How to Distinguish Bacteria and Fungi: From Morphology to Sequencing

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When classifying bacteria and fungi, morphological features are v­ery relevant. Colony morphology is a useful tool widely used to classify and define them by researchers. Carefully studied and used during these experiments are the colony properties of individual bacterial and fungal colonies. Compared to fungi, bacteria easily thrive on nutrient-rich culture media. Phenotypically distinct-looking colonies are formed by various species of bacteria and fungi. The size, shape, texture, color, margins of the colonies vary. Bacteria and fungi should be cultivated on agar in Petri dishes to examine colony morphology by supplying all the nutrients and conditions required. On agar media, bacteria emerge as tiny oily spots. All over the agar plate, fungi develop as powdery mats. The major distinction between bacterial and fungal colonies is that the recognizable masses of bacterial cells emerging from single bacterial cells are bacterial colonies, whereas the visible masses of fungi emerging from a single spore or mycelial fragment are fungal colonies.

Bacterial Colonies

Bacterial colonies are a mass of bacterial cells on a dense medium, isolated from a single bacterium. All bacteria are genetically similar within the colony and may be considered a clone. Many colonies of bacteria are spherical or irregular in form. Some others are filamentous or rhizoid actinomycetes. Many colonies of bacteria are microscopic and are less than 1 mm in diameter. They are therefore known as punctiform (pin-point). They likewise have a given margin. In order to observe the tip, the microscope should be used. For the species, the color of the colony varies. White, buff, violet, purple, etc.

The bacterial colonies may have a smooth, glistening, rough, dull, or rugged surface (wrinkled). Butyrous (buttery), viscid (sticks to ring, difficult to get off), brittle/friable (dry, breaks apart) or mucoid may be their texture (sticky, mucus-like).

Fungal colonies

Fungi is a community of eukaryotic species such as yeast, filamentous fungi, and mushrooms. Under damp and warm conditions, fungi grow well. Based on their morphological and molecular attributes, they may be categorized. Forming fungi on solid media such as potato dextrose agar can clearly predict morphological characteristics (PDA). PDA is the tool widely used in labs to grow fungi. Fungi grow as colonies when grown on stable media. Among various types of fungi, fungal colony morphologies are different. From fungal colonies, characteristics such as pigmentation and texture may be observed.

Colonies of fungi are distinct from bacterial colonies. Fungi emerge as textured colonies that are powdery or fuzzy. Fungi hyphae run across the solid media, producing colonies of rhizoids or filaments. As tiny oily dots, fungal colonies may not surface. The colors of mycelium and spores also vary greatly among the fungal species. Similarities between bacterial and fungal colonies.

On solid nutrient agar, bacterial and fungal colonies can be grown. They display characteristics to the organism that develops the colony. The color of the colony depends on the kind of microorganism that the colony produces. It is also possible to use both for the detection of microorganisms.

Differences between bacterial and fungal colonies


Bacterial colonies correspond to a recognizable mass of cells from a single bacterial colony, while a mass of thread-like hyphae corresponds to fungal colonies.

Number of cells

Bacterial colonies consist of unicellular cells, whereas unicellular or multicellular organisms may be made up of fungal colonies.


Bacterial colonies consist of a mass of bacterial cells arising from a single bacterium's fragmentation, while fungal colonies consist of fungal hyphae made up of a single spore.

Colony size

Bacterial colonies are tiny, whereas most hyphae-developing fungal colonies are huge.


While fungal colonies have a hairy look, bacterial colonies have a smooth or rough texture. This is one major distinction between colonies of bacteria and fungi.


Bacterial colonies have a fixed margin, whereas a filamentous margin can be seen in fungal colonies.


While fungal colonies are powder-like, bacterial colonies appear damp and glossy.


While fungal colonies are filamentous or rhizoid, bacterial colonies are spherical or irregular.

pH compatibility

The colonies of bacteria develop within pH 5-9 (optimum 7) while the colonies of fungi thrive within pH 5-6.

Summary of Differences between bacterial and fungal colonies

As an observable mass of microorganisms, a colony can be identified. A single mother cell derives from each colony. The cells in a colony are also genetically similar. On solid media, bacteria and fungi emerge as colonies. On the surface of the agar, bacterial colonies occur as tiny creamy spots. Fungal colonies form on the surface of the agar as molds. This is the main distinction between colonies of bacteria and fungi. Colony morphologies are helpful in bacterial and fungal recognition and differentiation.

Sequencing: A Leap for Microbiology Research

The initial microbial research mainly relied on morphology. Although this approach has opened the door to a rich and colorful microbial world, let us know all kinds of microbes and allowed for preliminarily classification. This process took a lot of effort, but these understandings still have certain limitations. With the continuous development and improvement of sequencing technology, microbiology has developed rapidly in a short period of time. These techniques include targeted sequencing, metagenomics, transcriptomics, epigenomics and even more. These methods are not only fast and efficient, but also have greatly improved accuracy. With our deeper understanding of microorganisms, research on microbial metabolic pathways, gene utilization, and microbial modification has become much easier.

CD Genomics is a genomics service company with a good reputation in providing reliable sequencing, genotyping, microarray, and bioinformatics services. Our fungal sequencing solutions vary from taxonomic profiling to discovering complex metabolic pathways to identifying metabolites that are beneficial to human health and more. Our platform provides data on the fungal genome sequence, helping to improve medical science, agriculture science, ecology, bioremediation, bioenergy, and biotech industries.


  1. Hibbett DS, Ohman A, Glotzer D, et al. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal biology reviews. 2011, 25(1).
  2. Minerdi D, Bianciotto V, Bonfante P. Endosymbiotic bacteria in mycorrhizal fungi: from their morphology to genomic sequences. InDiversity and Integration in Mycorrhizas, 2002
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