Microbes: A brief intro.

Fiyin Akinsiku
Sep 7, 2018 · 8 min read
credit: PHD Comics

Welcome to my first microbiology post. This is a really, really broad and complex topic so I will start with general basic information (definition and taxonomy) then narrow it down to focus on Kingdom Bacteria.

What are microbes and how were they discovered?
Microbe, a shorter name for microorganism, can be simply defined as a very small (micro) living thing (organism) that can only be seen with the aid of a microscope. There are different types of microscopes used in viewing microbes however the light microscope is the most commonly used and as the name implies, it makes use of visible light coupled with a magnifying lens. Human beings are multi-cellular organisms that have organ systems made up of organs; these organs are made up of tissues which are in turn made up of cells. The list goes on but this is just so we can imagine and understand how small microorganisms are compared to humans. The study of microorganisms is called Microbiology. Microorganisms differ from each other not only in size, but also in structure, habitat, metabolism, and many other characteristics.

credit: Pinterest

Fun fact: There are more microbes than body cells in the average human being, majority of them in the gut and on our skin.

Antonie van Leeuwenhoek is one name that always comes to mind. The first time I came across this name was in 2012 when I was preparing for my undergraduate studies. I got the Prescott’s Microbiology textbook ahead and was trying to read as much as possible before school, obviously I got bored and did not even get halfway but this name sounded weird to me then plus he was described as the “Father of Microbiology” so I memorized it and dropped the book. However, in the course of reading up more on the history of microbiology, I found out that it was actually the joint effort of Robert Hooke and Leeuwenhoek (notice how they rhyme?). Hooke presented the first published depiction of a microorganism, the micro-fungus Mucor, in his book Micrographia (1665)and about nine years later Leeuwenhoek observed and described microscopic protozoa and bacteria. This interesting article gives more insight on the specific roles they played.


How are they grouped? What are the types? How are they identified?

Taxonomy is a branch of science that deals with classification based on shared characteristics. This includes the identification and scientific naming(nomenclature) of living things. This grouping makes it easier for us to identify similarities among organisms in a particular group. There are presently eight main taxa: Domain, Kingdom, Phylum, Class, Order, Family then Genus and Species; the groupings used for formation of a scientific name, the highest taxonomic rank being Domain. The three domains are: Bacteria, Archaea and Eukarya. Viruses are not included in this.

I found this website with funny mnemonics for taxonomy and I think it would really help in remembering.

My favorite: Drunken-Kangaroos-Punch-Children-On-Family-Game-Shows

If you imagine it long enough, I promise you will never forget it.

Permit me to digress a bit. Every living thing was initially divided into two groups: Plants and animals but technological advancements have made it easier to properly differentiate and classify accordingly mostly based on nutrition, reproduction and cell type. All cells are either prokaryotic or eukaryotic and although they have a few similarities, they differ in several ways. Prokaryotic cells are single-celled, have no membrane-bound nucleus, have a circular DNA shape, reproduce asexually, are much smaller than eukaryotes, and are divided into bacteria and archaea while eukaryotes can be multi-celled, have a membrane-bound nucleus, have linear DNA, are capable of reproducing sexually, are much larger than prokaryotes, and make up plants, animals, protists, and fungi.

Viruses are infectious, acellular, genetic entities that lie somewhere in the grey area between living and non-living states. That is, they cannot be categorically classified under either group. Viruses have qualities of both living and non-living things. A virus cannot reproduce or carry out metabolic processes on its own; it has to be inside a living cell/organism to do so. The entire infectious virus particle consists of the nucleic acid (DNA or RNA) and an outer shell of protein. Viruses cause a number of diseases in humans including: smallpox, the common cold, chickenpox, influenza, herpes, polio, rabies, Ebola and AIDS. They also cause disease in other microorganisms. One positive side is that they are useful in genetic engineering to transfer genetic material between different species of host.

photo credit: FunkyJunk

Now back to taxonomy. The three-domain classification basically recognizes the difference between bacteria and archaea. Both were previously classified as one under Prokaryota and archaea was called Archaebacteria but this changed after Carl Woose discovered that they had a different rRNA barcode hence, three different domains.

Next up is the Kingdom taxa. This is where most classification lectures begin. Most taxonomist recognize six kingdoms: two prokaryotic kingdoms previously classified under one kingdom Monera(Archaebacteria and Bacteria), a large unicellular eukaryotic kingdom (Protista) and three multicellular eukaryotic kingdoms (Fungi, Plantae and Animalia).

Protista: or protists, are mostly unicellular but some like Algae are multi-cellular. They can only move with the aid of water (one of them is responsible for malaria). Some create their own food like plants, through photosynthesis, others get their nutrients through absorption just like fungi while some get their nutrients through digestion but are neither plants, animals nor fungi. Some produce sexually by gametes while others produce asexually by binary fission. Basically, any microscopic organism that does not fall into any of the other kingdoms is considered a part of the Protista kingdom. There is really no specific quality binding all protists and proposals have been made to divide it among several new kingdoms, such as Protozoa and Chromista in the Cavalier-Smith system.

Fungi: were previously classified under plants but later separated after it was discovered that they do not carry out photosynthesis and have different cell wall and cell membrane components. This kingdom includes both unicellular (yeasts)and multicellular (molds, mushroom)organisms. Fungi are heterotrophic: they use complex organic compounds as a source of carbon and obtain nitrogen from their food just like animals but the difference is that they secrete enzymes to digest it outside before ingesting the obtained nutrients. They can reproduce sexually and/or asexually; Perfect fungi reproduce both both ways while imperfect fungi reproduce only asexually (by mitosis). They can occur in air, water, soil and on plants and animals.

Plantae: or Plants are multi-cellular eukaryotes and unlike Fungi, contain highly specialized organelles in their cells, such as chloroplasts, which help them carry out photosynthesis and are autotrophic i.e. they feed by making use of simple substances (sun, water and carbon dioxide) present in the surroundings. Plants are probably the most important group to living organisms as they provide food, oxygen, shelter and so on, for most food chains in the planet’s major communities.

Animalia: as the name implies, includes all animals and is described as the largest, most complex and most studied group. They are heterotrophic, multicellular eukaryotes. They obtain nutrition by feeding on complex sources and most of them reproduce sexually.

Now, to the two kingdoms I’m interested in at the moment: Archaeabacteria and mostly Eubacteria

Archaebacteria: Although this is the most recent addition to the kingdoms of organisms, Archaebacteria are the oldest known living organisms. They were initially grouped together with Eubacteria under Kingdom Monera but that changed after major differences were noticed in their nucleic acid. I said something about that earlier. They are adapted to living in extreme environmental conditions, like near volcanic activity, deep oceans, etc, and do not need oxygen and light to survive, basically they are the “wild ones”.

Eubacteria: This kingdom makes up most of the bacteria in the world and they are considered to be true bacteria. They can be found in almost every type of environment, can be heterotrophic or autotrophic and can reproduce at an alarming rate under the right conditions (asexually by binary fission). Bacteria are the main microorganisms that make up the human microbiota with approximately 39 trillion bacterial cells in the human body, majority of them in the gut and on our skin. This is quite a large number considering the fact that there are 30 trillion human cells in the body. A lot of people hear “bacteria” and automatically think “disease”. While it is true that a lot of them cause disease, a number of them are actually beneficial, even necessary, for some of our bodily functions.


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The remaining six taxa:Phylum, Class, Order, Family, Genus and Species are further classification of an organism and the last two, like I mentioned earlier, are employed in binomial/binary nomenclature i.e two-name naming system, just like we have our first name and surname. This system was formalized by Carl Linnaeus. There are various rules that govern this naming system. The first name is the genus the organism and the first letter is always capitalized while the second name, the specie, is not. The names are also always written in a font different form that of the surrounding text; when typing it is italicized and when writing they are underlined. Examples:

  1. The scientific name of Beans is Phaseolus vulgaris.
  2. The scientific name for the single-celled parasite which causes malaria is Plasmodium falciparum, the female anopheles mosquito is just a vector.