What are Microbes? Microbes are microscopic, single-celled organisms that are found everywhere in our world. There are five main groups of microbes populating earth – bacteria, archaea, protists, fungi and viruses. While many microbes can cause disease (e.g. the ‘flu virus or potato blight fungus), the majority are beneficial and in fact essential to life on earth.
What is a Microbiota? A microbiota is the entire collection of microbes in a specific ecological niche, such as in a human gastrointestinal tract or on a tree. In reality, living organisms such as animals (including humans), are not single individuals, but an ecosystem that includes a huge variety of microbial cells which live in symbiosis with their host.
What is a Microbiome? A microbiome is all the collective genes of the microorganisms that reside in an environmental niche. The human genome has 23,000 genes, but it is estimated that the human microbiome has 3 million genes, many of which interact with, and at times even control, our human genes and contribute to human survival. So each microbiome is very complex. Here an excellent video by the Microbiology Society on “What is a microbiome” and a report they have published on unlocking the potential of the microbiome
Bacteria were among the first forms of life to appear on Earth and are present everywhere, from the glaciers to hot springs. Bacteria also live in symbiotic and parasitic relationships with plants and animals. There are typically 40 million bacterial cells in a gram of soil and one million bacterial cells in a millilitre of fresh water. It is estimated that there are 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants and animals. Bacteria are single-celled microbes that do not contain a nucleus, but rather have their genes floating free in a twisted, thread like mass called a nucleoid. Bacteria are essential for many processes that we take for granted – e.g. lactobacilli curdle milk into yogurt, decomposition of dead plants or animals. Some bacteria are pathogenic, causing infections like pneumonia and MRSA.
Bacteria can be killed by antibiotics, which are important for curing bacterial infections. However in recent years, the improper or unnecessary use of antibiotics has promoted the spread of several strains of bacteria which are resistant to antibiotics, which is termed Anti-Microbial Resistance (AMR), leading to a situation today where some infectious bacteria are no longer susceptible to antibiotics. AMR is a global challenge. A very promising tool in this fight against AMR are Bacteriophage.
Archaea are also single celled organisms, and were initially classified as bacteria, but since then have been separated into the domain Archaea, which share properties with both bacteria (morphology (how they look) and presence of a single circular chromosome) and eukaryotes (similar metabolic pathways, and machinery for DNA replication). Archaea are found in a wide range of habitats, and are particularly abundant in the sea where the archaea in plankton are thought to be one of the most plentiful groups of organisms on the planet. Archaea are also found in the human microbiota e.g. methanogens are present in the colon where they aid digestion.
Protists: The simplest definition of protists is all the eukaryotic organisms (containing a nucleus) that are not animals, plants or fungi. The majority of protists are unicellular, or come together to form colonies of a one or a couple of distinct cell types. Protists have nuclei that contain their genes and internal structures, called organelles, that carry out specific functions e.g. mitochondria to generate energy, plastids that carry our photosynthesis (use sunlight to convert carbohydrates into nutrients). Protists include algae, amoebas and ciliates such as paramecium.
Fungi are eukaryotes that include yeasts, moulds and mushrooms. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. The discipline of biology devoted to the study of fungi is mycology (from the Greek “mykes” mushroom). Fungi are abundant worldwide, but often inconspicuous due to their small size and hidden locations (e.g. in soil).They perform an essential role in the decomposition of organic matter and have long been used as a direct source of human food, e.g. mushrooms and truffles; as yeast in bread making; and in the fermentation of various foods, such as wine, beer, and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and are also used as biological pesticides to control weeds, plant diseases and insect pests. Fungi can be significant pathogens of humans (e.g. athlete’s foot, candidiasis) and other animals. Losses of crops due to fungal diseases (e.g. rice blast disease) or food spoilage can have a large impact on human food supplies and local economies.
Viruses are microscopic infection machines. Virus comes from a Latin word meaning “slimy liquid” or “poison.” Viruses are quintessential parasites – they can’t grow or multiply on their own and can only replicate (make copies of themselves) inside other living cells. Viruses infect all cell types, from animal to plant to bacteria – viruses that infect bacterial cells are called bacteriophage. There are millions of types of virus, which are found in almost every ecosystem on Earth and are the most numerous type of biological entity. The average virus is 100 times smaller than an average bacterium, so most are too small to see with an optical microscope, and need electron microscopes to be visualised. Viruses cause widespread diseases in plants, and it is estimated they cause over €60million loss in crops each year. Human infections caused by viruses include polio, encephalitis, smallpox, ‘flu, common cold, measles, AIDS.