A glossary of bench microbiology terms

This glossary is a working order of words for one afternoon with a non-pathogenic E. coli cloning strain. The decision it supports is whether the notebook and the bench refer to the same object. If you call a lawn a colony, every later step inherits the lie. The culture and the transformation those words describe are in bacterial culture and transformation. How an insert becomes one of those colonies is plasmid cloning from insert to colony. Antibiotic and colour language is in antibiotic selection and blue-white screening.

The reagents the words point at are specified from the reagents and chemicals catalogue. Method context is the molecular biology pathway. Naming a designed gene precisely is what the custom gene synthesis reference is for, as an enquiry. Use the quote request when a term in this list is also a purchasing line. A method can be discussed. A public companion for the same vocabulary is the Addgene molecular biology reference.

Colony

A colony is a visible pile of cells on solid medium, ideally the daughters of one cell. It is the unit you pick, not a guarantee of one plasmid sequence. "Isolated colony" means bare agar around the pile so a tip can touch it without a neighbour. Without that margin you have a region, not a single colony.

Lawn

A lawn is confluent growth. Individual piles are no longer separable. On non-selective agar a lawn can mean the cells were alive. On selective agar it usually means the drug failed or the inoculum was enormous. A lawn cannot be picked as clones. Streak it out, or discard it if the no-DNA plate looks the same.

Streak

A streak is a deliberate dilution of cells across agar, done so that the last sector contains separated colonies. The Addgene streak-plate protocol draws the usual pattern. The word is also abused for any scribble of a loop. If you did not dilute, say "smear" or "patch" and do not expect single colonies tomorrow. Streaking is how a glycerol scrape or a turbid broth becomes something you are allowed to call a colony again.

Patch

A patch is a spot you inoculate on purpose, often in a numbered grid, after you have already picked a colony. It is a way to hold many candidates on one plate. The patch inherits the purity of the pick. It does not create purity. Patches that run together in condensation are mixtures, and the grid on the lid will lie about them. Use the word when you mean the grid, and keep colony for the pile you originally touched.

Inoculum

The inoculum is the living material you transfer into the next vessel. A single colony is a clean inoculum. A loop dipped through a lawn is a mixed one. Write the source down. The Addgene protocol for inoculating a culture starts from a colony because that source is the whole point.

Overnight

An overnight is a culture incubated so that, by the next working day, it is dense enough for the step you planned. It is not a fixed number of hours. A small inoculum may still be exponential at breakfast, and a huge one may have been stationary since midnight. If the shaker stops, say so, and record the temperature you actually held.

Pellet

The pellet is the cell mass at the bottom of a tube after you centrifuge a culture. For a miniprep it is the fraction you keep and lyse. A pellet from a clear culture is a speck, and a speck is a fair warning that the culture did not grow. A huge pellet from a non-selective broth may be the wrong cells. The pellet is biomass. It is not plasmid DNA until the prep says so.

Supernatant

The supernatant is the liquid above that pellet. In a routine plasmid prep from a cloning strain you discard it, carefully, without losing the pellet. In other methods the product is in the liquid and the pellet is waste. Say which fraction carries the thing you want before you tip. "Pour off the supernatant" is a safe sentence only when you have identified the supernatant correctly. Pouring off the pellet because the tube was inverted is a common way to lose a clone and keep the word.

Competent

Competent means the cells are in a state that allows plasmid uptake. Chemical competence and electrocompetence are different states, both cold, with different salt rules. The strain was already your cloning strain. Competence is not a new species name and not a change in institutional risk group. A tube labelled competent is a reagent with a handling sheet. If it warmed, it may still be E. coli and no longer competent. Those two facts can be true together.

Transformant

A transformant is a cell, and then a colony, that took up the DNA you added and survived selection because of it. You earn the word when a no-DNA control stays clear and colonies appear where DNA was added. You do not earn it from a lawn, from a satellite, or from a colony on the wrong antibiotic. Even a real transformant may carry the wrong insert. The word means uptake under selection. It does not mean sequence-confirmed. Use "candidate" until the digest or the trace agrees.

Satellite

A satellite is a small colony in the zone around a large resistant colony, classically on ampicillin, where beta-lactamase has destroyed the drug locally. Satellites are usually not transformants. They are the reason the phrase "small colony" is not automatically "nice clone". If you are speaking about kanamycin, do not reach for this word by habit. A field of tiny colonies with no large neighbour is a failed plate, not a sky full of satellites.

Antibiotic marker

The antibiotic marker is the gene on the plasmid that lets a sensitive host grow on a particular drug. The drug, the gene and the host genotype are a set. bla pairs with a beta-lactam. A kanamycin gene pairs with kanamycin. The marker is not "antibiotic resistance" in the abstract. Name the gene and the molecule. A host that already carries the same resistance on its chromosome does not become a transformant by growing. It was already able to grow. Read the genotype before you praise the plate.

Ori

Ori is the origin of replication, the plasmid sequence that tells the cloning strain how to copy the circle, and roughly how many copies to keep. A high-copy ori gives more plasmid DNA per cell and is the usual choice for a simple clone. A low-copy ori is chosen when the plasmid is a burden, and it is easier to lose by segregation if selection slips. The ori is not the insert and not the marker. When a prep yields less DNA than you expected, the ori is one of the honest explanations, alongside a culture that lost the plasmid entirely.

Empty vector

An empty vector is the plasmid backbone without your insert. It still has the ori and the marker, so it still forms colonies on the right antibiotic. It is the correct control for a ligation and a miserable outcome if it is what you archived by mistake. Blue-white screening, when the vector supports it, is one screen against empty vector, not a proof. A colony of empty vector is a real transformant of the wrong plasmid. Say "empty" when the backbone is what you recovered, and keep "failed transformation" for the plate that grew nothing.

The object those words point at

Using the words in one afternoon

Streak so that colony will be true tomorrow. Pick one colony and call it the inoculum of a numbered tube. Grow an overnight under the marker's drug. Name the pellet as the cells you lyse and the supernatant as the liquid you discard. Say transformant only after the no-DNA plate stayed clear, empty vector if the backbone is what grew, and satellite if you stopped at the halo. The NCBI Bookshelf is a public reference for the cell biology under these objects. Used in that order, the words keep the afternoon auditable.

The institution still owns the risk

Every term here applies to K-12-style cloning strains the institution has already accepted. None of the words is permission to grow a different organism because the same flasks fit the shaker. Competent, transformant and marker are laboratory words, not a clinical vocabulary. Waste is inactivated by the existing route. This page is not medical advice. The WHO Laboratory Biosafety Manual is for the people who decide what may be streaked at all.

An overnight that a power cut redefined

In a building where the power fails, an overnight can be two cultures: the one that grew until the shaker stopped, and the one that sat warm and still until morning. The pellet is still a pellet. It is not the biomass the word usually promises. Write the outage in the notebook and do not call the result a normal overnight when you interpret a thin plasmid yield. Heat and humidity also smear patches into each other, so a patch grid read in the monsoon needs a look at the agar, not only at the lid. The word on the lid is a claim. The agar is the evidence.

What to name in an enquiry

Use marker, ori class, strain class, and whether you need broth, agar or a recovery medium. Say colony-picking tips if that is the consumable, and say so plainly. Put the specification on the quote request. A method can be discussed. The custom gene synthesis reference is how you name an insert when "the gene" is too vague for the vector. It is an enquiry prompt, not a statement that a synthesis is already running.