CLASSIFICATION / GROUPS OF MICROORGANISMS ACCORDING TO THEIR TAXONOMY

There are billions of microorganisms in the face of the planet earth, and these organisms are ubiquitously distributed. To make sense of the diversity of microorganisms around us in terms of their types or varieties, it is important to group microbes together according to some similarities and features that exist amongst them. This is the basis of microbial taxonomy – which identifies, puts a name to a microbe and classifies microorganisms so that they will be no ambiguity in microbial classification. Microorganisms are usually placed in five (5) taxonomic groups including bacteria, fungi, algae, protozoa and viruses. These different groups of microorganisms (both beneficial and harmful microbes) are further expanded in this section. However, the medical and non-medical significance of these organisms are explained in details in Microbiologyclass’s Basic Bacteriology. Microorganisms are a diversity of microscopic organisms that play various roles in the environment as well as in man and animals. They encompass bacteria, fungi, viruses, protozoa and algae; and these are expanded in this section.  

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Bacteria

Bacteria (singular: bacterium) are unicellular (single-celled) prokaryotic organisms with varying shapes and sizes (ranging between 1-10 µm) including cocci (spheres), rods (bacillus), spirals (Spirillum) and coccobacillus (i.e., curved or bent rods). They reproduce by a type of asexual reproduction known as binary fission, and they are ubiquitous in the environment. Bacteria are one of the smallest living cells which are capable of independent replication. The majority of bacterial species causes economically important diseases in man, wild animals and livestock’s while only a few cause diseases in plants (for example, Erwinia species). Others cause food spoilage and a handful of bacteria also help in the recycling of nutrients in nature. Some bacteria are anaerobic (i.e., they do not require oxygen) while others are aerobic (i.e., they require oxygen) in terms of their requirement for oxygen. Facultative bacteria are those that can grow in the absence or presence of oxygen. Bacteria are usually divided into two groups based on their Gram reaction: Gram positive bacteria and Gram negative bacteria. Though some bacteria are neither Gram positive nor Gram negative; and such bacteria are known as Gram variable organisms because the orientation of their cell wall makes them to be unresponsive to the stains (dyes) used in Gram staining technique. Examples of Gram variable organisms include Mycobacteria and mycoplasmas. Gram reaction is the basic universal technique used for the classification of bacteria into two groups, either as Gram positive or Gram negative bacteria.

Based on Gram stain reaction, bacteria can further be classified into four (4) other classes viz: Gram positive cocci, Gram positive rods, Gram negative cocci and Gram negative rods. Bacteria lack nucleus but has a structure known as nucleoid (that contains the nucleic acid) which directs the activities of the cell. Most bacterial species are free-living in the environment (occurring in water and soil) while the others are found in association with humans and animals. Actinomycetes are a different group of bacteria that form mycelium (a fungal structure). These bacteria have mycelial morphology, and they are very important in the production of antibiotics. Other bacterial forms are Chlamydia and Rickettsia which ismorphologicallydifferent fromthe normal prokaryotic cells and/or other forms of bacteria. Chlamydia and Rickettsia are obligate intracellular parasites (i.e., they live inside the cells of their host). Both exhibit virus-like characteristics, and cannot grow outside a living host cell like other bacteria (for example, Escherichia coli). Thus, Chlamydia and Rickettsia cannot be easily cultured on bacteriological media in the microbiology laboratory as is the case with other bacterial forms such as Mycobacterium tuberculosis, Staphylococcus aureus and Escherichia coli.

Fungi

Fungi (singular: fungus) are eukaryotic cells with rigid cell wall and cell membranes that contains ergosterol. They include the molds, yeasts and mushrooms. Fungi are heterotrophic, spore-bearing organisms which are widely distributed in nature, and are usually found in moist or wet environments. They are non-phototrophic (i.e., they lack chlorophyll) eukaryotes, and their mode of nutrition is usually absorptive i.e., they are saprophytic organisms. As saprophytes they feed on dead organic matters in the environment. Fungi exist primarily as hyphae, and they reproduce both sexually and asexually. Hyphae is a tubular, branching filament of fungal cells which bears the reproductive structures of fungi and also help fungal cells to absorb nutrients from their substrates. Hyphae can also occur in mass known as mycelium or mould colony. Fungi also form fruiting structures known as conidia (singular: conidium) or spores which help to disperse fungal cells to new environment. Conidia are fungal endospores and exospores that are asexual reproductive structures formed during the replication process of a fungus. Microconidia (small spores) and macroconidia (large spores) are the two types of conidia that exist. The spores of fungi are ubiquitous in the air, soil and dust, and they serve as route through which a given fungus is spread in a defined human or animal population. The size of fungi ranges from 2.0-1.0 µm (for moulds) and 5-10 µm (for yeasts). Most fungi act as decomposers by degrading the complex organic materials in their environment to simple inorganic molecules such as nitrogen, carbon and phosphorus which are finally made available for other living organisms. In order words, fungi are important agents of nutrient recycling in nature. Fungi have both beneficial and harmful effects which are felt by mankind, plants, and animals. They also cause damage on inanimate things such as clothes, food and furniture’s in the environment. While some group of fungi cause infections in humans, animals and crop plants; a considerable number of them are used industrially to produce bread, antibiotics, alcoholic and non-alcoholic beverages and wine.

Viruses

Viruses(singular: virus) are very small infective obligate intracellularparasites that consists of a capsid (protein coat) containing a nucleic acid (DNA or RNA). They only replicate inside a living host cell. The host cell is the cell (plant, animal, human or microbial cell) that the virus invades, and takes over its metabolic mechanism for its own benefit. Viruses lack the ability to replicate independently, and thus require the replication machinery of their host cell – which they take over to bring about their own reproduction. Outside the body of a living host, viruses are usually inert and inactive, and thus incapable of replication until they find a suitable living host to invade and begin replication. A virus is a genetic element that contains either an RNA or DNA as its genetic material, and its genome is enclosed inside a protein coat. They are not cells like other microorganisms because they lack some of the basic characteristics of a cell which include lack of autonomous metabolic ability, lack of ribosomes and lack of self-directed replication. Viruses are usually much smaller than other cells including prokaryotes and eukaryotes, and they only exhibit the features of a living organism when they infect other living organisms or cells including bacteria.

Bacteriophages are viruses that infect bacterial cells. Viruses are quite different from prokaryotic and eukaryotic organisms, and they are parasites of animals, humans and plants, bacteria and some protists. Their sizes vary from 0.015µm-0.2µm with the smallest virus measuring about 10 nm. Viruses are so minute that they could not be seen by a light microscope except with the aid of electron microscopes. Viruses exhibit different shapes including icosahedron, spherical, rod and flexuous shapes. The complete virus particle that exists outside a living host cell is called a virion. A virion is a complete virus particle, and it consists of a single-stranded (ss) or double-stranded DNA or RNA that is enveloped in a protein coat that may contain carbohydrates and lipids. Outside the body of a living system, viruses remain inactive because they are deficient of cellular components necessary for independent reproduction or metabolism. However, they are viable, and can go on to infect susceptible host cells when the opportunity arises. The term virion and virus are usually both used synonymously, but virion is often used to describe the form in which the virus moves from the cell in which it was produced to a new host cell in which it replicates its genetic material (DNA or RNA). Viruses cause plethora of diseases in plants, animals and humans. The dreaded acquired immunodeficiency syndrome (AIDS) which is caused by human immunodeficiency virus (HIV) is an example of the disease in which viruses can be implicated as causative agents. Those that study viruses are called virologists while virology is the study of viruses. Viruses unlike prokaryotic and eukaryotic cells can only be cultured in tissue (cell) cultures containing some elements of living systems such as tissues and cells from animal cells. They can also be propagated in embryonated egg cells or suitable animal hosts.

Algae

Some microorganisms contain photosynthetic machinery (i.e., they have chloroplasts containing chlorophyll), and thus can thrive in environments with sunlight, water, and carbon dioxide (CO2). However, some algae are heterotrophic in nature (i.e., they cannot manufacture their own food). This group of microorganisms that possess photosynthetic ability unlike bacteria, viruses and fungi are generally termed algae. Algae are photosynthetic microorganisms. However, algae lack some of the basic features of plants, and thus cannot be characterized as plants. Algae are ubiquitous eukaryotic microorganisms, and can be found in both aquatic and non-aquatic environments. They exhibit both sexual and asexual mode of reproduction. The study of algae is called algology or phycology. Algae are autotrophs, and are among the major primary producers of food in the food chain of nature due to their phototropic potential. They are mostly found in moist environments such as swimming pools, drainages, river side’s, streams, and even in pipes where they can clog water distribution pipes. Some algae species can serve as source of agar which is used as solidifying agents in the compounding and preparation microbial media. Algae are common contaminants in water bodies (including fresh and marine water bodies) where they can form algal blooms that destroy the aesthetics of the water body. Algal blooms adversely affect aquatic life, and thus can cause the death of other living things in the water body such as fishes.

Algae can partner with other eukaryotic microorganisms to form a community of organisms that share mutual benefits. Typical example of this is lichen, formed by the association of an algae and a fungus. Lichens are often found on the surfaces of rocks and trees, and they are classic example of mutualism that is often exhibited in a microbial community. Lichen can also be formed between a fungus and a prokaryote (for example, cyanobacterium). While the fungus provides an attachment upon which the algae grow, the latter provides food through its photosynthetic machinery for the former. Some algae grow and live within other living things such as plants, mollusks and worms. Algae that live inside other living organisms are generally known as endosymbionts. Only few algae are known to be parasitic in nature. Cyanobacteria (singular: cyanobacterium) are very different from algae and should not be classified as such. They are prokaryotes like bacteria; and cyanobacteria are the only prokaryotes that have the ability to carry out photosynthesis like algae, and thus they are autotrophs.    

Protozoa

Protozoa (singular: protozoan) are single-celled eukaryotic microorganisms that lack cell wall. They are motile and move by means of cilia, flagella and pseudopodia. Protozoa may include multicellular helminthic parasites or worms that use other animals including humans as their intermediate hosts and reservoirs. Their sizes vary from 5-200 µm, and they usually live in moist environments like soil, water and marshy environments. Protozoa are animal-like in nature, and can also feed on ready-made food in their surrounding environments. They lack chlorophyll, and are usually differentiated from other microorganisms on the basis of their morphological, physiological and nutritional characteristics. Protozoa have varying importance in nature including those that are found in the stomach of animals and helps in their digestion, and Plasmodium parasites which are one of the commonest protozoa because they cause disease in humans (i.e., malaria), and have been widely studied. Typical examples of protozoa include amoeba, Plasmodium and Trypanosome parasites. The study of protozoa is called protozoology.

OTHER INFECTIOUS BODIES

There are other infectious entities which are known to cause disease in humans and other animals, and which do not fall under any of the above taxonomic group or class of microorganisms. These infectious bodies are usually very small and sub-cellular in nature, and they are smaller than the known viruses that cause diseases in humans. These other infectious entities cause very rare, miscellaneous and fatal but progressive degenerative diseases in humans, plants and animals. They lack nucleic acids (excluding viroids which are made up of single-stranded RNA), and they are majorly made up of infectious protein particles that primarily affect the central nervous system (CNS) of their hosts (humans and animals inclusive).

Prions and viroids are examples of these other infectious bodies which are quite different from viruses, bacteria, fungi, protozoa and algae. Viroids for example are small, single-stranded (ss) circular RNA molecules that chiefly cause diseases in plants. Prions are proteinous molecules which are neither viruses nor viroids, and which cause a range of diseases in humans (for example, Creutzfeldt-Jacob disease, CJD) and animals (for example, scrapie and bovine spongiform encephalopathy, BSE). Prions are sub-cellular infectious entities that lack nucleic acids, and they cause a range of degenerative disease that affects parts of the central nervous system (CNS) of both animals and man.

PATHOGENIC ANIMALS THAT CAUSE INFECTIOUS DISEASES IN HUMANS

Infectious diseases in humans and other animals are majorly caused by infectious particles or entities (i.e., microorganisms which are too small to be seen by the naked eyes) which are generally termed pathogenic microorganisms including bacteria, viruses, fungi and protozoa. But they also exists other infectious bodies, some of which can be seen under the microscope and which can also be visible by the naked eyes because of their presumed larger forms or sizes. These pathogenic animals are referred to as parasitic worms (for example, helminthes) and arthropods (for example, mites). Helminthes and arthropods are invertebrates, and they are found in the Kingdom Animalia. They are known to cause a variety of infectious diseases in humans and animals. Arthropods which may include insects usually serve as vectors which help to transmit pathogenic microorganisms (for example, bacteria) to humans usually through a bite. Microorganisms can also reach humans and cause disease through arthropods when they come in direct contact with their food or defaecate on the body of humans. Helminthes includes all parasitic worms such as roundworms (nematodes), tapeworms (cestodes), and flatworms or flukes (which are trematodes), and they are known to cause a variety of gastrointestinal infections in humans. 

Further reading

Brooks G.F., Butel J.S and Morse S.A (2004). Medical Microbiology, 23rd edition. McGraw Hill Publishers. USA.

Gilligan P.H, Shapiro D.S and Miller M.B (2014). Cases in Medical Microbiology and Infectious Diseases. Third edition. American Society of Microbiology Press, USA.

Madigan M.T., Martinko J.M., Dunlap P.V and Clark D.P (2009). Brock Biology of Microorganisms, 12th edition. Pearson Benjamin Cummings Inc, USA.

Mahon C. R, Lehman D.C and Manuselis G (2011). Textbook of Diagnostic Microbiology. Fourth edition. Saunders Publishers, USA.

Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, Michael A. Pfaller (2007). Manual of Clinical Microbiology, 9th ed.: American Society for Microbiology.

Wilson B. A, Salyers A.A, Whitt D.D and Winkler M.E (2011). Bacterial Pathogenesis: A molecular Approach. Third edition. American Society of Microbiology Press, USA.

Woods GL and Washington JA (1995). The Clinician and the Microbiology Laboratory. Mandell GL, Bennett JE, Dolin R (eds): Principles and Practice of Infectious Diseases. 4th ed. Churchill Livingstone, New York.

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