L3, L5, L7- Microbiome and Biology of Gram +/- Bacteria Flashcards
___________ bacteria are commonly ubiquitous on the skin
Staphylococcus
microbiota are also known as….
commensal flora
very high numbers of bacteria are found in the mouth and large intestine, especially…
Escherichia coli
microbiota are importantly absent in (1) or (2) locations (include examples)
1- non-epithelial
2- mucosal
ex. blood, CSF
_______ is a common opportunistic gut infection that follows from the death of numerous gut flora due to antibiotic use
C. diff (clostridium difficile)
list 4 general characteristics of microbiome
- protection against disease
- important for barrier and immune modulation
- influences host metabolism and drug interaction
- possible source of infection (endogenous E.coli in Colon)
define dysbiosis and its effects
this is usually a transient effect resulting from long-term or repeated antibiotic use leading to the loss of beneficial species, altering microbiota
associated with chronic diseases like Crohn’s or IBS
describe prokaryotic DNA
circular, ~1 mil. BPs + many Plasmids with ~50k BPs
breakdown prokaryotic vs eukaryotic ribosomes
Pro: 30S + 50S = 70S
Euk: 40S + 60S = 80S
plasmids in bacteria contain DNA coding for….
- antibiotic resistance
- toxins
- mobile gene transfer
list in order the stages of bacterial growth
1) lag phase
2) log / exponential phase
3) stationary phase
4) death phase
describe the features of Lag phase
- newly inoculated cells, adjust to environment (is there food, space, etc)
- cells not multiplying at maximum rate
- population is sparse or dilute
describe the features of Log or exponential phase
- growth occurs at exponential rate and cells are at maximal rate of cell division
- continues as long as environment is favorable (nutrients present, etc)
describe features of stationary phase
- population at maximum number
- rate of cell inhibition/death = rate of cell multiplication
- accumulation of toxic waste products
describe features of death phase
- decline in growth rate
- caused by depletion in nutrients, O2
- excretion of toxic waste products
- increased density of cells (limited space)
describe how and why bacteria obtain Fe
- Fe is required for cytochromes
- most Fe is sequestered in Hb, therefore bacteria must have mechanisms to extract Fe from Hb
list the three ways bacteria generate ATP
- aerobic respiration
- anaerobic respiration
- fermentation
_______ levels are usually measured in urine samples to serve as an indicator of infection since the humans cannot break it down
nitrates (E.coli can convert it to nitrites)
if bacteria deplete enough O2 during an infection, the anoxic conditions can lead to….
- host tissue damage
- immune cells work poorly
- antimicrobials are less effective
most pathogens have an optimal temperature of growth at (1) and are referred to as (2)
1- 37C
2- mesophiles
define obligate aerobe
O2 necessary, only aerobic respiration is used (die w/o O2)
define obligate anaerobe
can’t use O2 and die in its presence
define facultative anaerobe
uses both aerobic and anaerobic respiration, although thrive more in aerobic conditions
define microaerophiles
require lesser amounts of O2 (5-10%)
mycobacterium tuberculosis is considered a (obligate aerobe / obligate anaerobe / facultative anaerobe / microaerophile)
obligate aerobe
clostridium difficile and other clostridiums are considered a (obligate aerobe / obligate anaerobe / facultative anaerobe / microaerophile)
obligate anaerobes
E.coli is considered a (obligate aerobe / obligate anaerobe / facultative anaerobe / microaerophile)
facultative anaerobe
most human pathogens are considered a (obligate aerobe / obligate anaerobe / facultative anaerobe / microaerophile)
facultative anaerobe
Helicobacter pylori is considered a (obligate aerobe / obligate anaerobe / facultative anaerobe / microaerophile)
microaerophile
describe where obligate aerobes, obligate anaerobes, and facultative anaerobes are found in sample vials
- Ob. Aero.- at top near cap (O2 needed)
- Ob. Anaero.- at bottom, furthest from cap (no O2)
- Fac. Anaero- throughout vial, although most near cap
superoxide dismutase reaction
2O2- + 2H+ —> H2O2 + O2
catalase reaction
2H2O2 —> 2H2O + O2
aerobic bacteria must have one or both of these enzymes to survive the ROS produced from cellular respiration
- superoxide dismutase (O2 radicals)
- catalase (H2O2)
by adding (1) to clinical samples, catalase can serve as a basis for the classification of (2)
1- H2O2
2- Staphylococcus
(Cat +)
most human pathogen live at pH between 6-8 and are termed (1), otherwise they may be (2) or (3)
1- neutrophiles
2- acidophiles (obligate acidophiles)
3- alkalinophiles
two common acidophiles found in the body are….
1) Lactobacillus (GI infection, vaginal canal to maintain acidic environment)
2) H. Pylori (GI infection)
‘picky’ bacteria or ones that require a special, or (1), media are called (2)
1- defined media
2- fastidious
samples for cultures that are taken from easy to access areas in the body have (a lot/little/no) endogenous microbes and require a (2) media
1- a lot
2- selective media
samples for cultures that are taken from difficult to access areas in the body have (a lot/little/no) endogenous microbes and require a (2) media
1- little (lungs) to none (CSF)
2- rich media
describe MacConkey Agar
- selective and differential media for fecal samples
- allows for growth of E.coli and Salmonella
- lactose is present: E.Coli will react and turn it pink, Salmonella doesn’t react => no color change
describe Blood Agar
- selective, rich media (with 5% sheep’s blood)
- α, β, γ- hemollysis determined
describe α-hemolysis of Blood Agar
- lysis of RBCs, incomplete breakdown of Hb
- appears greenish/tan around the colony
describe β-hemolysis of Blood Agar
- complete lysis of RBCs and breakdown of Hb
- clear zone around each colony
- indicates Staph. aureus
describe γ-hemolysis of Blood Agar
no hemolysis, appears as faint clear area
describe Chocolate Agar
heated Blood Agar
describe Nutrient Agar
rich media for non-fastidious bacteria
describe the agar required for Mycobacterium Tuberculosis
Lowenstein-Jensen Agar- rich in lipids and O2
-takes weeks to grow in BSL-3
describe the agar required for Neisseria Gonorrhea
Thayer-Martin Agar: Chocolate Agar (heated Blood Agar) with antibiotic added (selective) to restrict growth of usual flora (cervical or urethral)
describe media needed for throat swabs and what is usually trying to be determined
- selective media due to presence of numerous endogenous microbes (commensal flora)
- usually to Dx Streptococcus infections
describe media needed for sputum samples (include best method for obtaining)
- rich media due to very few commensal flora (endogenous microbes)
- best obtained through bronchial/trans-tracheal aspiration rather than cough
define bacteremia
- presence of bacteria in blood (symptomatic or asymptomatic)
- may indicate deeper infection like meningitis
define septicemia
serious immunological hypersensitivity response to bacteria, viruses, or fungi
infection/inflammation of CNS membranes is termed (1), of the brain tissue is termed (2), and of both is termed (3)
1- meningitis
2- encephalitis
3- meningoencephalitis
MRSA = …
methicillin resistant Staphylococcus aureus
fecal specimens are usually put into _________ agar
MacConkey Agar- promotes E.Coli and Salmonella growth
list some of the possible states opportunistic bacteria take advantage of
- weakened immune system
- altered microbiota (GI, vaginal)
- breach of integumentary barrier
define virulence
pathogen’s ability to infect or damage host (what mechanism or tools does it have)
list the four outcomes of a microbial host interaction
- communalization
- colonization
- disease
- latency
list some host factors that influence the outcome of an infection
age, EtOH use, coexisting disease, portal of entry, preexisting trauma, gender, immune status, malnutrition
list some pathogenic factors that influence the outcome of an infection
- antibiotic resistance
- duration of exposure
- infection dose
- virulence factors
most infections have an acute infection followed by (1) or (2) [describe each]
1- persistent infection: slow, long-term growth of microbe
2- latent infection: repeated acute infections with dormant periods in between (i.e. HSV(
list some microbial factors that lead to clinical signs and symptoms observed in a patient
- ability to grow in numbers at specific location
- damaging products: enzymes, toxins, cellular components
- ability to sense/respond to host counter measures
list some host factors that lead to clinical signs and symptoms observed in a patient
cytokines, interleukins, respiratory bursts
describe the features of an exotoxin
- released by pathogen (works at distant sites)
- heat stable (usually)
- highly specific
- very toxic
describe the features of an endotoxin
- part of pathogen’s structure
- heat stable
- low specificity
- low toxicity
define the 3 classes of exotoxins/endotoxins
- Class I: binds to cell surface –> triggers intracellular response
- Class II: binds to cell membrane, causes membrane damage
- Class III: enters cell
list the bacterial enzymes that contribute to virulence
- catalase
- urease- breaksdown Urea
- IgA protease- breaksdown IgA
- Neuraminidase- cleaves neuraminidase
- Coagulase
describe function and effect of coagulase in a pathogen
convert fibrin to fibrinogen –> fibrinogen wraps around microbe for protection (from immune cells)
list the steps of an infectious disease process
1) exposure and entry
2) adhesion and colonization
3) invasion and multiplication
4) spread and dissemination
describe the two types of adhesion from bacteria
Nonspecific = reversible: hydrophobic interactions, electrostatic attraction, biofilm attachment
Specific = irreversible: specific bonds between pathogen and host cells
the availability of micro-/macro- nutrients for pathogens allows the following evasive enzymes to be produced for the invasion/multiplication and spread/dissemination in other parts of the body
- hyaluronidases
- proteinases
- nucleases
- lipases
Fe uptake into bacteria is completed via….
sidophores- cell membrane structures allowing for the binding and influx of Fe
list three methods pathogens use to evade host defenses
- capsules
- antigenic variance (changes rapidly)
- host mimicry (host like antigens)
some bacteria have enzymes that convert plasminogen to plasmin for….
breaking down blood clots –> spread and dissemination of bacterial infection
attachment of bacteria contributes to pathogenicity by….
preventing removal
these 4 factors help bacteria evade immune system and contributes to its pathogenicity
- secreted toxins
- antigenic variation
- biofilm formation
- exotoxins
urine specimens are added to agar plates via….
calibrated loop, transfers ~0.01-0.001 mL
estimating the number of viable bacteria present from a specimen on a plate is through….
(colony count) Colony Forming Units, ~1000 bacteria
describe the results of a urine culture and what it indicates (hint 4 results)
Negative: no growth after 16-24 hrs OR 2 or more types of urogenital flora isolated (<10000 CFU/mL)
Positive: >100000 CFU/mL isolated
Depends: single type of urogenital flora isolated (<10000 CFU/mL)
bacterial quantification can be determined through _______, which record optical density / absorbance
spectrophotometer
Note- inaccurate in lag and death phases for viable cells
describe the benefits of live count serial dilutions
- more accurate than loop calibrated loop at high and low concentrations
- important for testing growth rate curves
- good for testing if a drug is working or not (tests for quantity, not just for presence)
describe the process of live count serial dilutions
- created a series of diluted samples (in 1:9 ratios)
- spread or pour each onto growth media
- count the CFUs of the plate with 30-300 colonies
- determine [bacteria] in original sample via dilution calculation
Staphylococcus are Gram (+/-)
gram +
Escherichia Coli are Gram (+/-)
gram -
describe the process of a gram stain and the two possible results
1) heat fix bacteria onto glass slide
2) stain with Purple Crystal Violet
3) de-stain with alcohol
4) counter-stain with Pink Safranin
Purple = Gram + Pink = Gram -
the two predominate bacterial shapes are….
- Coccus sphere
- Bacillus rod
(then there is spirochete or atypical shaped)
cell wall of bacteria is made of….
peptidoglycan
list the optional features of bacterial cell structure that can enhance or determine its ability to cause disease
- Capsule
- Appendages: Flagella, Pili
list layers of Gram+ bacteria
- thick peptidoglycan layer
- plasma membrane
list layers of Gram- bacteria
- outer membrane
- thin peptidoglycan layer
- periplasmic space
- plasma membrane
Gram(+/-) are more resilient and can survive without moisture, therefore they can be found on (2). Gram(+/-) die quickly is dry areas and are mostly found in (4).
1- Gram+
2- skin
3- Gram-
4- GI tract, Urogenital tract
Peptidoglycan is made of repeating (1) and (2) units, cross-linked by (3) long AA bridge via (4) enzyme
1- NAG (N-acetyl glucosamine)
2- NAM (N-acetyl muramic acid)
3- tetrapeptide (cleaved from pentapeptide via (4))
4- transpeptidase or Penicillin Binding Proteins (PBPs)
in Gram+ bacteria, peptidoglycan layer is about (1) layers thick, and has (2) and (3) molecules serving as scaffold with (4) as the only difference
1- 4-10 layers
2- Teichoic acid
3- LipoTeichoic acid
4- Lipotechoic acid is connected to lipid on plasma membrane, techoic acid has no such connection
the outer membrane of Gram- bacteria is primarily made of (1) with the following three subunits: (2)
1- LPS (LipoPolySaccharide)
2- Lipid A, core polysaccaride, O antigen (variable unite)
_____ part of LPS in Gram- bacteria has a toxic effect and is recognized by immune cells
Lipid A
LPS also functions as an Endotoxin, causing….
inflammation –> sepsis
what happens in the periplasmic space in Gram- bacteria
respiration / fermentation
______ are trans-lipid and modulate cell transport, especially antimicrobials (out of cell)
Porins
a bacterial cell capsule is made of (1) and functions to (2); note if it is thin and not well organized it is termed (3)
1- glycocalyx (gelatinous sugar material)
2- help organism resist environmental and immunlogical conditions
3- Slime layer
encapsulated bacteria are termed (1) since they aren’t recognized by WBCs and are a major virulence factor for dissemination, particularly in (2) patients
1- anti-phagocytic (non-encapsulated are easily phagocytosed by macrophages / neutrophils)
2- asplenic
describe the two types (or 2.5 types) of adhesins found on bacteria
(function in attachment role)
- Fimbriae: numerous, short
- Pili: few, long, usually has specific host receptor
- Sex Pili are involved in gene transfer
describe the aspects / functions of flagella in bacteria
- based in cell wall –> extends extracellular (can be multiple, and on one or more sides)
- function is motility –> contributes to virulence (ex. penetrates mucus layer)
- recognized by innate immune system
- present in Salmonella, E.Coli; absent in Shigella
______ is found based in cell wall of Gram- bacteria and acts as needles to inject effector proteins into host cell (contributes to virulence –> alters host cell characteristics)
T3SS, type 3 secretion system
name two important Endospores
- Bacillus
- Clostridium
describe an endospore
- highly resistant form of bacteria due to a harsh environment
- usually/often found in soil
- germinates into vegetative bacteria once in suitable environment
- if spores gain access to inner tissues –> serious infections / disease
Staphylococcus aureus is a Gram (+/-) (cocci/bacillus)
Gram+ cocci
serial dilution calculation formula
number of CFUs (original sample) = CFUs measured / (mL * dilution)
-note keep everything in 10^ form
what is a key function of lack of cell wall feature for Mycoplasmas
allows it to withstand osmotic pressure (thick cervicitis)
lactobacillus is a (large/small) Gram (+/-) (cocci/bacillus)
large Gram+ bacillus (rod)
Mycobacterium species are recognized through…..
- neither Gram +/- stain
- positive Acid-Fast stain
Mycoplasma are recognized through…..
- neither Gram +/- stain
- no cell wall
Chlamydia species are recognized through…..
- neither Gram +/- stain
- positive Giemsa stain
