Microbiology

Microbiology Glossary

Every term used across all 57 Microbiology tracks, defined and alphabetized. Search it, or jump by letter.

258 terms

1

16S rRNA
A component of the small ribosomal subunit whose gene sequence is present in every living cell and changes very slowly over evolutionary time. Because it is essentially universal and highly conserved, comparing 16S rRNA sequences between organisms lets scientists estimate how closely related they are, which is how the three-domain system (Bacteria, Archaea, Eukarya) was built and how unidentified bacteria are identified in the clinical lab today.

3

30S/50S
The two subunits that make up the bacterial 70S ribosome. The small 30S subunit reads the mRNA code, while the large 50S subunit catalyzes peptide-bond formation. Several antibiotic classes are selective because they bind one of these subunits specifically: aminoglycosides and tetracyclines bind 30S, while macrolides, clindamycin, and chloramphenicol bind 50S — none of which affects the structurally different human 80S ribosome.

7

70S ribosome
The bacterial ribosome, made of a 30S and a 50S subunit. It is smaller and structurally distinct from the eukaryotic 80S ribosome, which is the basis for selective toxicity of many protein-synthesis-inhibiting antibiotics — they can shut down bacterial translation without touching the patient's own ribosomes.

A

A-B toxin
A two-part secreted bacterial toxin. The B (binding) subunit attaches to a specific receptor on the host cell surface, and the A (active) subunit is the piece that actually enters the cell and causes damage, often by disrupting a critical cellular process such as protein synthesis or signaling. Diphtheria toxin, cholera toxin, and tetanus toxin are all classic A-B toxins.
Abscess
A localized, walled-off collection of pus, formed when the immune system encloses an infection with fibrous tissue rather than letting it spread. Staphylococcus aureus is the classic cause because it tends to produce localized, contained infections rather than diffuse spreading ones.
Acetyl-CoA
The two-carbon molecule produced when pyruvate (the end product of glycolysis) is oxidized and loses one carbon as CO2. Acetyl-CoA is the entry point into the Krebs cycle, linking the breakdown of glucose to the energy-generating reactions that follow.
Acid-fast
A property of bacteria whose cell walls contain large amounts of waxy mycolic acid, which makes them resistant to standard Gram staining. Once these organisms take up carbolfuchsin dye, they hold onto it even when washed with an acid-alcohol decolorizer — hence 'acid-fast.' Mycobacterium tuberculosis is the classic acid-fast organism, and the acid-fast stain (Ziehl-Neelsen) is used specifically to identify it.
activated sludge
A wastewater treatment method in which a dense community of aerobic bacteria and other microbes is mixed with sewage in an aeration tank; the microbes digest and break down the organic waste, and the resulting biomass ('sludge') is then settled out, leaving cleaner water.
Active/passive immunity
Active immunity is protection your own immune system builds by responding to a real infection or a vaccine — it takes time to develop but is long-lasting because memory cells are formed. Passive immunity is protection from antibodies made by someone (or something) else and given directly to you, such as maternal IgG crossing the placenta, IgA in breast milk, or an antitoxin injection — it works immediately but fades within weeks to months because no memory cells are created.
active/passive transport
Passive transport moves substances across the membrane down their concentration gradient (from high to low concentration) and requires no cellular energy — examples include simple diffusion, facilitated diffusion, and osmosis. Active transport moves substances against their gradient (low to high concentration) and requires ATP, allowing a cell to accumulate nutrients even when they are scarce outside.
Adhesin
A bacterial surface molecule (often part of a pilus or fimbria) that binds tightly to specific receptors on host cells. Adhesins are usually the very first step of infection, since a pathogen that cannot attach is typically washed away by mucus, urine flow, or peristalsis before it can cause disease.
adjuvant
A substance added to a vaccine to boost the immune response it triggers. Adjuvants are especially important in non-live (inactivated, subunit) vaccines, which on their own tend to stimulate a weaker immune response than a live pathogen would.
agglutination
The visible clumping that occurs when antibodies bind to antigens present on particles (such as bacteria or red blood cells), cross-linking them into a lattice. Agglutination reactions are the basis of blood typing and many rapid diagnostic tests.
Ames test
A laboratory screening test that uses a strain of Salmonella unable to make histidine (His-negative). If a chemical is a mutagen, it will cause enough DNA mutations that some bacteria revert back to being able to make histidine (His-positive) and grow on histidine-free media — the more revertant colonies, the stronger the mutagen. Because most mutagens are also carcinogens, this test is widely used to screen new chemicals for cancer risk.
anaphylatoxin
A complement fragment (C3a or C5a) that triggers inflammation by causing mast cells to release histamine and by attracting immune cells to the site — essentially a chemical alarm signal generated as a byproduct of the complement cascade.
antibiogram
A local hospital or regional report summarizing what percentage of bacterial isolates were susceptible to each tested antibiotic over a given period. Because resistance patterns vary by geography and change over time, clinicians use the antibiogram to choose the most likely-to-work empiric antibiotic before culture results are back.
Anticodon
The three-nucleotide sequence on a tRNA molecule that is complementary to, and base-pairs with, a specific mRNA codon, ensuring the correct amino acid is added at each step of translation.
Antigenic drift
The slow, gradual accumulation of small mutations in a virus's surface antigens over time — the reason influenza vaccines need to be reformulated most years, and the mechanism behind ordinary seasonal flu.
antigenic shift
An abrupt, major change in a virus's surface antigens, most notably seen in influenza when two different flu strains infect the same cell and swap whole gene segments (reassortment). Because the immune system has never seen the resulting combination, shift can trigger pandemics — unlike antigenic drift, which is the slow accumulation of small mutations responsible for ordinary seasonal flu.
antimetabolite
A drug that mimics a molecule the microbe needs for normal metabolism and blocks the real molecule's pathway. Sulfonamides and trimethoprim are classic antimetabolites — they block sequential steps of bacterial folate synthesis, which humans don't make on their own (we get folate from diet), giving the drugs selective toxicity.
Antiparasitic drugs
Drugs targeting parasite-specific biology, such as antimalarials (chloroquine, artemisinin) that interfere with Plasmodium's ability to detoxify heme inside red blood cells, and other agents targeting the distinct metabolism of helminths and protozoa.
antiseptic
A chemical agent that reduces the number of microorganisms on living tissue (skin, wounds) to a safe level, as opposed to a disinfectant, which is used only on non-living surfaces because it is generally too harsh for tissue.
Antiviral drug classes
Drugs that target steps unique to viral replication: acyclovir inhibits viral DNA polymerase (herpesviruses), oseltamivir blocks the influenza neuraminidase enzyme needed to release new virus particles, and HIV is treated with combination antiretroviral therapy (ART) drawn from reverse transcriptase inhibitors, integrase inhibitors, and protease inhibitors, each blocking a different step of the HIV replication cycle.
APC
Antigen-presenting cell — a cell (dendritic cell, macrophage, or B cell) that engulfs a pathogen, breaks it into peptide fragments, and displays those fragments on MHC class II molecules to activate helper (CD4) T cells, linking the innate and adaptive immune responses.
Archaea
One of the three domains of life, made up of single-celled prokaryotes that lack a nucleus like bacteria but have distinct biochemistry — including ether-linked membrane lipids and no peptidoglycan cell wall. Many archaea are extremophiles, thriving in extreme heat, salt, or acidity, and none are established as human pathogens.
arrangement
The pattern in which bacterial cells remain grouped together after dividing, based on the plane and completeness of cell separation — described with prefixes like diplo- (pairs), strepto- (chains), and staphylo- (irregular grape-like clusters).
aseptic technique
A set of practices designed to prevent the introduction of unwanted microorganisms into a sterile field, culture, or patient — for example, flaming an inoculating loop before touching sterile media, or using sterile gloves during a procedure.
ATP
Adenosine triphosphate, the universal 'energy currency' of the cell. Energy released from breaking down nutrients (glucose, fats) is captured by adding a phosphate group to ADP to make ATP; that stored energy is then released when ATP is broken back down to power cellular work.
ATP synthase
A membrane-embedded enzyme that generates ATP by allowing protons (H+) to flow back down their concentration gradient through it, using that flow like a turbine to physically drive the synthesis of ATP from ADP and phosphate — the final step of chemiosmosis.
attenuated
Weakened. A live-attenuated vaccine uses a version of the pathogen that has been altered so it can still replicate and trigger a strong, durable immune response, but causes little to no disease in a healthy person. Because the organism is still alive, these vaccines are generally avoided in immunocompromised patients.
atypical pneumonia
Pneumonia caused by organisms that don't behave like typical bacterial pneumonia — they don't Gram stain or culture well on standard media, and they tend to cause a milder, more diffuse ('walking pneumonia') illness rather than a lobar consolidation. Mycoplasma pneumoniae and Legionella are classic examples.
Autoclave
A device that sterilizes equipment using pressurized steam, typically at 121°C for 15–20 minutes. The combination of heat and pressure is what allows it to kill even the most resistant bacterial endospores, which is the benchmark for true sterilization.
autoinducer
A small signaling molecule that bacteria release into their environment as part of quorum sensing. As the bacterial population grows, the autoinducer concentration rises; once it crosses a threshold, it triggers coordinated changes in gene expression across the whole population, such as forming a biofilm.
Autotroph/heterotroph
An autotroph makes its own organic carbon molecules from an inorganic source like CO2 (as plants and cyanobacteria do). A heterotroph must consume organic carbon made by other organisms, as fungi, protozoa, and animals — including most disease-causing microbes — do.

B

bacillus/bacilli
A rod-shaped bacterium (bacillus, plural bacilli). This describes overall cell shape and is one of the two most common bacterial morphologies, alongside cocci (spheres).
Baltimore classification
A system that groups all viruses into seven classes based on their genome type (DNA or RNA, single- or double-stranded) and the pathway each uses to produce mRNA: dsDNA, ssDNA, dsRNA, +ssRNA, −ssRNA, ssRNA reverse-transcribing (retroviruses), and dsDNA reverse-transcribing viruses.
beta-lactam
A large family of antibiotics — including penicillins, cephalosporins, and carbapenems — that share a four-membered beta-lactam ring in their structure. They work by binding penicillin-binding proteins and blocking the final cross-linking step of peptidoglycan (cell wall) synthesis, which causes the bacterial cell to lyse.
beta-lactamase
A bacterial enzyme that breaks open (hydrolyzes) the beta-lactam ring of penicillins and related drugs, inactivating them before they can reach their target. It is the single most common mechanism of resistance to beta-lactam antibiotics, and drugs are often paired with a beta-lactamase inhibitor to overcome it.
Binary fission
The primary method of bacterial reproduction, in which a single cell copies its circular chromosome, grows in size, and then splits into two genetically identical daughter cells. Repeated rounds of binary fission are what drive the doubling seen during log (exponential) phase of the growth curve.
Binomial nomenclature
The standardized two-part naming system for species, consisting of a capitalized genus name followed by a lowercase species name, with the whole name italicized (e.g., Escherichia coli). After it has been written out in full once, convention allows the genus to be abbreviated to its first letter for the rest of a passage (E. coli).
biofilm
A structured community of bacteria attached to a surface and encased in a self-produced matrix of extracellular polymeric substance (EPS). Biofilms are far more tolerant of antibiotics and host defenses than free-floating (planktonic) cells, which is why device-related infections (catheters, prosthetic joints) are so hard to clear without removing the device.
biological vs. mechanical vector
A biological vector (like the Anopheles mosquito for malaria) is one in which the pathogen actually develops or multiplies inside the vector before being transmitted. A mechanical vector (like a housefly carrying bacteria on its legs) simply physically transports the pathogen from one place to another without the pathogen changing or reproducing inside it.
bioremediation
The use of microorganisms to break down and neutralize environmental pollutants — for example, using naturally occurring or engineered bacteria to digest spilled oil or industrial solvents into less harmful byproducts.
Biosafety level (BSL 1-4)
A four-tier classification (BSL-1 through BSL-4) for laboratories working with infectious agents, based on how dangerous the organism is and how it spreads. Higher levels require progressively more containment equipment and stricter practices, from basic precautions at BSL-1 up to fully isolated, positive-pressure suit facilities at BSL-4 for agents like Ebola virus.
broad vs. narrow spectrum
A narrow-spectrum antibiotic targets a limited range of bacteria (often just Gram-positives or just Gram-negatives), sparing the rest of the normal microbiota. A broad-spectrum antibiotic kills a wide range of both Gram-positive and Gram-negative organisms, which makes it useful when the causative organism is unknown but raises the risk of disrupting the microbiome and allowing opportunists like C. difficile to overgrow.

C

CAP/cAMP
Catabolite activator protein (CAP) is a positive regulatory protein that binds DNA and boosts transcription of certain operons (like lac) when it is bound to cyclic AMP (cAMP). Glucose levels control cAMP: when glucose is scarce, cAMP rises, CAP becomes active, and the cell is primed to use alternative sugars like lactose more efficiently.
Capsid
The protein shell that encases and protects a virus's genetic material (DNA or RNA). It is built from repeating protein subunits and gives the virus its structural shape.
carbolfuchsin
A deep red dye used in the acid-fast (Ziehl-Neelsen) staining procedure. Its small molecular structure and the use of heat during staining allow it to penetrate the waxy, mycolic-acid-rich walls of Mycobacterium species, where it becomes trapped and resists the subsequent acid-alcohol wash.
catalase
An enzyme that breaks down hydrogen peroxide (a toxic byproduct of oxygen metabolism) into water and oxygen gas. Its presence — tested for by the bubbling reaction it produces — helps organisms survive in oxygen-containing environments and is used as a lab test to distinguish, for example, Staphylococcus (catalase-positive) from Streptococcus (catalase-negative).
CD4/helper T
CD4 is a surface marker on helper T cells that binds MHC class II. Helper T cells don't kill infected cells directly; instead, they coordinate the immune response by releasing cytokines that activate B cells, cytotoxic T cells, and macrophages. HIV specifically targets and depletes CD4 T cells, which is why untreated HIV progressively cripples the whole immune system.
CD8/cytotoxic T
CD8 is a surface marker on cytotoxic T cells that binds MHC class I. Cytotoxic T cells directly kill cells that are infected with viruses or are cancerous, by recognizing abnormal peptides displayed on that cell's MHC I and triggering it to undergo apoptosis.
cellulitis
A spreading, non-abscessed bacterial infection of the skin and underlying soft tissue, typically caused by Streptococcus pyogenes or Staphylococcus aureus, presenting as redness, warmth, and swelling that expands outward rather than staying walled off like an abscess.
Central dogma
The fundamental flow of genetic information in a cell: DNA is transcribed into RNA, and RNA is translated into protein. It describes the general direction information travels from the genetic code to a functional product.
chancre
A painless, firm ulcer that appears at the site of infection during primary syphilis. It typically heals on its own within a few weeks even without treatment, which can falsely reassure a patient while the infection silently progresses to later stages.
chemiosmosis
The process of generating ATP by using the energy stored in a proton (H+) gradient across a membrane. Protons pumped out during the electron transport chain flow back in through ATP synthase, and that flow drives ATP production.
Chemoautotroph (chemolithoautotroph)
An organism that obtains energy by oxidizing inorganic chemicals (like ammonia or sulfur) and fixes CO2 as its carbon source. Nitrifying bacteria are a classic example, and this class forms the energy base of ecosystems that never see sunlight, like deep-sea vents.
Chemoheterotroph
An organism that obtains both its energy and its carbon from organic molecules made by other organisms. This is the nutritional class of fungi, protozoa, animals, and the great majority of medically important bacteria.
chemolithotroph
An organism that gets its energy by oxidizing inorganic chemicals (such as ammonia, nitrite, sulfur, or iron) rather than from sunlight or organic molecules. Chemolithotrophs are important in nutrient cycling and can form the base of ecosystems in places sunlight never reaches, like deep-sea hydrothermal vents.
chemotaxis
Directed movement of a motile organism toward a favorable chemical (like a nutrient) or away from an unfavorable one (like a toxin), guided by chemical receptors that control the direction of flagellar rotation.
clonal selection
The process by which an antigen 'selects' the one lymphocyte (out of an enormous pre-existing pool with different receptor specificities) whose receptor happens to fit it. That single cell is then triggered to proliferate rapidly, producing a large clone of identical cells — some that fight the current infection and some that become long-lived memory cells for faster response next time.
Coagulase test
A rapid biochemical test that detects whether an organism produces coagulase, an enzyme that clots blood plasma. Staphylococcus aureus is coagulase-positive, distinguishing it from coagulase-negative staph species such as S. epidermidis — a distinction used constantly in lab reports and antibiotic decisions.
Coccus/cocci
A spherical bacterium (coccus, plural cocci). This describes overall cell shape and, combined with arrangement (chains, clusters, pairs) and Gram stain result, is one of the first clues used to narrow down bacterial identity under the microscope.
Codon
A three-nucleotide sequence on mRNA that specifies either a single amino acid to add to the growing protein or a stop signal to end translation.
colonization resistance
The protection provided by the normal, resident microbiota against invasion by pathogens, achieved by physically occupying space and nutrients, producing inhibitory substances, and maintaining a hostile local environment that outcompetes newcomers.
Colony morphology
The visible characteristics of a bacterial colony growing on solid media — its size, shape, color, texture, and edge — which experienced microbiologists use as a first clue toward identifying the organism, alongside Gram stain and biochemical tests.
complement
A group of roughly 30 blood proteins that circulate in an inactive form and, once triggered, cascade through a sequence of activations to lyse pathogens, tag them for phagocytosis (opsonization), and trigger inflammation. It is part of the innate immune system but also interacts with antibodies from the adaptive system.
Complement cascade
The sequential activation of complement proteins, triggered through one of three pathways (classical, lectin, or alternative) that all converge on cleaving C3. This produces C3b (opsonization), C3a/C5a (inflammation/anaphylatoxins), and ultimately the membrane attack complex (cell lysis).
concentration gradient
The difference in concentration of a substance between two regions — for example, across a cell membrane. Substances naturally tend to move down their gradient, from an area of higher concentration to lower, unless a cell spends energy to move them the opposite way (active transport).
conjugation
A form of horizontal gene transfer in which one bacterium (the donor, carrying an F plasmid) forms a direct physical connection with another cell (the recipient) via a sex pilus and transfers a copy of DNA through it. This can transfer just a plasmid or, in an Hfr donor, part of the chromosome itself.
counterstain
A second dye applied after the primary stain and decolorization step, used to color cells that lost the primary stain so they remain visible under the microscope — in the Gram stain, safranin serves this role, turning decolorized Gram-negative cells pink.
crepitus
A crackling or popping sensation felt under the skin, caused by gas produced by bacteria (classically Clostridium perfringens) within infected tissue — a hallmark physical exam finding of gas gangrene that signals a surgical emergency.
CRISPR-Cas9
A gene-editing tool adapted from a natural bacterial immune defense against viruses. A short guide RNA directs the Cas9 enzyme to a specific matching DNA sequence, where Cas9 cuts both strands; the cell's own repair machinery then fixes the cut, allowing genes to be disabled or precisely edited.
CSF
Cerebrospinal fluid — the clear fluid surrounding the brain and spinal cord, sampled by lumbar puncture. Its appearance, glucose, protein, and white cell count are analyzed to help distinguish bacterial meningitis (cloudy, low glucose, high neutrophils) from viral meningitis (clear, normal glucose, lymphocyte-predominant).
cycle threshold
In real-time PCR, the number of amplification cycles needed before the target DNA/RNA signal becomes detectable above background. A lower cycle threshold means more starting genetic material was present in the sample (higher pathogen load), while a higher threshold indicates a smaller starting amount.
Cyclic fever
A fever pattern that rises and falls at regular intervals rather than staying constant, classically seen in malaria, where synchronized rupture of infected red blood cells (releasing Plasmodium merozoites and toxins) causes fever spikes every 48 or 72 hours depending on the species.
cytokine
A small signaling protein released by immune cells that influences the behavior of other cells nearby, coordinating processes like inflammation, cell growth, and immune activation. Helper T cells rely heavily on cytokines to direct the rest of the immune response.
cytoplasm
The gel-like interior of the cell, contained within the plasma membrane, where most metabolic reactions and, in prokaryotes, transcription and translation take place.

D

decolorizer
The step in a staining procedure that removes unbound or loosely bound dye, used to distinguish between cell types based on how tightly they retain the primary stain — in the Gram stain, alcohol or acetone serves this role and is the critical step determining the final result.
decomposer
An organism (mostly bacteria and fungi) that breaks down dead organic material, releasing the carbon and other nutrients it contains back into the environment where they can be reused by other living things — a critical role in the carbon cycle.
delayed-type
Describes a hypersensitivity reaction (Type IV) that is mediated by T cells rather than antibodies, and therefore takes hours to days to develop rather than occurring immediately — the tuberculin skin test and poison ivy contact dermatitis are classic examples.
denitrification
The conversion of nitrate (NO3-) back into nitrogen gas (N2) by certain bacteria, typically under low-oxygen conditions. It completes the nitrogen cycle by returning fixed nitrogen to the atmosphere.
dermatophyte
A type of fungus that infects keratinized tissue — skin, hair, and nails — causing conditions commonly called ringworm or tinea, without invading living tissue beneath the keratin layer.
differential media
See Colony morphology/media entries — culture media that doesn't necessarily restrict growth but instead reveals a visible difference (often a color change) between organisms based on a biochemical property, such as the ability to ferment a particular sugar.
dimorphic
Describes a fungus that can exist in two distinct forms depending on temperature — typically a mold form in the environment (at room temperature) and a yeast form inside the human body (at body temperature). Histoplasma is a classic dimorphic fungal pathogen.
diplococci
Bacteria that occur characteristically in pairs. Neisseria gonorrhoeae and Neisseria meningitidis are classic Gram-negative diplococci, often described as 'kidney bean-shaped' pairs on Gram stain.
disinfectant
A chemical agent strong enough to kill or inactivate microorganisms on non-living surfaces, but generally too harsh or toxic to use safely on living tissue (which is what an antiseptic is for instead).
Domain
The highest level of biological classification, above kingdom. Based on molecular (16S rRNA) evidence, all life is grouped into three domains: Bacteria, Archaea, and Eukarya.
dysbiosis
An imbalance in the normal microbial community of the body, in which the usual protective, competitive balance is disrupted — often by antibiotics — allowing normally suppressed organisms (like Clostridioides difficile) to overgrow and cause disease.
dysentery
Diarrheal illness characterized by blood and mucus in the stool, caused by organisms that invade and damage the intestinal lining rather than simply secreting a toxin — Shigella and Entamoeba histolytica are classic causes.

E

efflux pump
A membrane transport protein that actively pumps a drug back out of the bacterial cell before it can reach a high enough internal concentration to be effective, making it one of the four general mechanisms of antibiotic resistance.
electron acceptor
The molecule at the very end of the electron transport chain that receives the electrons passed down the chain. In aerobic respiration this is oxygen; some anaerobic bacteria use alternative acceptors such as nitrate or sulfate instead.
ELISA
Enzyme-Linked Immunosorbent Assay — a diagnostic test in which an antigen or antibody is bound to a plate, and a detection antibody linked to an enzyme is added; the enzyme reacts with a substrate to produce a color change proportional to how much target was present. It is typically used as a sensitive first-line screening test.
emerging vs. re-emerging infection
An emerging infection is one caused by a pathogen newly identified or newly capable of infecting humans (often via zoonotic spillover). A re-emerging infection is one that was previously under control (through vaccination, treatment, or public health measures) but has increased in incidence again, often due to declining vaccination rates, drug resistance, or changing ecology.
endogenous/exogenous antigen
An endogenous antigen originates from inside the cell itself (such as a viral protein made by an infected cell) and is displayed on MHC class I to be recognized by CD8 T cells. An exogenous antigen comes from outside the cell and is taken up, processed, and displayed on MHC class II to be recognized by CD4 T cells.
endospore
A dormant, extremely resistant structure formed by certain Gram-positive bacteria (Bacillus and Clostridium species) in response to harsh conditions. It is not a reproductive structure — one vegetative cell forms one endospore — but rather a survival strategy that can withstand heat, drying, radiation, and many disinfectants for years until conditions improve enough for it to germinate.
endotoxin/LPS
Lipopolysaccharide (LPS), also called endotoxin, is a component of the outer membrane found only in Gram-negative bacteria. Unlike a secreted exotoxin, it is a structural part of the cell and is released when the bacterial cell dies and its membrane breaks apart, where it triggers a strong inflammatory response that can cause fever, and in high amounts, septic shock.
envelope
A lipid membrane, derived from the host cell, that surrounds the capsid of some viruses. Enveloped viruses are generally more fragile outside a host (susceptible to drying, soap, and disinfectants) than non-enveloped ('naked') viruses, which affects how easily each type spreads.
EPS
Extracellular polymeric substance — the slimy matrix of sugars, proteins, and DNA that bacteria secrete to build and protect a biofilm, physically shielding the embedded cells from antibiotics, disinfectants, and immune cells.
ER
Endoplasmic reticulum — a eukaryotic organelle that forms a network of membranes involved in the synthesis and processing of proteins and lipids; found in eukaryotic cells but absent from prokaryotes.
Ergosterol
The primary sterol found in fungal cell membranes, playing the structural role that cholesterol plays in human membranes. Because ergosterol differs from cholesterol, several antifungal drug classes (azoles, polyenes) can selectively target it without harming human cells.
ETC
Electron transport chain — a series of membrane-embedded protein complexes that pass electrons from carriers like NADH and FADH2 down an energy gradient, using the released energy to pump protons across the membrane and build the proton gradient that powers ATP synthase.
ether-linked lipids
A distinctive feature of archaeal cell membranes, in which the lipid tails are connected to the glycerol backbone by ether bonds (rather than the ester bonds found in bacteria and eukaryotes). Ether linkages are more chemically stable, helping archaea survive extreme environments.
exponential growth
The log (logarithmic) phase of bacterial growth, during which cells divide at their maximum, constant rate and the population doubles at regular time intervals — this is when cells are metabolically most active and, notably, most susceptible to antibiotics that target active processes like cell wall synthesis.
extremophile
An organism, most often an archaeon, adapted to thrive in conditions that would be lethal to most life — extreme heat, cold, salinity, pressure, or pH.

F

fastidious
Describes an organism with complex, specific nutritional requirements that must be met with specialized (enriched) growth media in order to culture it successfully in the lab.
fecal-oral
A route of disease transmission in which a pathogen shed in feces is ingested by another host, typically through contaminated food, water, or hands — the primary route for most gastrointestinal pathogens.
Fermentation
A metabolic pathway that regenerates NAD+ (needed to keep glycolysis running) without using an electron transport chain, by transferring electrons from NADH directly to an organic molecule such as pyruvate. It produces relatively little ATP compared to respiration but allows a cell to keep generating energy in the absence of a suitable final electron acceptor.
fluorescence
A property in which a molecule absorbs light at one wavelength and re-emits it at a longer wavelength, appearing to glow. In microscopy, cells or structures are tagged with fluorescent dyes or antibodies so they can be visualized with high specificity against a dark background.

G

Generation/doubling time
The time it takes for a population of cells to double in number during exponential (log-phase) growth — a measure of how fast an organism reproduces under given conditions.
germ theory
The scientific principle that specific microorganisms cause specific infectious diseases, established largely through the work of Pasteur and Koch. It replaced earlier ideas (like spontaneous generation and miasma theory) and remains the foundation of modern microbiology and infectious disease medicine.
Ghon focus
A small area of granulomatous inflammation and scarring in the lung, representing the site where Mycobacterium tuberculosis was originally contained by the immune system during primary infection — visible on imaging and, combined with an involved lymph node, forms the 'Ghon complex.'
Glycolysis
The metabolic pathway that splits one molecule of glucose into two molecules of pyruvate, occurring in the cytoplasm and producing a small net yield of ATP directly. It is the universal first step of both fermentation and respiration.
gnotobiotic
Describes an animal raised in a completely germ-free environment, or one deliberately colonized with only a defined, known set of microorganisms. Studies of germ-free animals reveal that the normal microbiome is essential for healthy immune and digestive system development.

H

halophile
An organism, often an archaeon, that requires or tolerates high salt concentrations to grow, having evolved cellular adaptations to survive the osmotic stress that would dehydrate most other cells.
hemolysis
The breakdown of red blood cells, used as a diagnostic feature on blood agar: alpha-hemolysis causes partial breakdown with a greenish discoloration, beta-hemolysis causes complete breakdown with a clear zone around the colony, and gamma-hemolysis means no red cell breakdown occurs at all.
Hepatitis A–E
Five distinct viruses that all primarily infect the liver but differ in transmission and course: hepatitis A and E spread via the fecal-oral route and are typically acute and self-limited; hepatitis B, C, and D spread via blood and body fluids and can become chronic infections, with B and C carrying a long-term risk of cirrhosis and hepatocellular carcinoma.
herd immunity
Indirect protection from an infectious disease that occurs when a high enough proportion of a population is immune (through vaccination or prior infection), making it statistically unlikely for the pathogen to reach and infect the remaining susceptible individuals, thereby slowing or stopping its spread.
Hfr
High-frequency recombination — a bacterial donor cell in which the F plasmid has integrated into the chromosome. During conjugation, an Hfr cell can transfer part of its chromosomal DNA (not just the plasmid) to a recipient, at high frequency.
Humoral immunity
The branch of adaptive immunity carried out by B cells and the antibodies they produce, most effective against extracellular (free-floating) pathogens like bacteria and toxins circulating in blood or mucosal secretions.
HUS
Hemolytic uremic syndrome — a serious complication of infection with Shiga toxin-producing E. coli (like O157:H7), in which the toxin damages blood vessels, causing red blood cell destruction, low platelets, and acute kidney injury. Antibiotics are avoided in these infections because killing the bacteria can release more toxin and worsen HUS risk.
Hypersensitivity
An exaggerated or inappropriate immune response that causes tissue damage, classified into four types (I–IV) based on the underlying mechanism — ranging from immediate IgE-mediated allergic reactions (Type I) to delayed T-cell-mediated reactions (Type IV).

I

immune complex
A cluster formed when antibodies bind to antigen and, instead of being efficiently cleared, gets deposited in tissues such as blood vessels, joints, and kidneys — triggering the inflammatory damage characteristic of Type III hypersensitivity.
Immunoglobulin
Another name for antibody — a Y-shaped protein produced by plasma cells that binds specifically to an antigen. There are five classes (isotypes): IgG, IgA, IgM, IgE, and IgD, each with distinct locations and functions.
Incidence vs. prevalence
Incidence is the number of new cases of a disease that occur in a population over a defined time period. Prevalence is the total number of existing cases (new and old) at a given point in time. A disease can have high prevalence but low incidence if it is chronic and long-lasting but not spreading quickly.
India ink
A staining technique used to visualize the polysaccharide capsule of Cryptococcus neoformans; the ink stains the dark background but is excluded by the capsule, leaving a clear 'halo' around the yeast cell — a classic rapid diagnostic finding in cryptococcal meningitis.
inducible vs. repressible
An inducible operon (like lac) is normally off and is switched on when a specific molecule (an inducer, like lactose) is present. A repressible operon (like trp) is normally on and is switched off when the end product it makes (like tryptophan) becomes abundant, through negative feedback.
infectious dose
The number of organisms typically required to establish an infection in a host. Some pathogens, like Shigella, have a very low infectious dose (as few as 10–100 organisms), making them highly transmissible even with minimal exposure.
inflammation
The body's protective response to injury or infection, producing the cardinal signs of redness, heat, swelling, and pain, driven by increased blood flow, vascular permeability, and recruitment of immune cells to the affected area.
Innate immunity
The immune system's first line of defense, present from birth, that responds rapidly to a broad range of threats without needing prior exposure, and does not create lasting memory. It includes physical barriers, phagocytes, complement, and inflammation.
interferon
A signaling protein released by virus-infected cells that warns neighboring cells of the infection, prompting them to activate antiviral defenses and reduce their own susceptibility. It does not cure the already-infected cell but limits the spread of infection to nearby cells.
isotype
A distinct class of antibody (IgG, IgA, IgM, IgE, or IgD), each defined by a different structure of the antibody's constant region, which determines its function and location in the body.

K

Koch's postulates
A set of four criteria used to establish that a specific microorganism causes a specific disease: (1) the microbe must be found in every case of the disease and absent in healthy individuals, (2) it must be isolated in pure culture, (3) it must reproduce the disease when introduced into a healthy host, and (4) it must be re-isolated from that host and match the original organism.
KOH prep
A rapid diagnostic technique in which potassium hydroxide is added to a skin, hair, or nail sample to dissolve human cells while leaving fungal cell walls intact, allowing fungal hyphae or yeast to be seen directly under the microscope.
Krebs cycle
Also called the citric acid cycle — a series of chemical reactions occurring in the mitochondrial matrix (or cytoplasm in bacteria) that fully oxidizes acetyl-CoA, releasing CO2 and generating the electron carriers NADH and FADH2, which feed into the electron transport chain.

L

latent
A stage of infection in which a pathogen persists in the body without causing active symptoms, often 'hiding' from the immune system, but capable of reactivating later — a key stage in syphilis and many viral infections like herpes.
lateral flow
A simple, rapid point-of-care diagnostic format (like a home pregnancy or rapid COVID test) in which a sample flows across a test strip and antibodies bound to the strip capture a target antigen, producing a visible colored line if it is present.
leukocyte esterase
An enzyme released by white blood cells, detected on a urine dipstick as an indirect marker of pyuria (white cells in the urine) — a supportive but nonspecific finding for urinary tract infection.
limiting nutrient
The nutrient in shortest supply relative to an organism's or ecosystem's needs, which therefore restricts growth even if all other nutrients are abundant. Phosphorus is often the limiting nutrient in ecosystems because it has no atmospheric gas phase and cycles very slowly.
lithotroph/organotroph
A lithotroph obtains electrons for its metabolism from inorganic sources (such as hydrogen sulfide or ammonia). An organotroph obtains electrons from organic molecules. This distinction is combined with energy source (photo-/chemo-) and carbon source (auto-/hetero-) to fully classify a microbe's nutritional strategy.
Lobar pneumonia
A pattern of bacterial pneumonia in which infection and consolidation fill an entire lobe of the lung fairly uniformly, classically caused by Streptococcus pneumoniae and associated with rusty-colored sputum.
LPS/endotoxin
Lipopolysaccharide (LPS), also called endotoxin, is a component of the outer membrane found only in Gram-negative bacteria. Unlike a secreted exotoxin, it is a structural part of the cell and is released when the bacterial cell dies and its membrane breaks apart, where it triggers a strong inflammatory response that can cause fever, and in high amounts, septic shock.
lumbar puncture
A procedure in which a needle is inserted into the lower spinal canal to collect cerebrospinal fluid (CSF) for analysis, used to diagnose meningitis and other central nervous system infections.
Lysogenic cycle
A bacteriophage replication pathway in which the phage's DNA integrates into the host chromosome as a dormant prophage and is passively copied along with the bacterium's own DNA at every division, rather than immediately producing new phage. A trigger such as cellular stress can later cause the prophage to excise and switch into the lytic cycle.
Lytic cycle
The bacteriophage replication pathway in which the phage immediately redirects the host cell's machinery to assemble many new phage particles, then lyses (bursts) the cell to release them. This rapid assembly step is when a phage can accidentally package bacterial DNA instead of its own, which is the basis of transduction.

M

MAC
Membrane attack complex — the end product of the complement cascade (C5b through C9), which assembles into a pore in a pathogen's membrane, allowing water and ions to rush in and lysing the cell.
malachite green
A green dye used in endospore staining. Because endospores have a dense, impermeable coat, malachite green must be forced in with heat, but it then resists the decolorizing wash, allowing spores to be seen distinctly from the surrounding vegetative cells (counterstained red with safranin).
MALDI-TOF
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry — a rapid identification method that vaporizes and ionizes bacterial proteins with a laser, then measures their mass to generate a unique protein 'fingerprint' that is matched against a reference database to identify the organism within minutes.
mast cell
A tissue-resident immune cell coated in IgE receptors that, upon antigen binding and cross-linking of that IgE, rapidly releases histamine and other inflammatory mediators — the central effector cell of Type I (immediate) hypersensitivity and allergic reactions.
MBC
Minimum bactericidal concentration — the lowest concentration of an antibiotic that actually kills (rather than merely inhibits) 99.9% of the starting bacterial population. A drug is considered bactericidal if its MBC is close to its MIC, and bacteriostatic if the MBC is much higher.
mecA/PBP2a
The mecA gene, carried by MRSA (methicillin-resistant Staphylococcus aureus), encodes an altered penicillin-binding protein called PBP2a. Beta-lactam antibiotics cannot bind PBP2a effectively, so cell wall synthesis continues even in the presence of the drug — the mechanism behind MRSA's broad beta-lactam resistance.
memory B cell
A long-lived B cell generated during an immune response that 'remembers' a specific antigen. On re-exposure, memory B cells can rapidly differentiate into antibody-producing plasma cells, producing a faster and stronger secondary response than the original infection triggered.
Meningitis
Inflammation of the meninges (the membranes surrounding the brain and spinal cord), most seriously caused by bacteria and diagnosed by analyzing cerebrospinal fluid obtained via lumbar puncture; it is a medical emergency requiring rapid antibiotic treatment when bacterial.
methanogen
A type of archaeon that generates methane gas as a metabolic byproduct, typically living in strictly anaerobic environments such as wetlands, animal digestive tracts, and sewage sludge.
MHC
Major histocompatibility complex — a set of cell-surface molecules that display peptide fragments so T cells can inspect them. MHC class I is present on virtually all nucleated cells and presents endogenous (internally made) peptides to CD8 T cells; MHC class II is present only on antigen-presenting cells and displays exogenous (engulfed) peptides to CD4 T cells.
MIC
Minimum inhibitory concentration — the lowest concentration of an antibiotic that visibly prevents bacterial growth in a lab test, used to guide dosing and determine whether an organism is susceptible or resistant to a given drug.
Microbiota
The full community of microorganisms — bacteria, fungi, and others — that normally and harmlessly (often beneficially) colonize a healthy person's body surfaces, including the skin, gut, and mucous membranes.
mitochondria
A eukaryotic organelle responsible for producing most of the cell's ATP through aerobic respiration; absent from prokaryotic cells, which instead carry out the equivalent reactions across their plasma membrane.
mode of transmission
The specific pathway by which an infectious agent moves from a reservoir to a susceptible host — such as direct contact, droplet, airborne, fecal-oral, vector-borne, or bloodborne routes — one of the six links in the chain of infection.
molecular clock
The concept that certain molecules (like 16S rRNA) accumulate mutations at a roughly steady, predictable rate over time, allowing scientists to estimate how long ago two species diverged from a common ancestor by comparing how different their sequences have become.
molecular Koch's postulates
A modern, gene-level adaptation of Koch's original postulates used to prove that a specific gene (rather than a whole organism) is responsible for virulence: the gene should be present in pathogenic strains, knocking it out should reduce virulence, and restoring it should restore virulence.
mordant
A chemical that helps a stain bind more firmly to its target — in the Gram stain, iodine acts as the mordant, forming a large crystal violet-iodine complex that becomes trapped inside thick-walled Gram-positive cells during the decolorization step.
morphology
The overall shape and structural form of a cell or organism, one of the first descriptive features used in bacterial identification (e.g., coccus, bacillus, spiral).
MRSA
Methicillin-resistant Staphylococcus aureus — a strain of S. aureus carrying the mecA gene, making it resistant to methicillin and virtually all other beta-lactam antibiotics; it requires alternative drug classes such as vancomycin for treatment.
Multiplex PCR
A PCR-based test that uses several different primer sets in a single reaction to simultaneously detect multiple different pathogens (or genes) from one sample, speeding up diagnosis when several organisms could plausibly be causing a similar clinical picture.
mutagen
Any physical or chemical agent that increases the rate of mutations in DNA — including UV light (causing thymine dimers), certain chemicals, and base analogs that get mistakenly incorporated during replication.

N

NAD+
Nicotinamide adenine dinucleotide — an electron carrier molecule that is reduced to NADH when it picks up electrons during glycolysis and the Krebs cycle. Because a cell has only a limited supply, NAD+ must constantly be regenerated (either via the electron transport chain or via fermentation) for glycolysis to keep running.
Negative-sense RNA (−ssRNA)
A viral RNA genome that is the complementary mirror-image of mRNA, so it cannot be directly translated. The virus must carry its own RNA polymerase into the cell to first transcribe it into a readable, positive-sense copy.
nematode/cestode/trematode
The three major groups of parasitic worms (helminths): nematodes are roundworms with a tubular body and complete digestive tract; cestodes are tapeworms, flat and segmented, that absorb nutrients directly through their body wall (having no gut of their own); trematodes are flukes, flat and leaf-shaped, that often require an intermediate snail host as part of their life cycle.
neutralization
An antibody function in which the antibody binds directly to a toxin or a virus's attachment site, physically blocking it from binding to and damaging or entering a host cell — without necessarily killing the pathogen itself.
Neutrophile
An organism that grows optimally in an environment with a neutral pH, around 7. It is important to distinguish this term from the similarly spelled 'neutrophil,' which is an entirely different concept — a type of white blood cell.
nitrification
The two-step microbial process of oxidizing ammonia first to nitrite (by bacteria such as Nitrosomonas) and then to nitrate (by bacteria such as Nitrobacter), part of the nitrogen cycle that converts nitrogen into a form plants can readily use.
nitrites
A chemical marker tested on a urine dipstick; certain bacteria (notably E. coli) possess an enzyme that converts urinary nitrates into nitrites, so a positive nitrite result is a fairly specific — though not universally sensitive — indicator of a bacterial urinary tract infection.
Nitrogen fixation
The conversion of atmospheric nitrogen gas (N2), which most organisms cannot use directly, into ammonia — a biologically usable form. Only certain prokaryotes (such as Rhizobium, using the enzyme nitrogenase) can perform this reaction, making them essential to virtually all other life on Earth.
Normal flora by site
The distribution of resident microbiota across the body: skin (dominated by Staphylococcus epidermidis and Cutibacterium acnes), mouth (a dense mixed community including Streptococcus species), gut/large intestine (the densest community in the body, dominated by anaerobes like Bacteroides), and the vagina (typically dominated by protective Lactobacillus). Blood, CSF, and the lower respiratory tract are normally sterile, so any organism recovered from them is treated as significant rather than normal.
nosocomial infection
An infection acquired in a healthcare setting (also called a healthcare-associated infection), often linked to invasive devices like catheters and central lines or to surgical procedures, and controlled through hand hygiene, isolation precautions, and sterile technique.
Nucleus
The membrane-bound compartment in eukaryotic cells that houses the cell's DNA, physically separating transcription (which happens inside) from translation (which happens outside in the cytoplasm) — a feature entirely absent in prokaryotes.

O

O&P exam
Ova and parasite examination — a laboratory stool test in which a sample is examined microscopically for the presence of parasite eggs (ova), larvae, or adult forms, used to diagnose intestinal parasitic infections.
obligate intracellular
Describes an organism (all viruses, and some bacteria like Chlamydia and Rickettsia) that cannot replicate on its own and must invade and use the machinery of a living host cell to reproduce.
Okazaki fragments
Short, discontinuous segments of newly synthesized DNA on the lagging strand during DNA replication. Because DNA polymerase can only build in one direction, the lagging strand must be synthesized in these short backward-facing pieces, which are later joined together by DNA ligase.
Oncogenic virus
A virus capable of driving the development of cancer, most notably certain high-risk strains of human papillomavirus (HPV), which are linked to cervical and other cancers — the basis for the cancer-preventing HPV vaccine.
One Health
An approach recognizing that human, animal, and environmental health are deeply interconnected, and that effectively preventing disease — especially emerging zoonotic infections — requires coordinated efforts across all three domains rather than treating human medicine in isolation.
Operon
A cluster of genes in bacteria that are transcribed together as a single mRNA under the control of one shared promoter and operator, allowing coordinated on/off regulation of genes that function together, such as the enzymes needed to metabolize a particular sugar.
opsonization
The process of coating a pathogen with molecules (like complement protein C3b or antibodies) that phagocytes can recognize and bind to, dramatically increasing the efficiency with which the pathogen is engulfed and destroyed.
organelle
A specialized, usually membrane-bound structure within a eukaryotic cell that performs a specific function, such as the mitochondria (energy production) or endoplasmic reticulum (protein/lipid processing); prokaryotic cells lack true membrane-bound organelles.
outer membrane
An additional lipid bilayer found only in Gram-negative bacteria, located outside the thin peptidoglycan layer. It contains lipopolysaccharide (LPS/endotoxin) and acts as an extra barrier that makes Gram-negative organisms generally harder for certain antibiotics to penetrate than Gram-positive organisms.
Oxidase test
A rapid biochemical test that detects whether an organism produces cytochrome c oxidase, an enzyme used in aerobic respiration. A positive result (fast color change) helps distinguish organisms like Pseudomonas (oxidase-positive) from Enterobacteriaceae such as E. coli (oxidase-negative).
Oxygenic/anoxygenic photosynthesis
Oxygenic photosynthesis (performed by plants, algae, and cyanobacteria) splits water molecules to obtain electrons, releasing oxygen gas as a byproduct. Anoxygenic photosynthesis (performed by purple and green bacteria) uses other electron sources, like hydrogen sulfide, and does not produce oxygen.

P

PCR
Polymerase Chain Reaction — a laboratory technique that exponentially amplifies a specific segment of DNA through repeated cycles of heating and cooling (denature, anneal, extend), using a heat-stable DNA polymerase (Taq) to make millions of copies from a tiny starting sample, enabling rapid, sensitive detection of a pathogen's genetic material.
pentamer
A structure made of five identical subunits joined together — IgM circulates as a pentamer of five antibody units, giving it ten antigen-binding sites and making it extremely effective at agglutination even though each individual binding site has relatively low affinity.
Peptidoglycan
A mesh-like polymer of sugars and amino acids that forms the rigid bacterial cell wall, giving the cell its shape and protecting it from bursting due to osmotic pressure. Gram-positive bacteria have a thick peptidoglycan layer; Gram-negative bacteria have a much thinner layer, located between the plasma membrane and an additional outer membrane.
persister cell
A small subpopulation of bacterial cells, often found within biofilms, that enter a dormant, slow-metabolizing state. Because most antibiotics target active cellular processes, persister cells survive treatment even though they are not genetically resistant — they simply aren't 'awake' enough to be killed, and can repopulate the infection once treatment stops.
petechiae
Tiny, pinpoint, non-blanching red or purple spots on the skin caused by small blood vessel bleeding, classically associated with Neisseria meningitidis infection (meningococcemia) as a warning sign of a rapidly progressing, life-threatening illness.
phagocyte
An immune cell — such as a neutrophil or macrophage — specialized in engulfing (phagocytosing) and destroying pathogens, cellular debris, and other foreign material.
Phagocytosis
The process by which a phagocyte engulfs a pathogen or particle by surrounding it with its membrane, pulling it inside into a vesicle, and then destroying it using digestive enzymes and reactive molecules.
Phospholipid bilayer
The two-layered structure of phospholipid molecules that forms the basic framework of all cell membranes, with hydrophilic (water-loving) heads facing outward and hydrophobic (water-fearing) tails facing inward, described by the 'fluid mosaic model' because proteins float within this flexible lipid layer.
Photoautotroph
An organism that uses light as its energy source and fixes CO2 as its carbon source — the nutritional class of plants, algae, and cyanobacteria.
Photoheterotroph
An organism that captures energy from light but must obtain its carbon from pre-made organic molecules rather than fixing CO2 — an uncommon strategy seen in some purple and green non-sulfur bacteria.
phototroph/chemotroph
A phototroph captures energy from light (as plants and cyanobacteria do). A chemotroph obtains energy by breaking down chemical compounds, either organic (chemoorganotroph) or inorganic (chemolithotroph).
Planktonic
Describes bacteria existing as free-floating, individual cells suspended in a liquid environment, as opposed to being attached to a surface within a biofilm.
plasma cell
A fully differentiated B cell that functions as an antibody-secreting factory, producing large quantities of a single, specific antibody once a B cell has been activated by its matching antigen.
Plasmid
A small, circular piece of DNA, separate from the main bacterial chromosome, that replicates independently and often carries genes conferring useful traits such as antibiotic resistance. Plasmids can be transferred between bacterial cells, spreading these traits horizontally.
Point/frameshift mutation
A point mutation changes a single DNA base and may be silent (no amino acid change), missense (changes one amino acid), or nonsense (creates a premature stop codon). A frameshift mutation results from inserting or deleting a number of bases not divisible by three, shifting the reading frame for every codon downstream and typically scrambling the entire protein from that point on.
polycistronic mRNA
A single mRNA molecule that encodes multiple different proteins, each with its own start and stop signal, transcribed together from an operon — a feature common in bacteria but essentially absent in eukaryotes.
Positive-sense RNA (+ssRNA)
A viral RNA genome with the same sequence as mRNA, meaning host ribosomes can translate it directly into protein immediately upon entry — no extra enzyme needed first.
PPV/NPV
Positive predictive value (PPV) is the probability that a person who tests positive truly has the disease. Negative predictive value (NPV) is the probability that a person who tests negative truly does not. Unlike sensitivity and specificity, both values change depending on how common the disease is in the population being tested.
Prion
An infectious agent made entirely of misfolded protein, with no nucleic acid (DNA or RNA) at all. The abnormal prion protein (PrP) converts normal PrP molecules into the same misfolded shape on contact, causing a chain reaction that leads to progressive, fatal spongiform (sponge-like) degeneration of brain tissue, and resists standard sterilization methods.
probiotic
A live microorganism, typically a bacterium such as Lactobacillus, taken as a supplement or in fermented foods with the intent of restoring or supporting a healthy balance of gut microbiota.
Prophage
Bacteriophage DNA that has integrated into and become part of the host bacterium's chromosome during the lysogenic cycle, remaining dormant and being copied along with the host's own genes until it is triggered to re-enter the lytic cycle.
proton motive force
The stored energy of an electrochemical gradient of protons (H+) built up across a membrane, generated by the electron transport chain, which is then used to drive ATP synthesis (chemiosmosis) and, in some bacteria, to power flagellar rotation.
PrP
Prion protein — the normal cellular protein that, when misfolded, becomes the infectious prion. The disease-causing form is chemically identical in amino acid sequence to the normal form but folds into a different, self-propagating three-dimensional shape.
pseudomembranous colitis
A severe form of colitis caused by toxins from Clostridioides difficile, classically occurring after broad-spectrum antibiotic use disrupts the normal gut microbiota, allowing C. diff to overgrow; named for the characteristic yellow-white plaques ('pseudomembranes') that form on the inflamed colon lining.
pure culture
A population of microorganisms grown from a single original cell, containing only one species or strain, free of contaminants — a prerequisite for reliably identifying an organism or testing its properties.

Q

quorum sensing
A form of bacterial cell-to-cell communication in which cells release and detect a signaling molecule (autoinducer); once the population density (and therefore signal concentration) crosses a threshold, the whole population coordinately switches on group behaviors, such as forming a biofilm or releasing toxins together.

R

R-factor
A resistance plasmid — a plasmid that carries one or more genes conferring antibiotic resistance, which can spread that resistance to other bacteria through horizontal gene transfer (conjugation).
R0
The basic reproduction number — the average number of new infections one infected person generates in a fully susceptible population. An R0 greater than 1 means the outbreak is likely to grow; an R0 less than 1 means it is likely to shrink and eventually die out.
recombinant protein
A protein produced by genetically engineering a host organism (commonly E. coli or yeast) to carry and express a foreign gene — this technique is used to manufacture human proteins like insulin, growth hormone, and clotting factors at industrial scale.
repressor
A regulatory protein that binds to DNA (typically at an operator sequence) and physically blocks RNA polymerase from transcribing the downstream gene(s), turning that gene or operon off.
reservoir
The natural habitat where an infectious agent normally lives, grows, and multiplies — which may be a human, an animal, or the environment — and from which it can spread to a susceptible host.
Restriction enzyme
A bacterial enzyme that recognizes a specific, usually palindromic DNA sequence and cuts the DNA at or near that site. Bacteria naturally use these enzymes as a defense against invading viral DNA, but they are also a foundational tool in genetic engineering for cutting and splicing DNA.
reverse transcriptase
An enzyme, carried by retroviruses like HIV, that converts single-stranded RNA into double-stranded DNA — reversing the normal direction of the central dogma — so the viral genetic information can be inserted into the host cell's own chromosome.

S

Selective pressure
Any environmental factor (such as antibiotic exposure) that gives some individuals in a population a survival or reproductive advantage over others, causing the frequency of favorable traits (like resistance genes) to increase in the population over successive generations.
Selective toxicity
The principle that an ideal antimicrobial drug harms the target microbe while causing little or no harm to the host, achieved by targeting structures or processes unique to (or significantly different in) the pathogen compared to human cells.
selectively permeable
Describes a membrane that allows some substances to cross freely while restricting or completely blocking others, a property fundamental to the plasma membrane's ability to regulate what enters and leaves the cell.
Sensitivity
The proportion of people who truly have a disease that a test correctly identifies as positive. A highly sensitive test produces few false negatives, which is why sensitive tests are used for initial screening — you don't want to miss real cases.
sigma factor
A protein subunit that associates with bacterial RNA polymerase and directs it to recognize and bind specific promoter sequences, allowing transcription to begin at the correct starting point on the DNA.
Specificity
The proportion of people who truly do not have a disease that a test correctly identifies as negative. A highly specific test produces few false positives, which is why specific tests are used for confirmation after an initial positive screen.
spirochete
A distinctively shaped, flexible, corkscrew-spiraled bacterium that moves using internal flagella called axial filaments. Treponema pallidum (syphilis) and Borrelia (Lyme disease) are medically important spirochetes.
spongiform encephalopathy
A category of fatal, degenerative brain diseases caused by prions, in which the brain tissue develops a characteristic sponge-like appearance under the microscope due to the accumulation of misfolded protein and resulting neuronal loss — examples include Creutzfeldt-Jakob disease, kuru, and mad cow disease.
Spontaneous generation
A now-disproven historical theory that living organisms could arise directly from non-living matter (for example, that maggots simply appeared from rotting meat). Louis Pasteur's swan-neck flask experiments definitively disproved this idea and helped establish germ theory in its place.
standard precautions
A baseline set of infection-control practices — including hand hygiene, use of personal protective equipment, and safe handling of sharps — applied to the care of every patient regardless of known infection status, since any patient's blood or body fluids are treated as potentially infectious.
stationary phase
The phase of bacterial growth in which nutrients become depleted and waste products accumulate, causing the rate of new cell division to roughly equal the rate of cell death, so the total population size levels off rather than continuing to grow.
stewardship
Antimicrobial stewardship — the coordinated set of practices (prescribing the right drug, dose, and duration; discouraging unnecessary use) aimed at optimizing antibiotic use to treat infections effectively while slowing the development and spread of antimicrobial resistance.
superantigen
A toxin that bypasses the normal, highly specific process of antigen presentation and instead binds directly to and activates enormous numbers of T cells at once (regardless of their specific antigen receptor), triggering a massive, uncontrolled release of cytokines that can cause toxic shock.
Superoxide
A toxic, reactive form of oxygen produced as a natural byproduct of aerobic metabolism, capable of damaging cellular components; organisms living in oxygen must have enzymes (like superoxide dismutase) to detoxify it or they cannot survive.
superoxide dismutase
An enzyme that converts the toxic superoxide radical into hydrogen peroxide (which catalase can then further break down into water and oxygen), part of the detoxification system that allows organisms to safely live in the presence of oxygen.
surveillance
The ongoing, systematic collection and analysis of health data to detect and monitor patterns of disease in a population, allowing early identification of outbreaks and emerging threats so a public health response can be mounted quickly.

T

tape test
A simple diagnostic technique for pinworm infection in which a piece of clear adhesive tape is pressed against the skin around the anus (typically first thing in the morning) to collect eggs, which are then examined under a microscope.
Taq polymerase
A heat-stable DNA polymerase enzyme, originally isolated from the heat-loving bacterium Thermus aquaticus, that can withstand the repeated high-temperature denaturation steps of PCR without being destroyed — a discovery that made automated PCR practical.
target modification
An antibiotic resistance mechanism in which the bacterium alters the specific molecule the drug is designed to bind, so the drug can no longer attach effectively even though the bacterial process it would have blocked continues normally.
Thrush
A Candida yeast infection of the mouth and throat, appearing as white, adherent plaques on the tongue and oral mucosa, commonly seen in infants, immunocompromised patients, and after antibiotic use disrupts the normal oral microbiota.
thymine dimer
A type of DNA damage caused by ultraviolet light, in which two adjacent thymine bases on the same DNA strand become abnormally fused together, distorting the DNA helix and blocking normal replication and transcription unless repaired.
Titer
A measurement of the concentration of a specific antibody in a blood sample, typically expressed as the highest dilution at which the antibody can still be detected; rising titers over time can indicate an active or recent infection.
toxoid
An inactivated bacterial toxin that has been chemically or otherwise altered to remove its harmful, disease-causing activity while still retaining the antigenic shape needed to stimulate a protective immune response — the basis of vaccines against tetanus and diphtheria.
transduction
A form of horizontal gene transfer in which a bacteriophage (virus that infects bacteria) accidentally packages bacterial DNA instead of, or along with, its own genetic material, and transfers that DNA into the next bacterial cell it infects. Generalized transduction can transfer nearly any gene; specialized transduction transfers only genes located near where the phage DNA had integrated into the chromosome.
Transformation
A form of horizontal gene transfer in which a bacterium takes up naked DNA fragments directly from its surrounding environment (released, for example, when another cell dies and lyses) and incorporates them into its own genome. This was the mechanism demonstrated in Griffith's classic transformation experiment.
transposon
A mobile segment of DNA, sometimes called a 'jumping gene,' capable of copying or moving itself from one location in a genome to another, which can disrupt genes it inserts into or carry additional genes (including resistance genes) along with it.

U

urease
An enzyme that breaks urea down into ammonia and carbon dioxide, raising the local pH. Bacteria like Proteus that produce urease can alkalinize urine enough to promote the formation of struvite kidney stones.
Uropathogenic
Describes a strain of bacteria, most often a specific strain of E. coli, that has acquired specific virulence factors (like adhesins) allowing it to colonize and infect the urinary tract, making it the most common cause of urinary tract infections.

V

vaccine
A preparation containing an antigen (or the instructions to make one) designed to train the immune system to recognize and respond to a specific pathogen, so that if the real infection occurs later, the body can mount a fast, protective response before serious illness develops.
Vector
A living organism (typically an arthropod, like a mosquito or tick) that transmits an infectious agent from one host to another. See biological vs. mechanical vector for the distinction in how the pathogen behaves inside it.
Viral latency
A state in which a virus (classically a herpesvirus) persists inside host cells in a dormant, non-replicating form after the initial infection resolves, capable of reactivating later to cause recurrent disease — as seen when VZV reactivates from dorsal root ganglia to cause shingles.
viroid
A very small, naked (no protein coat), single-stranded circular RNA molecule that is infectious on its own — smaller and structurally simpler than a virus — and known to cause disease primarily in plants.
VRE
Vancomycin-resistant Enterococcus — a strain of Enterococcus that has altered its cell wall building block from D-alanine-D-alanine to D-alanine-D-lactate, which vancomycin can no longer bind effectively, allowing cell wall synthesis (and bacterial survival) to continue despite the drug's presence.

W

water activity
A measure of the amount of free, usable water available in a substance (like food), as opposed to water that is chemically bound and unavailable to microbes. Lowering water activity — through methods like salting, sugaring, or drying — is a classic food preservation technique because it deprives microbes of the water they need to grow.
Western blot
A laboratory technique that separates proteins by size using gel electrophoresis, then transfers them to a membrane and probes them with labeled antibodies to detect a specific target protein, producing a pattern of bands. It is often used as a highly specific confirmatory test following a positive screening test like ELISA.
Wobble
The relaxed, non-strict base-pairing allowed at the third position of a codon-anticodon match. Because the genetic code is degenerate (multiple codons can specify the same amino acid), wobble lets a single tRNA recognize more than one codon, reducing the total number of distinct tRNAs a cell needs.

Z

Zone of inhibition
The clear, bacteria-free ring that forms around an antibiotic-soaked disk on an agar plate in the Kirby-Bauer disk diffusion test; the diameter of this zone is measured and compared to a standardized chart to classify the organism as susceptible, intermediate, or resistant to that drug.
zoonosis/spillover
A zoonosis is a disease that can be transmitted from animals to humans. Spillover is the specific event of a pathogen jumping from its usual animal host into the human population for the first time, often driven by factors like deforestation, close human-animal contact, and travel that increase opportunities for exposure.
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