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Short answer
Culturing microorganisms means growing living microbes on or in a nutrient medium so they multiply enough to be observed, counted or used. Three choices shape every culture: the medium, the vessel, and the atmosphere, especially how much oxygen the organism tolerates. A fourth decision comes before all three: the biosafety level the organism requires.
Definition and scope
A microbial culture is a population of microorganisms propagated under controlled conditions, usually in a liquid broth or on a solid agar surface. Laboratories culture bacteria, yeasts and other microbes to isolate a single organism, to grow material for downstream work, or to see how an organism responds to a condition. This page covers the concepts that apply across those uses. It is not a bench protocol, and it does not replace the standard operating procedure or the risk assessment of your own laboratory.
How cultures are grown in practice
Each culture is built from the same three parts.
- Medium. The nutrient supply, either liquid or solidified with agar. Defined recipes are described in the dictionary entry on chemically defined media.
- Vessel. Solid cultures sit on an agar plate in a petri dish. Liquid cultures are grown in tubes or flasks, often on an incubator shaker that supplies aeration.
- Atmosphere and temperature. The gas environment the organism needs, covered in the next section.
Keeping a culture pure depends on aseptic technique. For selection antibiotics in culture medium, see ampicillin working concentration for one example.
Oxygen classes and how labs reveal them
Microbes differ sharply in their relationship to oxygen, and a culture set up in the wrong atmosphere simply will not grow. The OpenStax Microbiology textbook (section 9.2, checked 2026-10-29) describes five classes. The table below follows that chapter; every row is taken from it.
| Class | Relationship to oxygen (OpenStax wording) |
|---|---|
| Obligate (strict) aerobe | Cannot grow without an abundant supply of oxygen. |
| Obligate anaerobe | Killed by oxygen. |
| Facultative anaerobe | Thrives in the presence of oxygen but also grows in its absence. |
| Aerotolerant anaerobe | Indifferent to the presence of oxygen. |
| Microaerophile | Requires a minimum level of oxygen for growth, about 1%-10%. |
The same chapter describes two ways the requirement is handled in the laboratory. In a thioglycolate tube, the medium has strong reducing properties and autoclaving flushes out most of the oxygen, so oxygen diffuses in from the top and the position of growth in the tube shows what the organism needs. For organisms that cannot tolerate oxygen, anaerobic jars include chemical packs that remove oxygen and release carbon dioxide.
E. coli culture
E. coli is the most familiar laboratory culture, and it illustrates both the biosafety and the practical sides of the topic.
Biosafety level for E. coli
The CDC and NIH publication Biosafety in Microbiological and Biomedical Laboratories (BMBL), 6th edition, defines Biosafety Level 1 (BSL-1) as the basic level of protection, appropriate for defined and characterized strains of viable biological agents that are not known to cause disease in immunocompetent adult humans. BMBL describes BSL-1 work as typically conducted on open benchtops using standard microbiological practices, by staff trained in the procedures and supervised by a scientist with training in microbiology or a related science. The glossary lists K-12 derived strains of E. coli among the exempt organisms of Appendix C of the NIH Guidelines, which are generally considered not to pose a significant risk to health or the environment. That statement concerns K-12 derived strains specifically, not E. coli as a species. See the dictionary entry on Biosafety Level 1 (BSL-1).
Why an overnight E. coli culture can lag
Bitesize Bio, a practitioner site, describes a common surprise in its article on large E. coli cultures (J. Plank, updated 2025-04-15; a protocol-tips article, not a standard). An overnight culture contains dead, stationary and dividing cells, and stationary cells pause before they divide again. A Luria-Bertani (LB) overnight started in the early evening has usually left its log phase hours before morning, so the next day’s culture begins with a lag. The author suggests a buffered, richer medium (Terrific Broth) and a cooler starter, pre-warmed flasks, and as one example a 1:500 dilution of the starter, after which good aeration brings the culture to an optical density near 0.6 in about two to two and a half hours. These are one author’s figures and should be checked against your own laboratory’s validated protocol.
Which biosafety level does a culture need?
BMBL frames this as a protocol-driven risk assessment, and it states that it is not intended to be a regulatory document. Its introduction separates two entry levels by the agent. BSL-1 is for defined and characterized strains that are not known to cause disease in immunocompetent adult humans. BSL-2 is appropriate for handling moderate-risk agents that cause human disease of varying severity by ingestion or through percutaneous or mucous membrane exposure. The practical consequence for a laboratory is that the organism, not the equipment, sets the starting point: identify the strain, then decide the level, then choose the vessels and atmosphere.
Common misunderstandings
- “All E. coli is BSL-1.” BMBL ties the exempt status to K-12 derived strains. Other strains are assessed by the same agent-based risk assessment as any other organism.
- “Anaerobes just need the lid on.” An obligate anaerobe is killed by oxygen, so it needs the oxygen actively removed, as in the anaerobic jar described above.
- “Biosafety levels are regulations.” BMBL describes itself as advisory.
FAQ
What is an obligate anaerobe?
An organism that is killed by oxygen, according to the OpenStax Microbiology chapter on oxygen requirements. Such cultures are handled in conditions that remove oxygen, for example an anaerobic jar.
Is E. coli culture BSL-1?
For K-12 derived strains, BMBL lists them as exempt organisms under Appendix C of the NIH Guidelines, and BSL-1 covers defined strains not known to cause disease in immunocompetent adults. For any other strain, a documented risk assessment decides the level.
What is the difference between a facultative anaerobe and an aerotolerant anaerobe?
A facultative anaerobe thrives with oxygen but can also grow without it. An aerotolerant anaerobe is indifferent to oxygen, according to the same source.
Sources
- CDC and NIH, Biosafety in Microbiological and Biomedical Laboratories (BMBL), 6th edition, checked 2026-10-29.
- OpenStax, Microbiology, section 9.2 Oxygen Requirements for Microbial Growth (open textbook), checked 2026-10-29.
- Bitesize Bio, Eliminate the Growth Lag with Large E. coli Cultures, J. Plank, updated 2025-04-15, checked 2026-10-29 (practitioner article).
