Microbiology Essentials: 300 Terms You Get Tested On

Most marks are lost between two organisms that look alike on one test and differ on another.

300 cardsLast updated 2026-08-31

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A negative Gram stain does not exclude mycobacteria, because their waxy wall resists the stain entirely. A positive result on an old culture does not confirm a gram-positive organism either, because older cells decolourise. Microbiology is full of tests that answer one question and quietly fail at another, and knowing which is which is most of the subject. This deck is 300 cards, one organism group, structure, process or technique per card, with the back cut into three fixed lines. "Meaning" defines it in a sentence. "Detail" gives the structure, mechanism or method that makes it identifiable. "Watch for" names the organism or term it is confused with. The sections run from cell structure and staining through growth and metabolism, microbial genetics, control of microbes, viruses, fungi and parasites, and host interaction and immunity. No doses or treatment recommendations appear anywhere. The deck covers mechanisms of action, targets and resistance, which is what examinations test and what stays true regardless of local guidance. Once it is on a spaced-repetition schedule, the organisms you can already separate stop coming back and the pairs you keep confusing return until they stop being guesswork.

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What's inside

Showing 100 representative cards from the full 300-card deck.

Front	Back
Prokaryotic cell	Meaning: A cell without a membrane-bound nucleus or organelles. Detail: Its DNA sits in a nucleoid region and its ribosomes are smaller than eukaryotic ones. Watch for: Prokaryotic does not mean simple. Prokaryotes have highly organised internal structure.
Coccus	Meaning: A spherical bacterial cell. Detail: Arrangements include pairs, chains and clusters, depending on the plane of division. Watch for: Arrangement is a clue to identity, so it must be recorded along with shape.
Spirillum and spirochete	Meaning: Two kinds of helical bacterial cell. Detail: A spirillum is rigid with external flagella, while a spirochete is flexible with internal filaments. Watch for: The difference in motility structure is what separates them, not the degree of coiling.
Peptidoglycan	Meaning: The polymer that gives bacterial cell walls their strength. Detail: It consists of sugar chains cross-linked by short peptides. Watch for: It is found in bacteria but not in archaea, fungi or human cells.
Lipopolysaccharide	Meaning: A molecule in the outer membrane of gram-negative bacteria. Detail: Its lipid A portion is the endotoxin that triggers strong inflammation. Watch for: It is released mainly when the cell dies, not secreted during growth.
Acid-fast cell wall	Meaning: A wall containing large amounts of waxy mycolic acid. Detail: It resists staining and decolourisation by acid alcohol. Watch for: These organisms stain poorly by the Gram method, so a negative Gram result does not exclude them.
Capsule	Meaning: A well-organised polysaccharide layer outside the cell wall. Detail: It helps the organism resist being engulfed by immune cells. Watch for: A capsule is not a slime layer, which is loose and easily washed away.
Flagellar arrangements	Meaning: The pattern of flagella on a bacterial cell. Detail: Terms describe a single polar flagellum, tufts at the poles, or flagella all over. Watch for: Arrangement is a taxonomic feature and does not indicate how fast the cell moves.
Fimbriae	Meaning: Short hair-like appendages used for attachment. Detail: They allow bacteria to adhere to surfaces and host cells. Watch for: Fimbriae are for attachment, not motility, and are far more numerous than flagella.
Endospore	Meaning: A dormant, highly resistant structure formed inside certain bacteria. Detail: It survives heat, drying, radiation and many chemicals. Watch for: An endospore is a survival structure, not a means of reproduction.
Germination	Meaning: The return of an endospore to an actively growing cell. Detail: It is triggered by favourable conditions and by damage to the spore coat. Watch for: A germinating cell loses its resistance, which is the basis of some sterilisation methods.
Nucleoid	Meaning: The region of a prokaryotic cell containing the chromosome. Detail: It is not enclosed by a membrane. Watch for: It is a region, not an organelle, and has no defined boundary.
Plasmid	Meaning: A small circular DNA molecule separate from the chromosome. Detail: It often carries genes for resistance or virulence. Watch for: Plasmids are usually not essential for growth, which is why they can be lost.
Simple stain	Meaning: A staining method using one dye to make cells visible. Detail: It reveals shape, size and arrangement. Watch for: It gives no information about cell wall type or internal structure.
Gram stain	Meaning: The most widely used differential stain in bacteriology. Detail: Crystal violet, iodine, decolouriser and safranin are applied in that order. Watch for: Over-decolourisation makes gram-positive cells appear gram-negative.
Endospore stain	Meaning: A stain that reveals endospores within or outside cells. Detail: Heat drives the primary stain into the spore, and the cell is counterstained. Watch for: Unstained spores appear as clear areas in a simple stain, which can be mistaken for artefacts.
Flagella stain	Meaning: A method that thickens flagella so they become visible. Detail: A mordant builds up on the filament before staining. Watch for: Flagella are too thin to see with ordinary stains, so absence in a simple stain proves nothing.
Brightfield microscopy	Meaning: Microscopy in which specimens appear dark against a bright background. Detail: It is the standard method for stained preparations. Watch for: Unstained cells have too little contrast to be seen well this way.
Phase contrast microscopy	Meaning: Microscopy that converts differences in refractive index into contrast. Detail: It allows internal structures of living cells to be seen without staining. Watch for: It is not the same as darkfield, which relies on scattered light alone.
Electron microscopy	Meaning: Microscopy using a beam of electrons instead of light. Detail: Its far greater resolution reveals viruses and internal ultrastructure. Watch for: Specimens must be processed and cannot be viewed alive.
Immersion oil	Meaning: Oil placed between the slide and the highest power objective. Detail: It has the same refractive index as glass and prevents light being lost. Watch for: Using the oil objective without oil gives a blurred image that cannot be focused.
Binary fission	Meaning: The division of one bacterial cell into two. Detail: The chromosome is replicated and the cell divides by forming a septum. Watch for: It produces two cells of equal size, unlike budding in some yeasts.
Bacterial growth curve	Meaning: The pattern of population change in a closed culture. Detail: It has lag, log, stationary and death phases. Watch for: The curve describes a batch culture, so a continuous culture behaves differently.
Stationary phase	Meaning: The period when new cells balance dying cells. Detail: Nutrients are depleted and waste products accumulate. Watch for: The total count stays level while the viable count begins to fall.
Continuous culture	Meaning: A system in which fresh medium is added and culture removed continuously. Detail: It holds the population in the log phase indefinitely. Watch for: It requires balancing flow rate against growth rate, or the culture washes out.
Obligate aerobe	Meaning: An organism that requires oxygen for growth. Detail: It uses oxygen as the final electron acceptor in respiration. Watch for: It grows only at the surface of a liquid medium tube.
Aerotolerant anaerobe	Meaning: An organism that does not use oxygen but is not harmed by it. Detail: It ferments regardless of whether oxygen is present. Watch for: It grows evenly throughout a tube, unlike a facultative anaerobe.
Psychrophile	Meaning: An organism that grows best at low temperatures. Detail: Its enzymes and membranes function in the cold. Watch for: It can spoil refrigerated food, so refrigeration slows but does not stop all growth.
Thermophile	Meaning: An organism that grows best at high temperatures. Detail: Its proteins and membranes are stabilised against heat. Watch for: Thermophiles do not cause human infection, since body temperature is too low for them.
Acidophile and alkaliphile	Meaning: Organisms adapted to low and high pH. Detail: They maintain a near-neutral internal pH despite the external value. Watch for: Most bacteria are neutrophiles, so extreme pH values inhibit them.
Halophile	Meaning: An organism that requires high salt concentrations. Detail: It maintains internal solute levels that match the environment. Watch for: Salt-tolerant organisms are not necessarily halophiles, which require salt rather than tolerate it.
Complex medium	Meaning: A medium whose exact chemical composition is not known. Detail: It contains extracts and digests that supply many nutrients. Watch for: Batch to batch variation makes it unsuitable for precise nutritional studies.
Differential medium	Meaning: A medium that makes colonies of different organisms look different. Detail: Indicators reveal fermentation or enzyme activity. Watch for: A medium can be both selective and differential, and the two roles must be identified separately.
Streak plate	Meaning: A method for obtaining isolated colonies from a mixture. Detail: Successive strokes dilute the sample across the agar surface. Watch for: A colony arises from one cell only if separation was successful.
Colony forming unit	Meaning: A unit representing one viable cell or clump that produces a colony. Detail: It is used to express viable counts from plate methods. Watch for: A clump of cells produces one colony, so counts underestimate cell number.
Direct microscopic count	Meaning: Counting cells in a known volume under the microscope. Detail: It is rapid and requires no incubation. Watch for: It counts living and dead cells together unless a viability stain is used.
Chemoheterotroph	Meaning: An organism using organic compounds for both energy and carbon. Detail: Most bacteria of medical importance belong to this group. Watch for: It contrasts with autotrophs, which use inorganic carbon.
Photoautotroph	Meaning: An organism using light for energy and carbon dioxide for carbon. Detail: Cyanobacteria and algae are the main microbial examples. Watch for: Photosynthetic bacteria do not all produce oxygen.
Glycolysis	Meaning: The pathway converting glucose into pyruvate. Detail: It yields a small amount of energy and occurs with or without oxygen. Watch for: It is the shared starting point for both fermentation and respiration.
Fermentation end products	Meaning: The organic compounds produced by different fermentation pathways. Detail: Acids, alcohols and gases vary by organism and are used in identification. Watch for: Detecting acid production requires an indicator, since the product itself is invisible.
Anaerobic respiration	Meaning: Respiration using an inorganic molecule other than oxygen as the final acceptor. Detail: Nitrate and sulphate are common acceptors. Watch for: It is respiration, not fermentation, because an electron transport chain is used.
Catabolism and anabolism	Meaning: The breakdown of molecules for energy and the building of new ones. Detail: Catabolism supplies the energy and building blocks anabolism needs. Watch for: The two occur simultaneously, not in alternating phases.
Bacterial chromosome	Meaning: A single circular DNA molecule carrying the essential genes. Detail: It is supercoiled and packed into the nucleoid region. Watch for: A few bacteria have linear or multiple chromosomes, so the circular form is typical rather than universal.
R plasmid	Meaning: A plasmid carrying genes for antimicrobial resistance. Detail: It often carries several resistance genes together. Watch for: Transfer of one plasmid can confer resistance to several unrelated agents at once.
Bacterial DNA replication	Meaning: Copying of the circular chromosome from a single origin. Detail: Two forks proceed in opposite directions and meet on the far side. Watch for: One origin serves the whole chromosome, unlike in eukaryotes.
Spontaneous mutation rate	Meaning: The frequency of mutations arising without an external agent. Detail: It is low per gene but significant across a large population. Watch for: A culture of billions of cells will contain mutants even without any mutagen.
Frameshift mutation	Meaning: An insertion or deletion that shifts the reading frame. Detail: It usually abolishes the function of the encoded protein. Watch for: It has a far larger effect than a substitution at the same position.
Ames test	Meaning: A test using bacteria to screen chemicals for mutagenic activity. Detail: Reversion of a mutant strain indicates mutagenic potential. Watch for: It detects mutagenicity, which correlates with but does not prove carcinogenicity.
Replica plating	Meaning: A technique transferring colony patterns from one plate to another. Detail: It identifies mutants that fail to grow under a particular condition. Watch for: It was used to show that mutations arise before exposure to the selecting agent.
Horizontal gene transfer	Meaning: The movement of genetic material between organisms other than by descent. Detail: It spreads resistance and virulence genes rapidly through populations. Watch for: It differs from vertical transfer, which passes genes to offspring.
Competence	Meaning: The physiological state allowing a cell to take up external DNA. Detail: Some species develop it naturally at particular growth stages. Watch for: Laboratory treatments can force competence in species that lack it naturally.
Generalised transduction	Meaning: Transduction in which any part of the host chromosome can be transferred. Detail: Random fragments are packaged during virus assembly. Watch for: Any gene can move, unlike in specialised transduction.
Conjugation	Meaning: The transfer of DNA between bacteria through direct contact. Detail: A sex pilus draws the cells together and plasmid DNA passes across. Watch for: Conjugation requires cell contact, unlike transformation.
Transposon	Meaning: A DNA segment that can move to a new location in a genome. Detail: It often carries additional genes such as resistance determinants. Watch for: It moves within and between DNA molecules, so it is not confined to one chromosome.
Integron	Meaning: A genetic element that captures and expresses gene cassettes. Detail: It accumulates multiple resistance genes under one promoter. Watch for: It is a capture system, not a mobile element in itself, although it often sits on one.
Intrinsic resistance	Meaning: Resistance that is a natural property of a species. Detail: It arises from features such as an impermeable outer membrane. Watch for: It is not acquired, so it is present in every member of the species.
Efflux pump	Meaning: A membrane protein that expels compounds from the cell. Detail: Some pumps export many unrelated agents. Watch for: A single pump can produce resistance to several drug classes at once.
Genome sequencing in microbiology	Meaning: Determining the complete DNA sequence of an isolate. Detail: It identifies species, resistance genes and outbreak relationships. Watch for: Carrying a resistance gene does not always mean the gene is expressed.
Sterilisation	Meaning: The removal or destruction of all microorganisms including endospores. Detail: It is the standard required for surgical instruments and culture media. Watch for: Sterile is an absolute term. Almost sterile is not sterilisation.
Sanitisation	Meaning: Reducing microbial numbers to a level judged safe by public health standards. Detail: It is applied to food service and other everyday equipment. Watch for: The standard is a defined reduction, not the elimination of all organisms.
Decimal reduction time	Meaning: The time required to kill ninety percent of a population. Detail: It allows treatments to be compared quantitatively. Watch for: Microbial death is exponential, so no finite time gives absolute certainty of sterility.
Moist heat sterilisation	Meaning: The use of steam under pressure to kill microorganisms. Detail: Steam denatures proteins far faster than dry air at the same temperature. Watch for: Water must reach every surface, so packing and loading matter as much as time.
Dry heat sterilisation	Meaning: Sterilisation using hot air rather than steam. Detail: It requires higher temperatures and longer times than moist heat. Watch for: It is used for materials that steam would damage, such as powders and oils.
Desiccation	Meaning: The removal of water to prevent microbial growth. Detail: It is used to preserve food and to store cultures. Watch for: Many organisms survive drying and revive when moisture returns.
HEPA filtration	Meaning: High efficiency filtration of air to remove particles and organisms. Detail: It is used in safety cabinets and clean rooms. Watch for: It removes organisms from air but does not kill them, so filters remain contaminated.
Phenolics	Meaning: A group of disinfectants that disrupt membranes and denature proteins. Detail: They remain active in the presence of organic matter. Watch for: Their strong odour and tissue irritation limit where they can be used.
Aldehydes	Meaning: Agents that cross-link proteins and nucleic acids. Detail: They are among the few chemicals that can achieve sterilisation. Watch for: Their toxicity and irritant vapour require careful handling and ventilation.
Antimicrobial drug	Meaning: A substance used to treat infection by inhibiting or killing microorganisms. Detail: It must show selective toxicity toward the pathogen. Watch for: Selective toxicity is hardest to achieve against eukaryotic pathogens.
Nucleic acid synthesis inhibitors	Meaning: Agents that block bacterial DNA replication or transcription. Detail: They target enzymes that differ from the human equivalents. Watch for: Single point mutations in the target enzyme readily confer resistance.
Disc diffusion susceptibility test	Meaning: A method measuring the zone of inhibition around an impregnated disc. Detail: Zone diameters are compared with standard interpretive criteria. Watch for: A larger zone does not always mean a better clinical choice, since criteria differ by agent.
Virus	Meaning: An obligate intracellular agent consisting of nucleic acid in a protein coat. Detail: It has no metabolism of its own and replicates only inside a host cell. Watch for: A virus is not a cell and cannot be cultured on agar.
Naked virus	Meaning: A virus without a lipid envelope. Detail: It survives longer in the environment and resists disinfectants better. Watch for: Alcohol-based agents are less reliable against these viruses.
Attachment	Meaning: The binding of a virus to a specific receptor on the host cell. Detail: It is the first and most specific step of infection. Watch for: Binding requires a matching receptor, which is why viruses show tissue preferences.
Eclipse period	Meaning: The interval when no infectious virus can be recovered from the cell. Detail: It corresponds to the biosynthesis stage. Watch for: The virus is present but disassembled, so absence of particles does not mean absence of infection.
Bacteriophage	Meaning: A virus that infects bacteria. Detail: It attaches to the bacterial surface and injects its genome. Watch for: The phage particle itself does not enter the cell in many cases.
Prophage	Meaning: A phage genome integrated into a bacterial chromosome. Detail: It is inherited by daughter cells during division. Watch for: It can carry toxin genes, so its presence may change the pathogenicity of the host.
Latency	Meaning: The persistence of a virus in a cell without producing new particles. Detail: The genome remains in the cell and can reactivate later. Watch for: The absence of symptoms does not mean the virus has been cleared.
Antigenic drift	Meaning: Gradual change in viral surface proteins from accumulated mutations. Detail: It allows a virus to escape existing immunity over time. Watch for: It produces small yearly changes rather than a sudden new virus.
Prion	Meaning: An infectious protein particle containing no nucleic acid. Detail: It converts normal host protein into the misfolded form. Watch for: It resists heat and chemicals that destroy conventional organisms.
Fungal cell structure	Meaning: The features of a eukaryotic fungal cell. Detail: The wall contains chitin and the membrane contains ergosterol. Watch for: Fungal walls contain no peptidoglycan, so cell wall agents used against bacteria do not work.
Dimorphic fungus	Meaning: A fungus that grows as a mould or a yeast depending on temperature. Detail: It grows as a mould in the environment and as a yeast in tissue. Watch for: Culture at the wrong temperature gives a misleading appearance.
Protozoa	Meaning: Single-celled eukaryotic organisms, many of which are motile. Detail: They are classified partly by their means of movement. Watch for: They are not fungi or bacteria and require different culture approaches.
Helminth	Meaning: A parasitic worm. Detail: Groups include roundworms, tapeworms and flukes. Watch for: Helminths are multicellular animals, so they are not microorganisms in the strict sense.
Definitive host	Meaning: The host in which a parasite reaches sexual maturity. Detail: It is used to define the parasite's life cycle stages. Watch for: The definitive host is not necessarily the host that suffers most.
Biological and mechanical vectors	Meaning: Vectors in which the pathogen develops and those that merely carry it. Detail: In a biological vector the pathogen multiplies or matures. Watch for: A mechanical vector transports the pathogen unchanged, as on its body surface.
Ova and parasite examination	Meaning: Microscopic examination of stool for parasite stages. Detail: Eggs and cysts are identified by size, shape and internal structure. Watch for: Shedding is intermittent, so several specimens may be needed.
Normal microbiota	Meaning: The community of microorganisms that normally live on and in the body. Detail: It competes with pathogens and helps train the immune system. Watch for: Its presence in a specimen does not indicate infection.
Pathogenicity and virulence	Meaning: The ability to cause disease and the degree of that ability. Detail: Virulence is measured by the dose required to cause disease or death. Watch for: Pathogenicity is a yes or no property, while virulence is a matter of degree.
Adhesion	Meaning: The attachment of a pathogen to host cells. Detail: Adhesins on fimbriae and surface proteins bind specific receptors. Watch for: Without adhesion most pathogens are removed before they can multiply.
Coagulase	Meaning: An enzyme that causes plasma to clot. Detail: The clot walls off the organism from immune cells. Watch for: It is also a laboratory test result, and a positive test is used for identification.
Exotoxin	Meaning: A protein toxin secreted by a living bacterium. Detail: It is often highly specific and active in tiny amounts. Watch for: Exotoxins are produced by both gram-positive and gram-negative organisms.
Neurotoxin	Meaning: An exotoxin acting on the nervous system. Detail: It interferes with the transmission of nerve signals. Watch for: The site of action is remote from where the organism grows.
First line of defence	Meaning: The physical and chemical barriers that prevent entry. Detail: Intact skin, mucus, cilia and secretions all contribute. Watch for: Breaching these barriers, as by a catheter, bypasses the strongest defence.
Inflammation	Meaning: The tissue response to injury or infection. Detail: Redness, heat, swelling and pain follow increased blood flow and permeability. Watch for: Inflammation is protective, although excessive inflammation causes damage.
Adaptive immunity	Meaning: The specific defence that develops after exposure to an antigen. Detail: It is specific, has memory and takes days to develop. Watch for: Its slower onset is why innate immunity must hold the infection at first.
Cell-mediated immunity	Meaning: Immunity mediated by T cells acting directly on infected cells. Detail: It is essential against intracellular pathogens. Watch for: It does not involve antibodies, so antibody tests may not reflect it.
Antibody	Meaning: A protein produced by B cells that binds a specific antigen. Detail: It neutralises toxins, tags organisms for phagocytosis and activates complement. Watch for: Antibodies rarely kill organisms directly, and mostly mark them for other mechanisms.
Active and passive immunity	Meaning: Immunity produced by the person's own response and immunity transferred from elsewhere. Detail: Active immunity lasts far longer because memory cells are formed. Watch for: Passive immunity acts immediately but fades as the transferred antibodies are cleared.
Incidence and prevalence	Meaning: The number of new cases and the total number of cases at a time. Detail: Incidence measures risk while prevalence measures burden. Watch for: A long-lasting disease has high prevalence even with low incidence.
Healthcare-associated infection	Meaning: An infection acquired in a healthcare setting. Detail: Invasive devices, procedures and resistant organisms all contribute. Watch for: The organisms responsible are often part of the patient's own flora.

Frequently asked

What is in each section of the deck?

Cell structure and staining has 50 cards, growth and metabolism 50, microbial genetics 45, control of microbes 45, viruses, fungi and parasites 55, and host interaction and immunity 55, for 300 in total. Every card carries section and subtopic tags, so you can drill only staining or only immunity.

Is this a clinical microbiology deck?

No. It covers the science that clinical practice rests on, including virulence factors, resistance mechanisms and susceptibility testing, but it contains no doses, no regimens and no treatment advice. Clinical decisions depend on local guidance and on a patient in front of you, neither of which belongs on a flashcard.

Who is it aimed at?

Students taking an introductory microbiology course, including those on nursing, laboratory science and biology programmes. The vocabulary is standard across those courses, so the deck transfers even where the syllabus order differs from the section order used here.

Can I import the whole deck on the free plan?

Yes. Importing a saved deck runs no new AI generation and spends no AI credits, so the free plan imports all 300 cards. You can study, edit and delete them afterwards.

Will importing it twice create duplicates?

No. Cards you already have are skipped and only cards added in a revision come through. Including re-imports after deleting it, one official deck can be imported three times per account.

Can I use it on the web and in the mobile app?

Yes. The deck is added to your account rather than to a device, so the same cards and the same progress are there on the web, on iOS and on Android.

Can I edit the cards after importing?

Yes. Imported cards are yours: you can edit both sides, delete cards you do not need, change tags, and move cards to another deck.