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
metabolically flexible and engages in horizontal gene transfer (can stay in host and environment)
nano cables
long appendages that are used to sense oxygen
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
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
(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
ex: S. epidermis on skin
mutualism
both organisms benefit
ex: E. coli bacteria in large intestine
parasitism
one organism benefits at the expense of the other
ex: influenza viruses on a host cell
neutralism
if neither of the symbiotic organisms is affected in any way
ex: Bacillus anthracis → produce endospores
amensalism
a type of symbiosis in which one population harms another but remains unaffected itself
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
bacterium provides luminescence to avoid predators, squid provides nutrients
Vibrio vulnificus
bacteria that causes cellulitis and involved in blood-borne infections
taxonomic hierarchy
domain → kingdom → phyla → class → order → family → genera → species
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
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
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
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
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
live in soil, water, digestive tract of mites
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)
evolved first before the syphilis subspecies
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
phototrophs that fix CO2
chlamydiae
obligate intracellular pathogens that grow as inclusion bodies within host cells
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
low guanine and cytosine content
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
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
peptidoglycan with an additional thick waxy coat (mycolic acid), most stain with acid-fast stain
high G+C content
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
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
resist drying, freezing and chemical disinfectants
Clostridium
endospore forming firmicutes, most species are obligate anaerobes
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
decrease pH
Listeria spp.
facultative anaerobic rods, found in soft cheeses and luncheon meats
intracellular pathogens that cause diseases affecting the GI tract and nervous system
ex: listeria monocytogenes
cell to cell projection
when a bacterium escapes phagocytosis in a cell, it can start to replicate
following replication = formation of long actin tails by using host machinery → move to another cell
ex: done by Shigella
G+ cocci (firmicutes)
enterococcus, streptococcus, staphylococcus
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
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
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
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
grow within tissue of host
M. tuberculosis
facultative intracellular pathogen that only infects humans and causes tuberculosis
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?
porins in envelope that enable nutrients to enter but slowly
bacterium grows slowly in a place with no competitor
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)
all share a common form of cell envelope
enterobacteriaceae
(under proteobacteria) family of enteric G- bacilli, facultative anaerobes that are motile
exists in commensals and pathogens (ex: E. coli)
Proteus mirabilis
enterobacteriaceae that causes serious bladder/kidney infection
heavily flagellated
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
aids in digestion
Salmonella typhi
(proteobacteria, enterobactericeae) causative agent of typhoid fever
Y. pseudotuberculosis
member of enterobacteriaceae
causes enteritis, a gastrointestinal disease that can mimic appendicitis
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
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
some use alternative electron acceptors like nitrate
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
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
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
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
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
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
Bdellovibrio finds host by chemotaxis
binds to host receptors on envelope
invades periplasm
DNA replication and spiral chain grows
chain fragments into flagellated cells
host lysis releases Bdellovibrio cells
bacteroidetes
phylum of obligate anaerobes, ferment indigestible sugar derivatives and break down toxins
produce polysaccharide A and other communication molecules to communicate with and direct the immune system
cyanobacteria
oxygenic photoautotrophs
photosynthesis that fixes most of the carbon dioxide in ecosystems, particularly marine ecosystems
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
can multiply rapidly and produce neurotoxins, resulting in blooms that are harmful to fish and other aquatic animals