Colony Morphology of Bacteria

Bacteria grow on solid media as colonies. A colony is defined as a visible mass of microorganisms originating from a single mother cell. Key features of these bacterial colonies serve as important criteria for their identification.

Figure: Characteristics of bacterial colonies

Colony morphology can sometimes be useful in bacterial identification. Colonies are described based on size, shape, texture, elevation, pigmentation, and effect on growth medium.

Why colony morphology matters in clinical microbiology

Colony morphology is the first observation a clinical microbiologist makes when examining an incubated culture plate — before any biochemical testing, before MALDI-TOF, before serology. Within seconds of opening an incubated plate, an experienced microbiologist can make immediate presumptive assessments that directly guide the next steps in identification.

The combination of:

• Medium (which agar the organism is growing on)
• Colony characteristics (size, colour, hemolysis, texture, odour)
• Gram stain of a representative colony

...gives a preliminary identification in most cases before any further testing is performed.

This article covers the universal descriptors used to characterise any bacterial colony. For organism-specific colony appearances on selective and differential media, see the dedicated articles:

→ Blood Agar: Colony Morphology

→ MacConkey Agar: Colony Morphology

→ EMB Agar: Colony Morphology

Find common criteria that are used to describe colony morphology;

Colony shape

It includes the form, elevation, and margin of the bacterial colony.

Form of the bacterial colony: The form refers to the shape of the colony. These four forms represent the most common colony shapes you are likely to encounter.

1. circular,
2. irregular,
3. filamentous, and
4. rhizoid

Elevation of the bacterial colony: It gives information about how much the colony rises above the agar. This describes the “side view” of a colony.

The six most common elevations of bacterial colonies are

1. flat,
2. raised,
3. umbonate (having a knobby protuberance),
4. crateriform,
5. convex, and
6. pulvinate (cushion-shaped).

Figure: Elevation of Bacteria colony

The margin of the bacterial colony: The margin or edge of a colony may be a vital characteristic in identifying organisms. Examples are

• entire (smooth),
• irregular,
• undulate (wavy),
• lobate,
• curled, and
• filiform.

Colonies that are irregular in shape and/or have irregular margins are likely to be motile organisms. Highly motile organisms swarmed over the culture media, such as Proteus spp.

Size of the bacterial colony

The size of the colony can be a useful characteristic for identification. The diameter of a representative colony may be measured in millimeters or described in relative terms such as pinpoint, small, medium, and large.

Figure: Punctiform and other types of bacterial colony

Tiny colonies are also referred to as punctiform (pin-point). Colonies larger than about 5 mm are likely to be motile organisms. Punctiform colonies are distinguished from circular colonies by their very small size.

Appearance of the colony surface

Figure: Mixed growth of mucoid Lactose fermenting colonies and NLF colonies in MacConkey Agar

Bacterial colonies are frequently shiny and smooth in appearance. Other surface descriptions might be: dull (opposite of glistening), veined, rough, wrinkled (or shriveled), or glistening. Bacillus species give dry, wrinkled colonies. Pseudomonas stutzeri also gives similar-appearing wrinkled colonies.

Consistency/Texture

Several terms that may be appropriate for describing the texture or consistency of bacterial growth are: dry, moist, viscid (sticks to loop, hard to get off), brittle/friable (dry, breaks apart), mucoid (sticky, mucus-like).

Color of the colonies (pigmentation)

Some bacteria produce pigment when they grow in the medium, e.g., green pigment produces by Pseudomonas aeruginosa,  buff-colored colonies of Mycobacterium tuberculosis in L.J medium, and red-colored colonies of Serratia marcescens.

The opacity of the bacterial colony

The opacity of a bacterial colony can be described as transparent (clear), opaque (not transparent or clear), translucent (almost clear, but distorted vision–like looking through frosted glass), or iridescent (changing colors in reflected light). A pinpoint translucent β-hemolytic colonies on blood agar is most probably a Streptococcus species. Staphylococci give opaque, smooth, and circular colonies on the agar plate surface.

Some important terminologies

Draughtsman colonies

Figure: Draughtmans colonies of S. pneumoniae

Young colonies of Streptococcus pneumoniae(pneumococci) have raised centers, but as the culture ages, they become flattened, with a depressed central part and raised edges giving them a ringed appearance also known as ‘draughtsman colonies’.

Colony Morphology of Clinically Important Bacteria

The following table summarises the characteristic colony appearances of clinically important bacteria on blood agar (the most informative primary plating medium) and nutrient agar after 18–24 hours of incubation at 35–37°C. These descriptions represent the most common presentations — individual strain variation occurs.

Gram-positive cocci

Gram-positive rods

Gram-negative cocci and coccobacilli

Gram-negative rods

How Colony Morphology Guides Clinical Identification — Step by Step

When a clinical microbiologist opens an incubated culture plate, they follow a systematic approach:

Step 1 — Assess overall plate appearance

• Is there one type of colony or a mixture? (pure culture vs mixed growth)
• What media are present and what are the selective agents?
• Any unusual odours? (Pseudomonas grape-like, Proteus putrid, C. difficile horse-barn)

Step 2 — Examine individual colonies

• On blood agar: is there haemolysis? What type and zone size?
• On MacConkey: lactose fermenter (pink) or non-fermenter (colourless)?
• Size — pinpoint (<0.5mm), small (0.5–1mm), medium (1–3mm), large (>3mm)?
• Surface — smooth/glistening (typical), rough/dry (Bacillus, Nocardia), mucoid (encapsulated organisms)?
• Pigmentation — yellow (S. aureus, Micrococcus), blue-green (Pseudomonas), red (Serratia at 25°C)?
• Swarming — Proteus on blood agar?

Step 3 — Gram stain a representative colony The combination of colony morphology + gram stain reaction + morphology gives a preliminary identification:

Step 4 — Select appropriate biochemical tests Based on the preliminary identification, choose a targeted battery of biochemical tests (catalase, coagulase, oxidase, TSI, urease, etc.) or send for MALDI-TOF identification.

Chromogenic Media — Colony Colour as Direct Identification

Modern chromogenic media incorporate enzyme-specific substrates that produce coloured products when cleaved by enzymes produced by specific organisms — allowing presumptive species-level identification directly from primary culture based on colony colour alone:

Chromogenic media significantly reduce the time to organism identification in high-volume settings such as urine culture laboratories — from 2–3 days with conventional methods to 18–24 hours. They also allow detection of mixed infections (two different organisms) by producing different coloured colonies on the same plate.

→ CHROMagar Candida for Candida Species Identification

References

1. Tille, P. M. (2017). Bailey & Scott's Diagnostic Microbiology (14th ed.). Mosby Elsevier.
2. Koneman, E. W., & Allen, S. D. (2006). Koneman's Color Atlas and Textbook of Diagnostic Microbiology (6th ed.). Lippincott Williams & Wilkins.
3. Garcia, L. S. (Ed.). (2016). Clinical Microbiology Procedures Handbook (4th ed.). ASM Press.
4. Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M., & Stahl, D. A. (2018). Brock Biology of Microorganisms (15th ed.). Pearson.