ch 4 (prokaryotes)

anaerobe jar

(for plates) where O2 is removed and CO2 is generated

anaerobic chamber

has glove ports that remove the atmosphere via vacuum and replace it with a precise mixture of N2 and CO2 gases

prokaryotes

ubiquitous organisms that are extremely resilient and adaptable

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metabolically flexible and engages in horizontal gene transfer (can stay in host and environment)

nano cables

long appendages that are used to sense oxygen

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ex: seen in Shewanella bacteria (lives in deep sea where there's little oxygen diffused in the water)

microbiome

all prokaryotic and eukaryotic microorganisms and their genetic material that are associated with a certain organism or environment

human microbiome

consists of both resident microbiota and transient microbiota

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hygiene and diet can alter both

resident microbiota

the organisms that constantly live in or on our bodies

transient microbiota

the organisms that are only temporarily found in the human body

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(can differ during pregnancy, during a course of antibiotics, etc.)

Staphylococcus

example of bacteria found in the skin microbiota and urinary/reproductive systems

Staphylococcus aureus

example of bacteria found on eye microbiota, nose and throat microbiota

Streptococcus

example of bacteria found in mouth microbiota

Escherichia coli

example of bacteria found in large intestine microbiota

commensalism

one organism benefits and the other is unaffected

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ex: S. epidermis on skin

mutualism

both organisms benefit

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ex: E. coli bacteria in large intestine

parasitism

one organism benefits at the expense of the other

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ex: influenza viruses on a host cell

neutralism

if neither of the symbiotic organisms is affected in any way

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ex: Bacillus anthracis → produce endospores

amensalism

a type of symbiosis in which one population harms another but remains unaffected itself

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ex: Lactobacillus makes lactic acid and lowers pH = inhibit growth of other bacteria

Aliivibrio fischeri

bioluminescent bacterium that lives in a mutualistic relationship with Hawaiian bobtail squid

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bacterium provides luminescence to avoid predators, squid provides nutrients

Vibrio vulnificus

bacteria that causes cellulitis and involved in blood-borne infections

taxonomic hierarchy

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domain → kingdom → phyla → class → order → family → genera → species

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classification based on similarities in rRNA nucleotide sequences

Bacteria, Archaea

prokaryotes are divided into two domains: _____ and _____

Bergey's Manual

provides a reference for identifying bacteria in the laboratory as well as a classification scheme for bacteria

eukarya

closer evolutionary relationship between archaea and \_______ than archaea and bacteria

atypical bacteria

bacteria that cannot be stained by the standard Gram stain procedure

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ex: Mycoplasma, Chlamydia

Rickettsia

also considered atypical bacteria because they are too small to be evaluated by the Gram stain

further classification

scientists have begun to further classify G- and G+ bacteria

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added a special group of deeply branching bacteria based on a combination of physiological, biochemical and genetic features

bacteria phyla

there are 30 from which species can be cultured in lab but more likely 1000+ we have yet to see

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seven major ones are known to impact human health and the ecosystem

G+ firmicutes and actinobacteria

thick cells that resist drying

includes:
- firmicutes → produce endospores
- actinobacteria → produce antibiotics

G- proteobacteria and bacteroidetes

proteobacteria → diverse phylum that includes species capable of a wide range of metabolism

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bacteroidetes → all G- negative rods, most are obligate anaerobes

spirochetes

tightly coiled cells enclosed by a sheath with periplasmic flagella that run underneath the sheath along the cell body

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live in soil, water, digestive tract of mites

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ex: Borrelia burgdorferi → causes Lyme disease

observation of spirochetes

usually observed using darkfield microscopy but electron microscopy provides a more detailed view of cellular morphology

Treponema pallidum pertenue

spirochete subspecies closely related to the strain that causes syphilis (the two can't be distinguished by morphology/physiology → differ in 0.4% of genome)

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evolved first before the syphilis subspecies

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transmitted by direct contact with a cut or a wound

cyanobacteria

include tiny marine bacteria, as well as massive filamentous species; only bacteria to produce oxygen

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phototrophs that fix CO2

chlamydiae

obligate intracellular pathogens that grow as inclusion bodies within host cells

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sexually transmitted diseases, eye diseases, etc.

incubators of pathogen evolution

pathogens today continue to evolve and occasionally a new version emerges that causes human or animal disease

- environment (soil)
- shelter species (worms, insects)
- zoonoses
- horizontal gene transfer

firmicutes

"tough skin" = several layers of peptidoglycan supported with teichoic acids

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low guanine and cytosine content

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endospore formers, non-spore formers or mollicutes (lack cell wall)

Clostridium difficile

(firmicutes) rod with bulging spots; causes intestinal disease (colitis, diarrhea) in patients whose normal biota are diminished by antibiotics

Clostridium botulinum

(firmicutes) rod with bulging spores, causes botulism

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produces Botox at a low dosage by relaxing muscle spasms and smoothening wrinkles

Clostridium acetobutylicum

(firmicute) rod, used industrially to produce butanol

actinobacteria

broad group that includes antibiotic producers, decomposes in natural environments and also pathogens

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peptidoglycan with an additional thick waxy coat (mycolic acid), most stain with acid-fast stain

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high G+C content

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actinomycetes or other bacteria

actinomycetes

form mycelia with branching filaments → arthospores that grow at tips of mycelia → released/dispersed into air to grow new colonies

Nocardia

actinomycetes known to cause pneumonia in patients

other actinobacteria

cell walls contain mycolic acid and cells stain acid-fast, don't form mycelia

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Gardnerella vaginalis, Corynebacterium diphtheria, Proprionibacterium, Cutibacterium acnes

Gardnerella vaginalis

actinobacteria that causes bacteria vaginosis

Proprionibacterium

actinobacteria that's responsible for Swiss Cheese flavor

Cutibacterium acnes

actinobacteria that causes skin infection/acne

arabinogalactan

a polymer of galactose and arabinose; an important structural component of the mycobacterial cell wall (builds on peptidoglycan to enhance waxiness)

Actinomycete israelli

(actinobacteria) forms branched mycelial filaments, causes actinomycosis

Corynebacterium diphtheria

(actinobacteria) irregular rod, causes diphtheria and has distinctive palisades

Löwenstein-Jensen agar

culture media that grows M. tuberculosis in distinctive colonies

endospores

inert heat-resistant spores that can remain viable for thousands of years → germinate when conditions become favorable again

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resist drying, freezing and chemical disinfectants

Clostridium

endospore forming firmicutes, most species are obligate anaerobes

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growing endospore swells at end of the cell, giving the cell a club shape

Clostridium tetani

causes tetanus

non-endospore forming firmicutes

include lactic acid bacteria and Listeria spp.

lactic acid bacteria

Lactococcus and Lactobacillus ferment milk to make yogurt and cheese

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decrease pH

Listeria spp.

facultative anaerobic rods, found in soft cheeses and luncheon meats

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intracellular pathogens that cause diseases affecting the GI tract and nervous system

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ex: listeria monocytogenes

cell to cell projection

when a bacterium escapes phagocytosis in a cell, it can start to replicate

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following replication = formation of long actin tails by using host machinery → move to another cell

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ex: done by Shigella

G+ cocci (firmicutes)

enterococcus, streptococcus, staphylococcus

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species can be distinguished by patterns of hemolysis on blood agar plates

alpha hemolysis

partial/incomplete lysis of RBCs \= green halo

beta hemolysis

complete lysis of RBCs = clear zone/halo

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ex: S. pyogenes

enterococcus

normally found in intestinal tract; poses a problem for immunocompromised patients and VRE is also problematic

VRE

vancomycin resistant enterococcus

staphylococcus

(grape clusters) facultative anaerobic cocci, grow in clusters

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ex: Staphylococcus epidermis

Staphylococcus epidermis

commonly found on skin, tolerant to salt and form small fatty acids to eliminate other microbes

streptococcus

chains, aerotolerant and metabolize by fermentation

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cause of strep throat, Scarlet fever

lancefield grouping

a method of grouping different species of streptococcus by the bacterial antigens found on their cell walls and cell surface glycoproteins

mycoplasma

bacteria that lack a cell wall (won't show up in a gram stain), fried egg shape, fall under class of Mollicutes

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grow within tissue of host

M. tuberculosis

facultative intracellular pathogen that only infects humans and causes tuberculosis

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became more and more resistant due to horizontal gene transfer from other mycobacteria

M. bovis

causes tuberculosis in cattle, used in the BCG vaccine (not in the US) and stimulates antibody production but interferes with tuberculosis testing

granulomas

nodules of inflammation

how does M. tuberculosis grow even though its thick envelope screens out most nutrients?

1. porins in envelope that enable nutrients to enter but slowly
2. bacterium grows slowly in a place with no competitor
3. intracellular within the macrophages

proteobacteria

show an amazing diversity of form and metabolism — as varied as cocci and spiral cells (includes heterotrophs, lithotrophs and photosynthesizers)

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all share a common form of cell envelope

enterobacteriaceae

(under proteobacteria) family of enteric G- bacilli, facultative anaerobes that are motile

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exists in commensals and pathogens (ex: E. coli)

Proteus mirabilis

enterobacteriaceae that causes serious bladder/kidney infection

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heavily flagellated

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when inoculated at center of blood agar plate, migrates out in rings (in host, can migrate along catheter and form biofilm with antibiotic resistance)

30%

bacteroides comprise up to ____ of the normal microbiota in the gut

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aids in digestion

Salmonella typhi

(proteobacteria, enterobactericeae) causative agent of typhoid fever

Y. pseudotuberculosis

member of enterobacteriaceae

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causes **enteritis**, a gastrointestinal disease that can mimic appendicitis

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transmitted from animals to humans by contaminated food or water

Y. pestis

member of enterobacteriaceae, cause plague that can be transmitted from animals to humans by an infected flea

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diverged from Y. pseudotuberculosis and became more virulent due to horizontal gene transfer

bacterial protease

activates host plasmin, dissolves clot → gets into bloodstream

peptide capsule

provides protection

pseudomonaceae

obligate aerobic bacilli related to enterobacteriaceae

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some use alternative electron acceptors like nitrate

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widespread in soil as decomposed, important in natural recycling and soil turnover

P. aeruginosa

(proteobacteria) commonly grows in soil as decomposed but in humans, it can infect surgical wounds or form biofilms in the lungs of cystic fibrosis patients

Legionella pneumophila

(proteobacteria) intracellular pathogen related to the pseudomonads, causes Legionnaires disease and thrives in warm water

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grows inside amoeba and human macrophages (dual lifestyle)

Legionella transmission

occurs through inhalation of aerosolized amoeba with Legionella inside → outbreaks often originate in air conditioning units

lithotrophy

mineral oxidation for energy

Vibrio cholerae

(proteobacteria) single flagellum, comma shaped

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cause diarrhea, attaches to villi in intestine → problematic in areas with poor sanitation

Neisseria gonorrhoeae

(proteobacteria) sexually transmitted, pair of cocci

Heliobacter pylori

(proteobacteria) corkscrew shape, thrives in low pH GI tract

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causes gastritis and stomach acid → can lead to ulcers and stomach cancer

Neisseria meningitidis

(proteobacteria) infection of the brain and spinal cord

Rickettsia

(proteobacteria) a small bacterium that lives in lice, fleas, ticks, and mites

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causes Rocky Mountain spotted fever

Ehrlichia

(proteobacteria) transmitted by ticks and causes Ehrlichiosis

Coxiella

(proteobacteria) causes Q fever, transmitted by inhalation of dust (animal feces and urine)

Brucella

(proteobacteria) in livestock, causes Brucellosis

Rhizobium, Bradyrhizobium and Sinorhizobium

(proteobacteria) endosymbiosis of plants that perform nitrogen fixation, forms distinct nodules on plant

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has leghaemoglobin that provides anaerobic conditions for carbon fixation

Bdellovibrio

(proteobacteria) comma shaped, single flagellum; predatory, attack other bacterial host cells such as E. coli

life cycle of Bdellovibrio

1. Bdellovibrio finds host by chemotaxis
2. binds to host receptors on envelope
3. invades periplasm
4. DNA replication and spiral chain grows
5. chain fragments into flagellated cells
6. host lysis releases Bdellovibrio cells

bacteroidetes

phylum of obligate anaerobes, ferment indigestible sugar derivatives and break down toxins

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produce polysaccharide A and other communication molecules to communicate with and direct the immune system

cyanobacteria

oxygenic photoautotrophs

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photosynthesis that fixes most of the carbon dioxide in ecosystems, particularly marine ecosystems

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also fixes much of the biosphere's nitrogen

bacteriochlorophylls

used by purple and green sulfur bacteria to perform photosynthesis

Microcystis aeruginosa

a type of cyanobacteria commonly found in freshwater environments

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can multiply rapidly and produce neurotoxins, resulting in blooms that are harmful to fish and other aquatic animals