Memly's USMLE Step 1 Microbiology: 300 Organism Cards

300 organisms by structure, virulence and how they are identified.

300 cardsLast updated 2026-08-21

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Microbiology collapses into a list of names unless each organism carries a small set of features that separate it from the one next to it. Catalase splits the gram-positive cocci, coagulase splits the staphylococci, and novobiocin splits what is left. Non-septate hyphae branching at wide angles is a different mold from septate hyphae branching at acute ones. Narrow-based budding with a capsule is a different yeast from broad-based budding without one. Learn the discriminating feature and the name follows. Learn the name first and you have a list. That is how these 300 cards are built. Every one opens with a classification or a definition, and beyond that the fields follow what the organism actually turns on: where two organisms are routinely mixed up, the card names the other one and says which single feature separates them. The weighting is 146 cards of bacteriology including 31 on laboratory identification alone, 74 on virology, 30 on parasites, 28 on fungi, and 22 on immunology and host defence patterns. Antimicrobials are not here. Mechanism, spectrum and adverse effects live in the Pharmacology Drug Classes deck, so the two fit together without repeating a card: this deck is the organism, that one is the agent. Cards are tagged by group and by sub-group, so you can drill just the gram negatives, just the DNA viruses, or just the helminths. Import it and the deck joins your spaced-repetition schedule, and what you end up with is the thing the subject is really testing: given a stain, a plate, and a growth condition, being able to say what it is and why.

What happens when you add it

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The button opens Memly and the whole deck lands in your account.
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Each card gets its own schedule, based on how well you actually recall it.
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They are your cards afterwards — rewrite, delete or reorganize them freely.

What's inside

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

Front	Back
Gram stain principle — what is it?	A differential stain separating bacteria by how well the cell wall retains crystal violet after an alcohol wash. The result is a property of wall structure, so it also predicts susceptibility to agents that act on the wall.
Periplasmic space — what is it?	The compartment between inner and outer membranes of a gram-negative cell, containing peptidoglycan and secreted enzymes. Beta-lactamases accumulate here, so an enzyme released into this space reaches its target before the agent does.
Catalase test — what is it?	Detection of the enzyme converting hydrogen peroxide to water and oxygen, seen as bubbling.
Optochin sensitivity — what is it?	A disc test separating alpha-hemolytic streptococci.
Bile solubility — what is it?	Lysis of an organism by bile salts, which activate its own autolysin.
Urease test — what is it?	Detection of the enzyme splitting urea into ammonia and carbon dioxide, raising the pH of the medium.
Citrate utilization — what is it?	Growth using citrate as the sole carbon source, raising the pH and turning the medium blue.
Chocolate agar — what is it?	Blood agar heated to lyse the red cells, releasing factor V and factor X.
Lowenstein-Jensen medium — what is it?	An egg-based selective medium for mycobacteria. Mycobacterial growth is very slow, so culture takes weeks rather than the overnight of routine bacteriology.
Obligate aerobe — what is it?	An organism requiring oxygen as its terminal electron acceptor.
Microaerophile — what is it?	An organism growing best at oxygen concentrations below atmospheric.
Staphylococcus aureus — what is it?	Gram-positive cocci in clusters, catalase positive and coagulase positive, beta hemolytic.
Staphylococcus saprophyticus — what is it?	Gram-positive cocci in clusters, catalase positive, coagulase negative, novobiocin resistant. Staphylococcus epidermidis, from which novobiocin separates it.
Streptococcus pyogenes — what is it?	Gram-positive cocci in chains, catalase negative, beta hemolytic, bacitracin sensitive, Lancefield group A.
Viridans streptococci — what is it?	Gram-positive cocci in chains, alpha hemolytic, optochin resistant, not bile soluble.
M protein — what is it?	A surface protein of group A streptococci extending from the cell wall.
Rheumatic fever mechanism — what is it?	Immune-mediated damage following group A streptococcal pharyngitis, attributed to antibodies cross-reacting with host tissue. The damage is immunological rather than infectious, which is why it appears weeks after the infection has cleared.
Bacillus anthracis — what is it?	Gram-positive spore-forming aerobic rod with a polypeptide capsule of D-glutamate.
Clostridium tetani — what is it?	Gram-positive spore-forming obligate anaerobe with a terminal spore.
Botulinum toxin mechanism — what is it?	A protease cleaving vesicle fusion proteins at the neuromuscular junction, preventing acetylcholine release. Tetanospasmin, which uses the same chemistry on the same protein family but acts on inhibitory neurons, so the two toxins produce opposite pictures.
Clostridioides difficile — what is it?	Gram-positive spore-forming obligate anaerobe. Its spores resist alcohol, which is why physical removal rather than alcohol matters for hand hygiene.
Diphtheria toxin mechanism — what is it?	An AB toxin that ADP-ribosylates elongation factor 2, halting protein synthesis. Exotoxin A of Pseudomonas aeruginosa, which modifies the same target by the same chemistry in an unrelated organism.
Actin rocket motility — what is it?	Polymerization of host actin at one pole of an intracellular bacterium, propelling it into the neighbouring cell. The organism never enters the extracellular space, so antibody has limited access to it.
Actinomyces israelii — what is it?	Gram-positive branching filamentous rod, anaerobic, not acid fast.
Spore-forming gram-positive rods — what is it?	The genera Bacillus and Clostridium, separated by oxygen requirement. Spores survive heat, drying, and many disinfectants, so the organisms persist in environments that would clear vegetative bacteria.
Neisseria meningitidis — what is it?	Gram-negative diplococci, oxidase positive, maltose and glucose fermenting, grown on Thayer-Martin.
Neisseria species compared — what is it?	Both are oxidase-positive gram-negative diplococci. The meningococcus ferments maltose and has a polysaccharide capsule, the gonococcus does neither. Capsule presence explains why one has a polysaccharide-based vaccine and the other does not.
Bordetella pertussis — what is it?	Gram-negative coccobacillus, highly fastidious, grown on charcoal-containing media.
Legionella pneumophila — what is it?	Gram-negative rod staining poorly, requiring iron and cysteine, grown on charcoal yeast extract.
Enterobacteriaceae common features — what is it?	Gram-negative rods that are oxidase negative, ferment glucose, and reduce nitrate. A negative oxidase result on a gram-negative rod points to this family, which is the first branch in enteric identification.
Enterohemorrhagic Escherichia coli — what is it?	A strain carrying shiga-like toxin, most recognized as serotype O157:H7.
Uropathogenic Escherichia coli — what is it?	Strains carrying P fimbriae that bind uroepithelial receptors. Adherence against urine flow is the limiting step, so the fimbria rather than a toxin defines this group.
Proteus mirabilis — what is it?	Gram-negative rod, non-lactose fermenting, highly motile with swarming growth, strongly urease positive. Urease raises urinary pH, which favours precipitation of struvite stones, so the enzyme links the organism to stone formation.
Non-typhoidal Salmonella — what is it?	Gram-negative rod, non-lactose fermenting, motile, hydrogen sulfide producing. Shigella, which is non-motile, produces no hydrogen sulfide, and has a human-only reservoir.
Yersinia enterocolitica — what is it?	Gram-negative rod growing at cold temperatures. It can inflame mesenteric lymph nodes, producing a picture that has been described as resembling appendicitis.
Vibrio cholerae — what is it?	Comma-shaped gram-negative rod, oxidase positive, growing in alkaline media.
Campylobacter jejuni — what is it?	Comma or S-shaped gram-negative rod, oxidase positive, microaerophilic, growing at higher than usual incubation temperature. It is a recognized antecedent of an immune-mediated demyelinating neuropathy through molecular mimicry.
Pseudomonas aeruginosa — what is it?	Gram-negative rod, oxidase positive, non-lactose fermenting, obligate aerobe, producing blue-green pigments and a grape-like odour.
Brucella — what is it?	Small gram-negative coccobacillus, facultative intracellular within macrophages. Intracellular survival produces an undulating fever pattern and a prolonged course.
Bartonella henselae — what is it?	Gram-negative rod.
Endotoxin — what is it?	Lipopolysaccharide in the outer membrane of gram-negative bacteria, released on cell lysis. Exotoxin, which is secreted, protein, heat labile, and often has a specific molecular target.
Lipid A — what is it?	The membrane-anchored lipid portion of lipopolysaccharide, and the component responsible for its biological activity. The toxic effects are host-derived, coming from the immune response lipid A provokes rather than from direct damage.
Superantigen — what is it?	A toxin cross-linking a class II molecule and the T cell receptor outside the normal antigen groove. It activates a large fraction of T cells regardless of specificity, so the damage is cytokine-driven rather than caused by the toxin itself.
Type III secretion system — what is it?	A needle-like apparatus injecting bacterial proteins directly into a host cell cytoplasm. Delivery bypasses the extracellular space entirely, so antibody cannot intercept the effector.
Mycobacterium tuberculosis — what is it?	Acid-fast rod, obligate aerobe, slow growing on Lowenstein-Jensen medium.
Cord factor — what is it?	A mycobacterial surface glycolipid causing organisms to grow in parallel cords.
Latent tuberculosis — what is it?	Persistence of viable organisms within granulomas without active disease, held in check by cell-mediated immunity. Loss of that immunity allows reactivation, which is why the balance rather than the organism determines the state.
Mycobacterium leprae — what is it?	Acid-fast rod that cannot be grown on artificial media, preferring cool body regions. The disease form follows the host response, with strong cell-mediated immunity limiting the organism and weak responses allowing extensive multiplication.
Treponema pallidum — what is it?	Spirochete too thin to be seen on Gram stain, visualized by darkfield microscopy, not culturable on artificial media. Its outer membrane carries few surface proteins, which is one explanation offered for its persistence despite an antibody response.
Borrelia recurrentis — what is it?	Spirochete transmitted by the body louse.
Mycoplasma pneumoniae — what is it?	The smallest free-living bacteria, with no cell wall and sterols in the membrane, growing slowly on enriched media. Having no peptidoglycan, it is unaffected by agents acting on the cell wall and is invisible on Gram stain.
Chlamydia trachomatis — what is it?	Obligate intracellular bacterium that cannot make its own ATP. Its wall lacks classical muramic acid, which is part of why it behaves unlike a typical gram-negative organism.
Chlamydophila psittaci — what is it?	Obligate intracellular bacterium.
Typhus group rickettsiae — what is it?	Rickettsia prowazekii transmitted by the body louse and Rickettsia typhi by the rat flea. Spotted fever, whose rash starts peripherally. The typhus rash characteristically begins centrally and spreads outward.
Biofilm — what is it?	A community of bacteria embedded in a self-produced polysaccharide matrix on a surface. Organisms inside divide slowly and are shielded from both phagocytes and diffusion, so the state rather than the species explains persistence.
Siderophores — what is it?	Secreted molecules that bind iron with very high affinity and are taken back up by the organism. The host withholds iron by binding it to transferrin and lactoferrin, so siderophore production is a counter to that defence.
Bacterial flagella — what is it?	A rotating filament of flagellin driven by the proton gradient, giving directed motility. Flagellin is strongly immunogenic and is recognized by innate receptors, so motility carries a cost in detection.
Catalase as a virulence factor — what is it?	A bacterial enzyme degrading hydrogen peroxide. It neutralizes part of the phagocyte oxidative burst, which is why catalase-positive organisms are the ones that trouble hosts whose phagocytes cannot generate that burst.
Facultative versus obligate intracellular bacteria — what is it?	Facultative organisms can grow inside or outside host cells, while obligate ones cannot be cultured without them. Both groups are controlled by cell-mediated rather than antibody-mediated immunity.
Viral genome classification — what is it?	Viruses grouped by nucleic acid type, strandedness, and sense, since those determine what must happen before proteins can be made. The grouping predicts whether the virus must carry its own polymerase, which is a structural requirement rather than a naming convention.
Viral uncoating — what is it?	Release of the genome from the capsid after entry, often triggered by endosomal acidification. The genome is inaccessible until this step, so anything blocking endosomal acidification blocks replication before transcription begins.
Negative-sense RNA genome — what is it?	A genome complementary to messenger RNA, which must be transcribed before anything can be translated. Host cells have no enzyme that copies RNA into RNA, so the virus must carry its own polymerase inside the particle.
Antigenic drift — what is it?	Gradual accumulation of point mutations in surface protein genes. It produces small annual changes, which is why immunity from a previous season is partial rather than absent.
Cytopathic effect — what is it?	Visible change in infected cells in culture, including rounding, fusion into multinucleate cells, or lysis. It is how viral growth was detected before molecular methods, and the pattern of change differs between virus families.
DNA virus general features — what is it?	Most are double stranded, linear or circular, and replicate in the nucleus using host machinery. The exceptions are the examinable part, since the general rule follows from needing host nuclear enzymes.
Varicella zoster virus — what is it?	Enveloped double-stranded DNA herpesvirus.
Human herpesvirus 8 — what is it?	Enveloped double-stranded DNA herpesvirus.
Human papillomavirus — what is it?	Non-enveloped double-stranded circular DNA virus.
RNA virus general features — what is it?	Most replicate in the cytoplasm and lack proofreading, so mutation rates are far higher than for DNA viruses. High mutation rate underlies antigenic change, quasispecies diversity, and rapid emergence of resistance.
Coxsackievirus — what is it?	Non-enveloped positive-sense RNA picornavirus, divided into groups A and B.
Dengue virus — what is it?	Enveloped positive-sense RNA flavivirus with four serotypes.
Hepatitis C virus — what is it?	Enveloped positive-sense RNA flavivirus. Its envelope proteins vary rapidly within one host, which is why infection frequently becomes chronic and why no vaccine has followed.
Influenza genome segmentation — what is it?	Eight separate RNA segments packaged together in one particle. Co-infection of one cell by two strains allows whole segments to be exchanged, which is the mechanism of antigenic shift and of pandemic emergence.
Parainfluenza virus — what is it?	Enveloped negative-sense RNA paramyxovirus.
Hantavirus — what is it?	Enveloped segmented negative-sense RNA virus of the bunyavirus group.
HIV effect on cell-mediated immunity — what is it?	Progressive loss of CD4-positive T cells, removing the helper function that coordinates both cellular and antibody responses. The organisms that appear as immunity declines are those normally controlled by cell-mediated immunity, which is why the pattern is predictable from the defect.
Arbovirus transmission — what is it?	Transmission by an arthropod vector in which the virus replicates before being passed on. Vector distribution and season determine where and when infection occurs, which is why these infections are geographically bounded.
Vertical transmission — what is it?	Passage from mother to child across the placenta, during delivery, or through breastfeeding. Which route an agent uses determines when in gestation or delivery the risk falls, so timing rather than the agent alone shapes the outcome.
Fungal cell wall — what is it?	A wall of chitin and glucans, with ergosterol rather than cholesterol as the principal membrane sterol. Both the wall polysaccharide and the membrane sterol are absent from human cells, which is why they are the two selective targets.
Potassium hydroxide preparation — what is it?	A specimen treated with alkali, which dissolves keratin and host cells while leaving fungal walls intact. The fungal wall resists the alkali because of its chitin, so the method works by removing everything else.
Histoplasma capsulatum — what is it?	Dimorphic fungus appearing as small yeasts within macrophages.
Candida albicans — what is it?	Yeast forming pseudohyphae and true hyphae at body temperature, part of normal flora of mouth, gut, and vagina. It is already present, so disease follows a change in the host or in competing flora rather than new acquisition.
Mucormycetes — what is it?	Molds with broad non-septate hyphae branching at wide angles, including Rhizopus and Mucor. The association is with acidosis and with high available iron, which is why the host state rather than exposure explains most disease.
Fungal spores and conidia — what is it?	Reproductive structures released into the environment, whose shape and arrangement identify many molds. Bacterial endospores, which are survival structures rather than reproductive ones and are formed inside the cell.
Giardia lamblia — what is it?	Flagellated protozoan with trophozoite and cyst forms.
Trichomonas vaginalis — what is it?	Flagellated protozoan with a trophozoite form only and no cyst stage. Having no cyst, it cannot survive long outside the host, which is why transmission is essentially direct.
Plasmodium falciparum sequestration — what is it?	Infected erythrocytes expressing adhesive proteins that bind capillary endothelium, so they are held in small vessels. Sequestration keeps mature stages out of the circulating blood and obstructs microvasculature, which is why this species produces the most severe disease.
Trypanosoma cruzi — what is it?	Flagellated protozoan.
Nematodes — what is it?	Roundworms with a cylindrical unsegmented body and separate sexes. Most intestinal species are acquired by ingesting eggs or by larvae penetrating skin, so the entry route separates them into two groups.
Strongyloides stercoralis — what is it?	Nematode whose larvae penetrate skin. That autoinfection can accelerate dramatically when cell-mediated immunity is suppressed.
Filarial worms — what is it?	Tissue nematodes including Wuchereria bancrofti and Onchocerca volvulus.
Echinococcus granulosus — what is it?	Tapeworm of dogs, with sheep as usual intermediate host.
Definitive versus intermediate host — what is it?	The definitive host harbours the sexually reproducing stage, while an intermediate host carries larval or asexual stages. For malaria the mosquito is definitive and the human intermediate, which reverses the assumption that the human is the main host.
Type I hypersensitivity — what is it?	An immediate reaction in which antigen cross-links IgE bound to mast cells, releasing histamine and other mediators. It requires previous sensitization, so the first exposure produces the IgE and a later one produces the reaction.
Toll-like receptors — what is it?	Innate receptors recognizing conserved microbial patterns such as lipopolysaccharide, flagellin, and unmethylated DNA motifs. They detect classes of organism rather than specific ones, which is why the innate response is immediate but does not improve with repeated exposure.
Natural killer cells — what is it?	Innate lymphocytes killing cells that display too little class I molecule or that are coated with antibody. They detect the absence of a normal signal, which covers the gap left when a virus downregulates class I to hide from T cells.
Antibody isotypes — what is it?	IgM as the first response and a strong complement activator, IgG the most abundant and the only one crossing the placenta, IgA in secretions, IgE on mast cells, and IgD on naive B cells. The heavy chain constant region rather than the binding site determines what an antibody can do once bound.
Mucosal secretory antibody — what is it?	Dimeric IgA transported across epithelium and carrying a secretory component that resists proteolysis. It neutralizes organisms at the surface before attachment, which is precisely why several mucosal pathogens produce a protease against it.
B cell defects and organism pattern — what is it?	Impaired antibody production, associated with recurrent infection by encapsulated bacteria and by enteroviruses. Encapsulated organisms need opsonizing antibody to be cleared, so the defect predicts the organism class.
Phagocyte defects and organism pattern — what is it?	Impaired killing or migration, associated with catalase-positive bacteria and with molds. The pattern follows the failed mechanism rather than exposure, so knowing the defect predicts the organism.

Frequently asked

How is each organism card built?

It opens with the classification, which for a bacterium means the Gram result, shape, arrangement and the key biochemical results. Under that, on the cards where it matters, comes the organism this one is most often confused with and the single feature that separates them.

Where do the antimicrobials fit?

In the Pharmacology Drug Classes deck, deliberately. That deck covers the mechanism and target of every antimicrobial class. Keeping the agent and the organism in separate decks means neither one repeats the other, and you can drill either side on its own. The only drug names here are optochin, bacitracin and novobiocin, which appear as identification discs rather than as therapy.

Does it cover the laboratory identification tests?

Yes, as its own block of 31 cards: Gram stain and acid-fast staining, catalase and coagulase, hemolysis patterns, the optochin, bacitracin and novobiocin discs, oxidase, urease, indole and citrate, lactose fermentation on MacConkey, and the special media from chocolate agar to charcoal yeast extract. Each says what the test detects.

Which groups get the most cards?

Bacteriology 146, made up of 31 laboratory identification, 35 gram-positive, 35 gram-negative, 23 virulence mechanisms and 22 mycobacteria, spirochetes and atypicals. Then virology 74, parasites 30, fungi 28, and immunology 22. Bacteriology is heaviest because that is where the discriminating features are densest.

How is it organized for studying one group at a time?

Every card carries a group tag and a finer sub-group tag, across laboratory identification, gram-positive bacteria, gram-negative bacteria, mycobacteria and spirochetes, bacterial virulence, virology, fungi, parasites and immunology. Filter by a tag to drill one group, or by the finer tag for a single block such as DNA viruses, helminths or biochemical tests.

Can I import the whole deck on the free plan?

Yes. Importing a saved deck runs no new AI generation and does not use your AI allowance, so the free plan imports every card. 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 edit the cards after importing?

Yes. Once imported they are your cards: edit either side, delete the ones you already know cold, retag them, or move them into another deck.