IUPUI K356 Exam 4 Final Test 2024\2025.
Niche
Habitat that an organism lives in. Includes location, available nutrients and what it interacts with.
Biogeochemical Cycling
The cycling of nutrients in the environment
Carbon Cycle
Organics <-> CO2 <-> CH4
Microbial Mat
Layers of microbes
Environmental Genomics
Only 1% of microbes can be cultivated in the lab, so we take a "census" of genes that are in the
environment. Marine microbiology has benefitted from this by discovering novel genes.
Mutualism
Two organisms that are dependent on each other. They would die without each other.
Cooperation
Two organisms that benefit from each other, but they could survive without each other.
Commensalism
Two organisms: One benefits and the other is indifferent.
Example: An organism feeds off the waste of another.
Predation
One organism attacks and KILLS the other.
Parasitism
Two organisms: one benefits and the other is harmed.
Amensalism
Two organisms: one adversely affects the other, but the first organism is neither harmed nor benefitted.
Example: bacteria make antibiotics that harm or kill others.
Competition
Organisms that compete in the same niche for the same nutrients.
Skin
A human colonization site for bacteria. This is our protective barrier: acidic and salty. Gram+ bacteria
(Staph. epidermidis) and yeasts and Gram- in moist areas.
Nose
A human colonization site for bacteria. Similar to skin. Staph. aureus, Haemophilus influenza, Neisseria
meningitides live here.
Eye
, IUPUI K356 Exam 4 Final Test 2024\2025.
A human colonization site for bacteria. Normally sterile, but some bacteria live on the conjunctiva. Staph.
epidermidis and Haemophilus live here.
Ear (external)
A human colonization site for bacteria. Similar to skin. Staph. and some fungus live here.
Respiratory Tract
A human colonization site for bacteria. Normally sterile due to mechanical intervention (Sharp turn where
large stuff gets stuck) and mucociliary escalator (Pushes stuff up and out of the trachea).
Mouth
A human colonization site for bacteria. Warm, moist, nutrient-rich and good pH. Over 500 different
species identified that live here.
Stomach
A human colonization site for bacteria. Low pH. Less than 10 viable microbes per mL. Helicobacter pylori:
Can survive here. excretes urease, which creates a bubble of ammonia that neutralizes the pH around it.
Can cause stomach ulcers.
Small Intestine
A human colonization site for bacteria.
Upper portion: few microbes.
Middle portion: E. faecalis, Lactobacillus
Lower portion: Enterobacteriaceae
Large Intestine
A human colonization site for bacteria. 10^12 microbes per gram. More than 400 species live here,
including Bacteroides thetaiotaomicron, which can degrade LOTS of stuff.
Genitourinary Tract
A human colonization site for bacteria.
Upper portion: normally sterile (kidney, ureter, bladder)
Lower portion: E. faecalis and Staph. can live here.
In females, genital tract has lots of microbes, including Lactobacillus acidophilus, which keeps the pH low.
Gnotobiotic Animals
"Germ-free" animals. Born via C-section and then kept in a sterile bubble. They help us understand the
effects of normal flora.
Professional Pathogen
A microbe that ALWAYS causes disease
Opportunistic Pathogen
A microbe that can cause disease if given the right opportunity, but can also just be normal flora.
Compromised Host
Niche
Habitat that an organism lives in. Includes location, available nutrients and what it interacts with.
Biogeochemical Cycling
The cycling of nutrients in the environment
Carbon Cycle
Organics <-> CO2 <-> CH4
Microbial Mat
Layers of microbes
Environmental Genomics
Only 1% of microbes can be cultivated in the lab, so we take a "census" of genes that are in the
environment. Marine microbiology has benefitted from this by discovering novel genes.
Mutualism
Two organisms that are dependent on each other. They would die without each other.
Cooperation
Two organisms that benefit from each other, but they could survive without each other.
Commensalism
Two organisms: One benefits and the other is indifferent.
Example: An organism feeds off the waste of another.
Predation
One organism attacks and KILLS the other.
Parasitism
Two organisms: one benefits and the other is harmed.
Amensalism
Two organisms: one adversely affects the other, but the first organism is neither harmed nor benefitted.
Example: bacteria make antibiotics that harm or kill others.
Competition
Organisms that compete in the same niche for the same nutrients.
Skin
A human colonization site for bacteria. This is our protective barrier: acidic and salty. Gram+ bacteria
(Staph. epidermidis) and yeasts and Gram- in moist areas.
Nose
A human colonization site for bacteria. Similar to skin. Staph. aureus, Haemophilus influenza, Neisseria
meningitides live here.
Eye
, IUPUI K356 Exam 4 Final Test 2024\2025.
A human colonization site for bacteria. Normally sterile, but some bacteria live on the conjunctiva. Staph.
epidermidis and Haemophilus live here.
Ear (external)
A human colonization site for bacteria. Similar to skin. Staph. and some fungus live here.
Respiratory Tract
A human colonization site for bacteria. Normally sterile due to mechanical intervention (Sharp turn where
large stuff gets stuck) and mucociliary escalator (Pushes stuff up and out of the trachea).
Mouth
A human colonization site for bacteria. Warm, moist, nutrient-rich and good pH. Over 500 different
species identified that live here.
Stomach
A human colonization site for bacteria. Low pH. Less than 10 viable microbes per mL. Helicobacter pylori:
Can survive here. excretes urease, which creates a bubble of ammonia that neutralizes the pH around it.
Can cause stomach ulcers.
Small Intestine
A human colonization site for bacteria.
Upper portion: few microbes.
Middle portion: E. faecalis, Lactobacillus
Lower portion: Enterobacteriaceae
Large Intestine
A human colonization site for bacteria. 10^12 microbes per gram. More than 400 species live here,
including Bacteroides thetaiotaomicron, which can degrade LOTS of stuff.
Genitourinary Tract
A human colonization site for bacteria.
Upper portion: normally sterile (kidney, ureter, bladder)
Lower portion: E. faecalis and Staph. can live here.
In females, genital tract has lots of microbes, including Lactobacillus acidophilus, which keeps the pH low.
Gnotobiotic Animals
"Germ-free" animals. Born via C-section and then kept in a sterile bubble. They help us understand the
effects of normal flora.
Professional Pathogen
A microbe that ALWAYS causes disease
Opportunistic Pathogen
A microbe that can cause disease if given the right opportunity, but can also just be normal flora.
Compromised Host
