Flagellates, bacteria and spore-forming parasites under the microscope

What kind of microscopic external parasites can you find on freshwater fish after a skin scraping and what do they look like under a microscope? In this second article and video we will show you flagellates, bacteria and spore-forming parasites. Stay tuned, because in upcoming videos we will look at ciliates, crustaceans, skin flukes and gill flukes.

Ichthyobodo necator

The parasite Ichthyobodo necator, also known as Costia, belongs to the genus Ichthyobodo, which is part of the class of Kinetoplastea, belonging to the family Ichthyobodonidae. The genus Ichthyobodo includes 3 to 5 species, depending on which scientific classification is used. Ichthyobodo necator is a dangerous fish parasite that causes mass mortality in aquariums and ponds. This tiny parasite ranges in size from 6 to 12 microns, so at 100-fold magnification under a microscope, they appear as rapidly moving large dots. At higher magnification we see that Ichthyobodo is flat and looks similar to a stretched pancake. Ichthyobodo can move in a sharply undulating or spiraling way, resembling the movement of a fishing lure.


Infected fish lie on the bottom or stay near the water surface, making oscillatory movements. Fish breathe fast, press their fins against their body, while white mucus may cover the skin. The fish hardly eat and appear apathetic. Often several types of parasites can be found in a scraping sample.


The genus Cryptobia also belongs to the class Kinetoplastea but is part of the family Cryptobiidae, which includes about 50 species of parasitic protozoa. The majority of them are endoparasites that live in the intestine and circulatory system of fish. Five species of Cryptobia parasitize on the gills and skin of fish. In size, Cryptobia is comparable to Costia and, at low magnification under a microscope, appears as mobile black dots. At high magnification, the difference between Ichthyobodo sp. and Cryptobia sp. is visible. Cryptobia have a slightly elongated shape and full body with a pointed nose, resembling mice with tails, and the parasites themselves are very pliable.


The symptoms that fish exhibit are similar to those of infection with Ichthyobodo necator: infected fish lie on the bottom or stay near the water surface, making oscillatory movements. Fish breathe fast, press their fins against their body, while white mucus may cover the skin. The fish hardly eat and appear apathetic. Often several types of parasites can be found in a scraping sample.


Oodinium sp. is a parasitic dinoflagellate belonging to the family Oodiniaceae, class Dinophyceae. Under a microscope, stationary oval-shaped Oodinium cells can be seen, which are dark brown or black in color. Members of the genus Oodinium affect both marine and freshwater species, causing symptoms that resemble an Ichthyophthyrius infection.


The fish’s body is covered with small golden-white spots, which looks like dust.

Myxosporea / Myxozoa

Myxosporea or Myxozoa is a large group of spore-forming organisms, all of which are parasites, mainly of freshwater and marine fish species. The class Myxosporea encompasses several thousand species, and scientists are constantly discovering new genera and species of these parasites. For example, there are already more than 2,000 species described in the genus Myxobolus. Myxosporea have a complex life cycle, in which, after several developmental stages, spores are formed in the final stage. Spores of different species have different shapes and structures: they can be round-, oval-, drop- or heart-shaped, elongated, with spines or without. But what unites them all is the presence of two polar capsules, containing ejector filaments. The detection of even only one spore in a smear confirms the diagnosis of myxosporidiosis. Parasites form cysts in various tissues and organs of the fish, where they develop and produce spores that are released into the environment. In infected tissues we can observe nodules or granulomas, white spots, tumors, sometimes with exudate, containing spores.


Microsporidia is another group of spore-forming parasitic organisms, of with currently about 1300 species are known and new species are still being discovered. All Microsporidia intracellularly parasitize eukaryotic organisms. A frequently occurring diseases in aquariums is pleistophorosis, caused by Pleistophora hyphessobryconis, which affects fish of the genus Hyphessobrycon, the tetra fish. Under the microscope, individual spores and cysts containing spores can be detected. Spores have a characteristic oval shape with an ejector capsule inside, which makes it resemble a slipper.


In affected fish, white patches form in the area of the back muscles. In these areas, the parasites develop and form cyst with spores.

Flavobacterium columnare

Flavobacterium columnare is one of the few species of pathogenic bacteria that can be identified using a microscope. This large (50-100 μm), gram-negative, rod-shaped bacterium forms colonies on the body of fish, ranging in color from white to yellow-orange due to the pigment contained within the cells. In a sample taken from the body of an infected fish, individual scales and normal transparent mucus can be seen, but special attention should be paid to the yellow-orange film surrounding the scales, which forms bumps. At high magnification, we can observe how the shape and size of these bumps change. The undulating, bending movements of individual cells in the colony create a wave-like motion, which is the hallmark of this type of bacteria, making accurate identification relatively easy. Flavobacterium columnare excrete enzymes and other substances that are toxic to fish, leading to tissue destruction and the formation of necrotic foci.


Visible signs include raised scales, accumulation of mucus and bacterial colonies in the interstitial space between scales, loss of pigment, destruction of the epidermis and shedding of scales in the affected area. We often see a clear border between healthy and affected tissue.

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