic infections
Proteusvulgaris – uti’s
Vibrio cholerae - cholera
Haemophilus influenzae -upper respiratory infections (epiglottitis, sinusitis,
ear infections),pneumonia, & meningitis.
Zymomonas -alcoholic fermentation;used to make tequilla
Klebsiellapneumoniae -pneumonia; uti’s
E. Section6 - AnaerobicStraight,Curved,&Helical Rods -most abundant microbes in mouth &
intestinal tract; Example: Bacteroides gingivalis -causes gingvivitis & peridontal disease. Other species
cause digestive & respiratory infections, uti’s, infections of wounds.
F. Section9 - TheRickettsias& Chlamydias -Oncethought to be viruses because of small size. Most
species are obligate intracellular parasites & can'tbe cultivatedoutside a living host cell. In general,
rickettsial pathogens are transmitted by arthropods (ticks,lice, mites, fleas); chlamydiae are spread
directly from one infectedhuman to another. Chlamydiae alternate between 2 cell types, elementary
bodies and vegetative cells. Elementary bodies are tiny, round structures released when an infected
host cell lyses. When phagocytized, they differentiate into rod-shaped vegetative cells that multiply
within the host cell [This is different fromother bacteria whichdo not invade the host cell!]. They then
differentiate into elementary bodies again before the host cell lyses. Examples:
Rickettsia spp. - typhus (transmitted by body lice & rat fleas), Rocky Mt.
Spotted Fever (transmitted by ticks)

17. Coxiella– Qfever
Chlamydiatrachomatis -trachoma, sexually transmissible nongonococcal
urethritis or NGU.
Chlamydiapsittaci- ornithosis (parrot fever) (a respiratory disease)
II. MYCOPLASMAS (eubacteria) -Section10 - All lack a rigid cell wall. To maintain turgor
pressure: 1.) their cellmembrane contain sterols to add strength (sterols are also found in eukaryotic cell
membranes), and 2.) they maintain their cytoplasm at the same pressure as their external environment by
actively pumping sodium ion out of the cell. All are parasites of humans, animals, or plants. Almost all are
obligate fermenters (they ferment even in the presence of oxygen). Their colonies have a distinctive fried
egg appearance. They have various shapes, but when growth conditions are suboptimal, they become
distorted, forming long strands that resemble fungi (thus accounting for the name myco , whichmeans
"fungus"). Their wall-less structure allows them to squeeze through even the tiny pores in filters used to
sterilize liquids. Mycoplasmapneumoniae -commoncold& primary atypical pneumonia (walking
pneumonia)
III. GRAM-POSITIVEBACTERIA (eubacteria) - lackan outer membrane & a periplasmic space; have a thick
peptidoglycan cell wall.
A. Section12 - Cocci - large group. Some examples:
Micrococcus spp. - normal inhabitant of human skin; often contaminants on
agar plates.
Staphylococcus spp. - normal inhabitant of human skin; many species produce
carotenoid pigments, giving colonies characteristic yellow & orange colors
Staphylococcusaureus - major human pathogen; can infect almost any tissue
in the body;causes impetigo, pneumonia, food poisoning; causes many nosocomial
(hospital-acquired) infections.
Streptococcus - S. pyogenes causes strep throat, scarlet fever, rheumatic
fever,endocarditis; S. pneumoniae causes life-threatening pneumococcalpneumonia &
meningitis; S. mutans causes dental plaque.
B. Section13 - Endospore-FormingRods&Cocci -These bacteria are the most heat-resistant living
things; they are used as an index of sterilization; locationof endospore can be used to distinguish
species. Some examples:
Clostridium spp. - all strict anaerobes, inhabiting soil & mud; C. tetani causes
tetanus (fatal rigid paralysis); C. perfringens causes gas gangrene & foodpoisoning, C.
difficile causes iatrogenic(medically induced) diarrhea when antibiotics upset the normal
balance of intestinal microbes; C. botulinum causes botulism (foodpoisoning); some species
are harmless.
Bacillus spp. - aerobes, some facultativeanaerobes; B.anthracis - causes
anthrax; B. cereus causes foodpoisoning.
C. Section14 - NonsporingRods -Listeriamonocytogenes – foodpoisoning (listeriosis); in young, old, &
immunocompromised patients it can cause a formof meningitis.
D. Section15 - IrregularNonsporingRods -Members have irregular shapes (branched, club-shaped,
etc.);shapes can change with growth phase of culture.
Propionibacteriumacnes -causes acne
Corynebacteriumdiptheriae -causes diphtheria.
IV. MYCOBACTERIUM(Section16) -have a waxy outer layer composed of polysaccharides & mycolic acids;
protects against hostile environments & affectsstaining; identified by the acid-faststain procedure;
Examples: Mycobacteriumtuberculosis -causes tuberculosis; Mycobacteriumleprae -causes leprosy
V. OTHERSECTIONS
A. Section27 - ActinomyceteswithMultiocularSporangia -Bacteriain this group grow as mycelia,
masses of branching filamentous cells that resemble a mycelialfungus. They form spores within
a multiocular sporangium, a many-chambered swelling at the end of a filament. Dermatophilus spp.
infects animals & sometimes human skin.
B. Section29 - Streptomyces & RelatedGenera- These bacteria are also actinomycetes. Abundant in
most soils (important in breakdown of organic matter). Odor of freshly turned soil comes fromvolatile
compounds produced by these bacteria. Colonies have pastel colors,soil-like odor, & are hard & stick
into agar. Members of this genus produce most of antibiotics in current use.