I. Domain: Bacteria

A. Taxonomic Classification 1. Bacteria are classified according to rRNA similarities morphological similarities biochemical similarities DNA similarities II. Phylum: Proteobacteria -largest taxonomic group -all are gram negative bacteria -divided into five classes

Bacteria and Archaea of Interest

A. Class: Alpha Proteobacteria

1. Rickettsia a. non-motile obligate intracellular parasite b. can be cocci ,bacilli or threadlike- highly pleiomorphic c. many members belong to the spotted fever group of diseases d. damage the permeability of capillaries e. pathogens are transmitted by arthropod vectors g. R. typhi- causes typhus and is transmitted by the rat flea vector h. R. rickettsii- causes Rocky Mountain spotted fever, is the most dangerous Rickettsia pathogen and transmitted by the ticks, Dermacentor variabilis and Dermacentor andersoni i. R. prowazekii- causes epidemic typhus is transmitted by the lice vector, and is the closest known relative to mitochondria through genome sequencing

Tick vectors for Rocky Mountain spotted fever- Dermacentor variabilis and Dermacentor andersoni

American dog tick Rocky Mountain wood tick

Mitochondrion Rickettsia

Genetic analysis indicates that the mitochondrial genome is most closely related to Rickettsia

Rickettsias are small encapsulated bacteria that are intracellular obligateparasites

Damage to the permeability of capillaries is demonstrated with Rocky Mountain spotted fever

Dr. Howard Taylor Ricketts -when researching the characteristics of Rickettsias, Ricketts

injected himself with R. rickettsii in order to measure its effects -later when studying the disease typhus, he ultimately died from

this disease

Dr. Stanislaus von Prowazek -von Prowazek’s study of typhus led to his dead also -R. prowazekii was named in his honor

2. Agrobacterium tumefaciens a. plant pathogen that causes crown gall disease (plant cancer) b. bacteria contains the Ti plasmid c. Ti plasmid has a T (tumor) gene for inducing crown gall in plants d. makes a protein called opines

Crown gall in tomato plant stems

Crown gall in the roots of a plant

A. tumefaciens invading plant cells

Ti plasmid with the T-DNA gene - tumors are inserted by the conjugative transfer of a DNA segment (T-DNA)

3. Azospirillum

a. grow in soil, using nutrients excreted by plants b. fix nitrogen for green plants

4. Rhizobium a. fix nitrogen and form nodules in the

roots of plants

Rhizobium forming root nodules

4. Rhodopseudomonas palustris a. purple non sulfur bacteria b. can grow with or without oxygen; it can use light, inorganic c. compounds, or organic compounds for energy; it can acquire carbon from either carbon dioxide fixation or green plant-derived compounds; and it also fixes nitrogen

B. Class: Beta Proteobacteria

1. Neisseria N. meningitidis causes a. meningococcal meningitis, is an inflammation of the meninges b. approximately 2500 to 3500 cases of meningitis infection occur annually in the United States c. lipopolysaccharide (LPS) of the cell wall acts as a powerful endotoxin

N. gonorrhoeae

a. sexually transmitted disease that causes gonorrhoea b. transmitted via sexual contact c. sometimes called "the clap"

N. gonorrhoeae attacking human tissue

C. Class: Gamma Proteobacteria -largest subgroup of Proteobacteria -includes the bacteria (enterics) that inhabit the intestine

1. Psuedomonas aeruginosa a. opportunistic microbe responsible for many nosocomial infections b. causes septicemia, meningitis, infections of urinary system, burn infections, and wound infections c. genome contains many novel genes not found in other bacteria d. produce enzymes digest pesticides, oil, soap residues, antiseptics e. can reside in soap residues, cap liner adhesive and some antiseptics f. show a great deal of resistance to antibiotics g. secretes a blue water soluble pigment h. spoils refrigerated foods

Psuedomonas aeruginosa and the characteristic blue, water soluble pigment it producers

P. aeruginosa is an opportunistic pathogen

2. Moraxella a. Moraxella lacunata can cause conjunctivitis or pink eye

b. Moraxella catarrhalis fastidious, nonmotile, diplococcus that can cause infections of the respiratory system, middle ear, eye, central nervous system, and joints

3. Legionella pneumophili a. sometimes called Legion Fever b. the disease caused by Legionella is called legionellosis, a

pneumonia-like condition c. first identified during a flu-like outbreak at a convention attended by the Legionaires (USA war veterans) in Philadelphia on July 1977 d. 221 Legionaires were hospitalized and 34 died e. finally isolated with buffered charcoal-yeast extract agar f. colonizes cooling towers of conditioning systems and hot air lines in buildings

Legionella pneumophili

4. Vibrio a. V. cholerae causes cholera b. transmission occurs primarily by drinking water or eating food that has

been contaminated by the feces of an infected person c. the severity of the diarrhea and vomiting can lead to rapid

dehydration and electrolyte imbalance, and death in some cases

Individual suffering with V. cholerae

5. Yersinia pestis a. discovered in 1894 by Alexandre Yersin b. infection takes three main forms: pneumonic, septicemic and bubonic plague c. high-mortality rates from all three forms- 30% to 60% lethality rate d. without treatment, the bubonic plague kills about two thirds of infected humans within 4 days. e. bubonic plague is responsible for the death of 1/3 of the population of Europe between 1347 and 1353 and is spread between rodents and fleas

Oriental rat flea, Xenopsylla cheopsis, the vector for bubonic plague

Yersinia pestis

Medieval scene of the bubonic plague

Enterobacteriales somewhere between 300 and 1000 different species of bacteria live in the gut 99% of the bacteria come from about 30 or 40 species facultative anaerobe inhabit intestine permanently by mutualism,

commensalism, or as pathogens all have fimbriae that helps them adhere to cell surface produce bacteriocins that cause the lysis of other bacteria coliforms are enterics that metabolize lactose, E. coli is a coliform bacteria coliforms are commonly used bacterial indicators of sanitary quality of foods and water coliforms are abundant in the feces of warm-blooded animals, but can also be found in the aquatic environment, in soil and on vegetation they are easy to culture and their presence is used to indicate that

pathogenic organisms of fecal origin may be present

7. Escherichia coli a. one of the most common human intestinal symbiotic bacteria and the most studied bacteria b. its presence in food and water is an indicator of fecal contamination c. not usually pathogenic but can cause urinary infections d. O157:H7 strain is a source of dangerous food poisoning

8. Salmonella

a. Daniel Salmon first to identify salmonella b. all considered pathogenic c. inhabits intestinal tract of poultry, cattle, and humans d. all Salmonella species are classified as S. enterica e. S. enterica is divided into 2400 serovars f. S. typhi causes typhoid fever g. S. typhimurium used by researchers in the Ames assay

Common foods harboring Salmoella

Mary Mallon- Carried the distinction of being the first “healthy carrier” of Typhoid Fever discovered in the US

9. Shigella

a. causes bacillary dysentery

10. Klebsiella a. K. pneumoniae capsulated bacteria that causes pneumonia

11. Serratia

-produces an orange-red pigment called prodigiosin -can cause urinary, respiratory, wound and eye infections

12. Proteus

-P. vulgaris are opportunistic microorganisms that can cause urinary and wound infections -peritrichous flagela make them highly motile bacteria

13. Enterobacter a. E. cloacae -sometimes associated with urinary tract and respiratory infections

14. Erwinia

D. Class: Delta Proteobacteria 1. Bdellovibrio a. lives in the periplasmic space of gram negative bacteria and causes lysis of host bacteria

E. Class: Epsilon Proteobacteria 1. Helicobacter pylori a. identified in 1982 by Barry Marshall and Robin Warren, who found that it was present in patients with chronic gastritis and gastric ulcers

b. H. pylori weakens the protective mucous coating of the stomach and duodenum, which allows acid to get through to the sensitive lining beneath c. both the acid and bacteria irritate the lining and cause a sore, or ulcer d. H. pylori is able to survive in stomach acid because it secretes enzymes that neutralize the acid allowing it to make its way to the protective mucous linings

Helicobacter pylori

III. Nonproteobacteria 1. Cyanobacteria (blue-green algae) -photosynthetic oxygenic bacteria a. Anabaena -filamentous cyanobacteria b. Gleocapsa -colonial cyanobacteria

Oscillatoria and a cyanobacteria “mat”

Rise in oxygen amounts in the ocean over time

IV. Chlamydiae

1. Chlamydia a. C.trachomatis b. C. pneumoniae

V. Spirochaetes -move by axial filaments

1. Borrelia burgdorferi causes Lyme disease a. predominant in North America, but also exists in Europe, and is the agent of Lyme disease b. it is a vector borne disease transmitted by the deer tick

Familiar “bulls eye” characteristic of Lyme disease and the deer tick vector

2. Treponema pallidum a. is a motile spirochete that causes syphilis b. it is generally acquired by close sexual contact

Primary syphilis Secondary syphilis

VI. Phylum: Firmicutes -low guanine-cytosine ratio -gram-positive

1. Clostridium -Clostridia are anaerobic, spore-forming rods

-produce powerful exotoxins

a. C. tetani -usually enters a host through a wound to the skin -produces the exotoxin, tetanospasmin -the genes that produce the toxins are encoded on a plasmid

-tetanospasmin is a neurotoxin that causes the clinical manifestations of tetanus

b. C. botulinum -tolerate very small traces of oxygen due to the enzyme superoxide dimutase (SOD) which is an important antioxidant defense when exposed to oxygen -C. botulinum is normally harmless to humans, but it can become infected by a virus and become dangerous -the virus DNA gets integrated into the bacterial genome, causing C. botulinum to produce the neurotoxin, botulinum, the most toxic exotoxin known

Botox is produced from botulism

c. C. perfringens -can cause food poisoning -is the most common bacterial agent for gas gangrene -gas gangrene is necrosis and putrefaction of tissues -the toxin involved in gas gangrene is known as alpha toxin which inserts into

the plasma membrane of cells, producing gaps in the membrane that

disrupt normal cellular function -gas production forms bubbles of gas in muscle (crepitus) -after rapid and destructive local spread (which can take hours), systemic spread of bacteria and bacterial toxins may result in death

Gas gangrene

d. C. difficile (C. diff) -causes the most severe diarrhea when gut flora have been wiped out by

antibiotics (broad spectrum) -can lead to pseudomembranous colitis, a severe inflammation of the colon -relapses of C. difficile in up to 20% of cases -transmitted from person to person by the fecal-oral -once spores are ingested by a patient, they pass through the stomach and germinate into vegetative cells in the colon upon exposure to bile acids, and multiply

C. difficile Pseudomembranous colitis

2. Mycoplasma

-Mycoplasma pneumoniae -extremely small, pleimorphic bacteria -atypical pneumonia -0.1 – 0.24 um

3. Staphylococcus

-S. aureus -can live at 60 degrees Celsius for one hour -lives 10 to 46 degrees Celsius -live in extreme pH environments -facultative halophile -very resistant to antibiotics -31 species -80,000 deaths per year in the US -produce many enterotoxins -produce biofilms -can cause food poisoning -commonly lives on the skin and mucous membrane

Methicillin Resistant Staphylococcus aureus (MRSA)

In simple terms it is a staph infection that has morphed over time making it resistant to the most used antibiotics.

Most people who contract MRSA do so in the hospital. This is because people in the hospital have weak immune systems from being sick and or they have open wounds which allow the bacteria to get in their body. It is also a problem in other confined setting such as prisons, daycare centers, nurseries and also in athletes who share locker rooms and gyms.

MRSA is highly contagious and can cause severe health problems and even death if not treated in time.

MRSA is a type of bacteria that causes a variety of infections that belong to the Staphylococcus family.

Although the bacteria are resistant to most antibiotics it does respond to vancomycin and some other antibiotics.

MRSA Infection

Osteomyelitis

Infective endocarditis inflammation of the innermost surface of the heart

Toxic shock syndrome (TSS) -is a very rare but potentially fatal illness caused by a bacterial toxin -different toxins may cause toxic shock syndrome -it is generally caused by Staphylococcus aureus bacteria and has been associated with the use of tampons which has since been taken off the market -Streptococcus pyogenes can also cause this illness

Carbuncles and Furuncles

-carbuncles are large, contagious -furuncles are boils on the skin that are abscesses with one or more smaller openings draining pus

4. Streptococcus

-Rebecca Lancefield identified 17

different types of streptococci (ABC….) -S. pyogenes is a very dangerous member of this group

Classification of Streptococcus by Rebecca Lancefield

Group A - Streptococcus pyogenes Group B - Streptococcus agalactiae Group C - Streptococcus equisimilis, Streptococcus equi, Streptococcus

zooepidemicus, Streptococcus dysgalactiae Group D – Enterococci, Streptococcus bovis Group E - Streptococcus milleri and mutans Group F - Streptococcus anginosus Group G - Streptococcus canis and Streptococcus dysgalactiae Group H - Streptococcus sanguis Group L - Streptococcus dysgalactiae Group N - Lactococcus lactis Group R&S - Streptococcus suis other Streptococcus species are classified as non-Lancefield Streptococci

Streptococcus pyogenes and advanced flesh-eating disease

Impetigo

Strep throat

Scarlet fever

5. Bacillus endospore producers endospores in particular are highly resilient, surviving extremes of temperature, low-nutrient environments, and harsh chemical treatment over decades or centuries.

a. B. anthracis capsulated causes anthrax

B. subtilis

B. cereus

B. polymyxa

B. megaterium

6. Listeria monocytogenes

-commonly found in soil, streams, sewage, plants, and food -listeriosis is a lethal food-borne infection (25% fatal) -vegetables can become contaminated from the soil, and animals can also be carriers. Listeria has been found in uncooked meats, uncooked vegetables, unpasteurized milk, foods made from unpasteurized milk, and processed foods -Listeria induces macrophage phagocytic uptake but escapes the destruction by lysing the vacuole

VII. Phylum: Actinobacteria -high guanine-cytosine ratio, gram positive

1. Gardnerella vaginalis -pleomorphic -cause vaginitis

2. Mycobacterium -M. tuberculosis -acid fast bacteria that causes tuberculosis

-M. leprae

causes leprosy

M. leprae and leprosy

VIII. Microbial Diversity A. Thiomargarita namibiensis - the largest bacteria (750 um)

B. Nanobes (nanobacteria)

-tiny filamentus structures first found in some rocks and sediments -smallest form of life, 1/10th the size of the smallest known bacteria -no conclusive evidence exists for whether these structures are, or are

not, living organisms, and their classification is controversial -0.02 um in size

http://en.wikipedia.org/wiki/Image:ALH84001_structures.jpg

IX. Domain Archaea

A. Phylum: Crenarchaeota 1. Sulfolobolus -hyperthermophiles

B. Phylum: Euryarchaeota 1. Methanobacterium -methanogens - inhabit the gut of humans and aid in the digestion of food 2. Halobacterium -extreme halophiles

Methanogens