I have a background in microbiology through both education and career, as such I am nearly consistently asked questions about microbes and their relative importance. In this post, I wanted to talk (broadly) about what microbes are, and why they are important, note that if I was to cover everything I would likely need to write for many lifetimes, so this post will be fairly basic and fairly high level.

What are Microbes?

Whilst this is not a great definition, for the purpose of this article you can consider microbes to be tiny living (some conjecture there) things that are found all around us but on their own, they are too small to be seen by the naked eye. The most common types of microbes can include bacteria, viruses, fungi, and a group known as protozoa. There are other types I have left out (i.e, Algae, Archaea and Prions) for simplicity. With this definition, it is worth noting that some microbes you can see (e.g., mushrooms) but that is because they are many microbes in one.

Whilst there are many different types of microbes, not all of them actually make us sick, and many of them are important for either our own health or for environmental processes (such as material breakdown i.e., in forests).

What are Bacteria?

Bacteria are a member of a huge group of unicellular microorganisms, these organisms have cell walls but lack organelles and an organised nucleus. In many ways, bacteria are much simpler than other organisms (i.e., fungi) and their genetic information is contained in a single loop of DNA. On some occasions, extra genetic information is stored in another (extra) circle called a plasmid (for example antibiotic resistance).

There are a significant number of different types of bacteria, so we classify them in different ways. This can be based on the content of their cell wall (we call this gram-negative or gram-positive), or we can also classify them based on their basic shapes (i.e. spherical – cocci, rod – bacilli, spiral – spirilla, comma – vibrios or corkscrew – spirochaetes).

Bacteria are found in every habitat on earth, from soil to oceans. In addition to those bacteria that live by themselves, some bacteria can also live on other organisms (i.e., there are bacteria that live on your skin), and other bacteria can live inside organisms (i.e., there are bacteria that live in your gut).

Some bacteria can be considered ‘good' in that they play an important role in the cycling of nutrients (i.e., bacteria that break down dead plant matter or live in the soil) whilst there are (a relatively smaller number) of bacteria that can also be pathogens and cause illness in animals and plants.

What are Fungi?

Whilst I am passionate about all types of microbes, Fungi have a special place in my heart and are one of my favourite groups of microbes. Whilst oversimplified fungi are either single-celled (i.e., yeasts) or can be very complex multicellular organisms, they are found nearly everywhere but mainly occur in soil, on plant material, and inland (rather than in water or oceans).

Fungi are grouped (or sub-divided) based on their life cycles, the presence or structure of their fruiting body, or the types of spores and their arrangement (spores can be considered simplistically as seeds). The three main groups of fungi are:

1. Multicellular filamentous moulds
2. Macroscopic filamentous fungi that produce large fruiting bodies (often known as mushrooms but note the mushroom is only one part which is above the surface that we can see)
3. Single-celled microscopic yeasts

(1) Moulds are a type of fungi that are also multicellular and filamentous. These are made up of very fine thread-like materials which we call hyphae. These hyphae grow and extend at the tip and divide along their length (usually) creating long branching chains and these chains intertwine and form a structure called a mycelium. Digestive enzymes are secreted from the hyphae and these break down organic matter into smaller molecules that can be used as food. An example of this is breaking down wood by wood rot fungi, but can also include nutrient cycling.

Some of the hyphae can provide spores which are essentially hardy seeds, since fungi can't really move the spores are a way to allow the fungi to spread (i.e., through the wind) and to germinate in other locations.

(2) Macroscopic fungi are a bit different to the filamentous moulds in that they have a hyphal structure but then they produce a visible fruiting body (often referred to as a mushroom or toadstool). The fruiting body contains lots of tightly packed hyphae which create the different parts of the structure (like the cap), and these usually have gills or gill-like structures underneath which are covered with spores and help the spread.

(3) Yeasts are a bit different to moulds and macroscopic fungi in that they are small single cells. They multiply through budding (like cell division) and can be important in common processes like making bread and brewing beer. Whilst years can be important in common processes (like Saccharomyces), there are also other species of yeast that are opportunistic pathogens and can cause infections in individuals without a healthy immune system (i.e., Candida)

What are Viruses?

Viruses are a very different type of microbe, a fully assembled virus is called a virion which is basically genetic information that is encapsulated within a protective layer (called a capsid) and occasionally another layer (called an envelope). Viruses are very different to many of the other microorganisms as they don't have the ability to reproduce on their own, rather require a host cell in order to replicate.

There are many different types of viruses, some infect bacteria (which are called bacteriophages) whilst others infect plant cells, and others infect animal cells.

Viruses require a host cell to replicate, and in general, there are six steps in the lifecycle of a virus. This includes:

• attachment where the virus attaches to the surface of a cell,
• penetration where the virus enters the host cell,
• uncoating where the protective coating (i.e., the capsid) around the genetic information is removed or broken down to uncover the genetic information,
• replication where the host cell starts to read the genetic information and starts to create viral proteins and copies of the genetic information of the virus (the genome),
• assembly where the components of the virus are put together to create fully assembled viruses,
• virion release where the fully assembled virus (virion) is released from the host cell (usually through the cell being ruptured) and can go and infect other cells.
• Some viruses also have a latent phase where the genetic information can be retained but the virus is not replicated and remains dormant until retriggered (i.e. cold sores).

There is a little bit of conjecture around if viruses are alive as they can't replicate on their own, and require a host cell in order to replicate, by themselves they are just a series of proteins and coded genetic information.

What are Protozoa?

Protozoa is an informal term for a group of single-celled microscopic animals that have a nucleus and other membrane-bound organelles. They have fairly complex internal structures and some even have structures for propulsion or other types of movement. As this is a large informal group there are lots of different types of species including ones like Amoebae which can change their shape through to others with a fixed shape and complex structure.

All of the protozoa use organic carbon as a source of energy rather than generating energy themselves so have to consume organic carbon from other organisms. This can include either ingesting the other smaller organisms whole or taking up dissolved organic matter or micro-particles.

There are a significant number of different types of protozoa, but these can include things like amoebas, flagellates, ciliates, sporozoans and foraminifers.

Some of the protozoa are parasitic and can live in other plants and animals where they can cause disease. An example of this is Plasmodium which causes malaria.

Am I exposed to microbes in my daily life?

Absolutely, in your everyday life, you are constantly exposed to microbes. These include (but are not limited to) the bacteria that live in or on our bodies (i.e., gut bacteria), viruses that we are constantly challenged with (i.e., SARS-CoV-2, Influenza, and other respiratory viruses), in addition to Fungi that are found in the natural environment. As previously mentioned the seed of fungi is known as a spore, and in your daily life, you are exposed to sores. Estimates suggest that spore concentrations in the air can range from 200 to 1 million spores per cubic metre of air, the mean spore content outdoors is often 100 to 1000 times greater than pollen.

If you touch fruits, soils, water from puddles/lakes/dams and other organic materials you are likely exposed to many more different types of microorganisms, which can include bacteria, protozoa and more.

Can microbes be ‘bad’ ?

This is a really tricky question, and it often depends on how you define ‘good' or ‘bad’. Whilst not always, in many cases microbes have evolved to carry out an evolutionary function (i.e., breakdown of timber) but often there are cases where this function is important but when it occurs in the wrong environment it is a problem.

Equally, there are many microbes that for a normal healthy person in a normal environment they are not an issue at all, but if the person has a weakened immune system then an infection can occur which can be deadly, it is not that these microbes are normally always an issue, just in some people they may be (I.e., an opportunistic infection).

That said, there are many microbes that are downright terrifying and I don't know that in my take I would consider them to be good (that said they do achieve a function). Take for example the fungal species Ophiocordyceps unilateralis which is known as the zombie ant fungus, this fungi has evolved to specifically infect ants, it is a pathogenic fungus that is found predominately in tropical forest ecosystems and causes infected ants to leave their canopy nests for the forest floor and then use their mandibles to attach themselves to a major vein of a leaf where the ant will remain until its eventual death (typically 4 – 10 days) where the fungi can reproduce, create fruiting bodies, and then eventually rupture to release the fungal spores.

Whilst some microbes are unusual (like the one above), there is also a range of microbes that are not usually a problem for medically healthy people, but in immune-weakened individuals, they can cause what is known as an opportunistic infection. Many bacteria, yeasts and other microbes fit into this category.

Can microbes be ‘good’ ?

Without many of the microbes that exist, I would suggest that life on this earth would not exist. So by that logic, I would say that many of the microbes are good, and play important functions.

These functions vary, in the environmental context microbes can be essential in the nutrient cycling process by removing carbon and other nutrients from organic material and releasing it into the environment, this role of being a recycler is essential to life.

They can also play important roles in controlling disease, in the human body many microbes exist that are a normal part of the microbial population and their presence aims to suppress the growth of bad bacteria. In fact, we also know that many of the things we rely on in everyday life (i.e., Penicillium and antibiotics) come from microbes such as the fungi Penicillium spp.

We also rely on microbes for many of the things we enjoy in everyday life, things like beer which is created by microbes, and even bread which requires yeast to be created, without these things life would be a little bit less interesting (and delicious).

I hope this gives a bit of an idea of the different types of microbes and their relative importance, in reality, we rely on microbes to undertake essential functions such as nutrient recycling and decay of dead organic material, in addition to creating many of the nice foods and drinks we consume. Not all microbes are ‘good' and can be detrimental to human health, but equally not all microbes are bad and some create useful things that keep us healthy hence are not really ‘bad'.