News: Bacteria, Viruses, Fungi ... All the Words You Need to Know to Understand Microbes

Bacteria, Viruses, Fungi ... All the Words You Need to Know to Understand Microbes

All fields of study have their own language. For people interested in learning about microbes, the language can sometimes be downright difficult — but it doesn't need to be. From antibiotics to xerophiles, we have you covered in an easy-to-understand glossary.

Terms are listed alphabetically, and if you're looking for a specific term, use the "Find" function in your desktop browser (Ctrl + F or Command + F) to jump right to it. You can browse for information and for interest. Just make sure to check back, because we are always updating our glossary and references.

adaptive immune system

Mounting a specialized response to specific pathogens, the adaptive or acquired immune system is one aspect of your immune system. The adaptive immune system enables your body to develop a long-lasting response, and to remember a particular pathogen after exposure such as chickenpox or a vaccination against infection by tetanus bacteria.

The other main aspect of the immune system is the innate immune system, which includes barriers like skin and mucous, as well as non-specialized immune system molecules like natural killer cells, and proteins like cytokines.


A class of drugs that inhibit or kill microorganisms, typically bacteria.


Manufactured by the immune system, antibodies are specialized proteins that are either released into the blood or located on the surface of white blood cells. They target material identified as foreign to the body, like viruses or dangerous bacteria, and mark it for destruction.


Looking a lot like bacteria, archaea are single-celled microorganisms that have no nucleus or other organelles bound by membrane inside their cytoplasm. Archaea are known for living in extreme environments, but are capable of living elsewhere — including in the human gut.

Archaea are one of the top three domains of life established in 1977 to categorize cellular forms of life. In addition to Archaea, the other domains are Bacteria, an extremely large group of microorganisms, and Eukaryota. Humans, plants, animals, and insects are in the Eukarya domain. The Bacteria domain is home to your favorite probiotics, as well as the bacteria that causes streptococcal pharyngitis (strep throat).

B cells

White blood cells that produce specialized proteins called antibodies to attack foreign pathogens in the body.


Much larger than viruses, bacteria are a diverse group of single-cell microorganisms that display a wide variety of shapes, including rods, spirals, or spheres. Bacteria divide and reproduce themselves through a process called binary fission.

There are a large number of bacteria, and some are dangerous while others are beneficial. The human body is home to trillions of bacteria that live on and in your body. Your gut microbiota, or microbiome, help your body regulate digestion and maintain healthy immune function.

Thermophilic bacteria, extremophiles that live at high temperatures. Image by Amateria1121/Wikimedia Commons


Even bacteria can have viral infections! Phage, or bacteriophage, are viruses that infect and replicate inside bacteria. Once attached to a bacteria, phages insert their genetic material into their host. The genetic material sets to work quickly dissolving and restructuring the cellular processes of the bacteria, making way to replicate the phage. Phages are common wherever bacteria are found, and may offer an additional option for targeting and reducing populations of harmful bacteria.

biological agent

If a microorganism is weaponized, it is called a biological agent. Biological agents, like a bacterium, virus, or other toxin, could be deployed for use in bioterrorism or biological warfare. They could be weaponized by making them hardier and more able to survive environments, or they could be changed in ways that make them easier to spread or to make them more deadly when they do infect someone.

bone marrow

The spongy tissue within bones that produce white and red blood cells and platelets. The synthesis of blood products within bone marrow is called haematopoiesis.


The smallest structural unit of a living organism. Cells are often called the "building blocks of life." Not all cells look the same, and different types of cells have different functions and express different proteins.

Cells can survive on their own, as single-celled organisms, though many create multicellular organisms made up of many cells working together. Within a multicellular organism, cells can organize into tissues, larger conglomerates of cell types that work together to perform a function.

Humans are made up of about 200 types of cells. The different cell types within a multicellular organism all have the same genetic material, but different proteins and genes are turned on in different combinations to enable the cells to carry out different functions.

cell culture

Cells raised in a lab in a controlled growing liquid (called the medium) are a tissue or cell culture. These cells can be from any species, or of any type, and can act differently than they would in a tissue or living organism. Cells in culture can often be from cancerous tumors or are adapted with genetic changes to live outside of the body, so they aren't always a great representation of how those cells work in an organism.

Cultured cells are used to study how the cell lives and grows, how its proteins work together, and how they are impacted by the environment or drugs. When a drug study is done or a research finding confirmed in cell culture, it doesn't necessarily translate to humans, especially if the cells tested are not human cells or are not from the right tissue.


A relationship between two organisms in which one participant benefits and the other receives no benefit but is not harmed.

Centers for Disease Control and Prevention (CDC)

A federal agency of the US government, the CDC has a broad mandate to protect national health through conducting research and responding to health threats.


A prominent player in mediating messages in the the immune system, cytokines are a group of proteins produced by several types of cells. Cytokines mediate signals between cells during pain response and inflammation, A cytokine storm, also known as cytokine cascade or hypercytokinemia, is a potentially fatal immune reaction caused by an overabundance of cytokine proteins produced in response to an infection or injury. Specifically, this causes septic shock, a dangerous and deadly condition.

deoxyribonucleic acid (DNA)

The hereditary material located in almost all cells of a living organism. DNA uses the cell's machinery to make copies of itself, and carries the genetic code that governs the growth and development of the organism within which it resides.


With many origins, a disease is a condition that causes damage to the cells and the function of a living organism.


A condition or illnesses that is endemic is native to and is continually transmitted in a specific geographic area. For example, malaria is endemic to many tropical parts of the world.


Essential for life, enzymes are protein molecules created by cells that are vital to biochemical actions. They typically have very specific purposes and interact with other proteins or genetic material to carry those actions out. Many enzymes acting in a linear fashion create an enzyme cascade.


An outbreak of new cases of a disease or illness in a population at a particular time.


Cells that contain internal structures called organelles. These internal structures include the nucleus (which holds DNA), the mitochondria (which turns molecules into energy for the cell), and others. Animals, plants, and fungi are all members of the Eukaryota domain.

European Centre for Disease Prevention and Control (ECDC)

Organized in 2004, the ECDC is an independent agency of the European Union tasked with supporting and maintaining European defense to infectious disease.


Bacteria are often called extremophiles when they live in extreme environments like volcanoes, heated undersea vents, the vacuum of space, or within solid rock. They often live off of non-organic materials, like sulfur or iron.


Mushrooms, yeast, and molds are common examples of fungi, which are important decomposers. Fungi have many uses, but can also be pathogens and cause disease and infection.

Yeast fungi, Saccharomyces cerevisiae. Image by Mogana Das Murtey and Patchamuthu Ramasamy/Wikimedia Commons

gastrointestinal tract

From mouth to rectum, the gastrointestinal tract is the system of the body that ingests, digests, absorbs, and excretes food. It contains a diverse variety of bacteria, archaea, viruses, and fungi that help break down and metabolize food.

genetically modified organism (GMO)

When genetic material within an organism is removed, added, or altered, it is called a genetically modified organism (GMO). While GMOs are usually discussed in the context of food, vaccines composed of genetically modified bacteria, like Salmonella, could someday save lives of those suffering virulent forms of pneumonia and other conditions. Every GMO is different. Health and environment testing needs to be done for each product individually, and there's no benefit or truth in a general overarching claims that GMOs are dangerous or unhealthy.


A microorganism that causes disease. A more academic term for a germ is pathogen, which is basically a disease-causing virus, bacteria, or fungi.


A type of white blood cell with small protein-containing granules. High numbers of granulocytes may signal the presence of infection, while chronically low granulocyte populations could hamper immune function.


The physical environment, or geography, in which an organism or microorganism lives.


See "bone marrow" above.

herd immunity

The vaccination, or acquired immunity, of a group of people against a contagious disease. In a community, the higher the numbers of immunized individuals, the lower the risk of outbreak, even for members of that community that aren't immune to a disease. The more people in the community are vaccinated, the less pathogen is spreading through the population.

Herd immunity is very important for protecting members of the group that can't get a vaccinations themselves: The immune-compromised and those that are too young. Herd immunity is also a term used to indicate a threshold of the population needed to dampen contagion or threat to the group in the event of an outbreak.


An organism in or on which another organism lives. Parasites that live on or in a host often cause disease or damage, though not all do. Humans and other plants and animals can be hosts not only to dangerous bacteria, viruses, and parasites, but to helpful ones as well, which can do jobs like digesting food or creating compounds the host can't make itself. Bacteria themselves can be hosts to smaller bacteria, archaea, or viruses.

immune system

A highly complex network of tissues, cells, organs, and molecular signals, the immune system protects living organisms against invasion of foreign particles or pathogens. The two aspects of the mammalian immune system are the innate and the adaptive immune system, which work in different ways to protect an organism. Other organisms, like bacteria, have their own immune systems as well, they're just less complex.


The physical ability of an organism to fight off a infectious agent without becoming sick. Immunity can be gained through exposure to a wild virus or pathogen, or through immunization, among other means.


A controlled process carried out by injection and other methods, immunization strengthens the immune system of a living organism against a pathogen.


When microbes penetrate or enter a living organism and replicate. During infection, symptoms arise from both the infectious agent and the immune system's response to it.


A front-line response by the innate immune system to invasion by a pathogen, injury, or irritant. Inflammation is characterized by dispatch of white blood cells, lymph fluid, and other cellular products (including cytokines) to a body area that is injured or under attack by pathogens. Inflammation generally causes redness, pain, heat, and swelling. Inflammation clears out dead and dying cells and begins the healing process.

innate immune system

The innate immune system offers constant protection from pathogens and organisms through physical barriers such as the skin, substances like mucous, shedding of skin cells, and chemical response — like the release of cytokines related to an inflammatory response after injury or during infection. The innate immune system responds quickly to pathogens or injury while the adaptive immune system takes longer to respond through synthesis of specialized antibodies to attack the infectious agent.


A type of white blood cell, leukocytes are part of an immune response to infection or injury.


Lymphocytes are also white blood cells in the immune system. Two major types of lymphocytes include B cells that produce specialized antibodies to attack pathogens, and T cells which destroy cells in the body that are damaged or infected.


White blood cells that circulate in your bloodstream continually and protect wounds from opportunistic germs seeking entry into the body.


Invisible to the naked eye, microbes (also called microorganisms) are visible with a microscope. A microbe could be a fungi, algae, bacteria, or other small living organism. Viruses, though not alive, are sometimes lumped into microbes.


The community of bacteria, viruses, fungi, and other microbes that live on and within our bodies is called the microbiome, or microbiota. Your microbiome is unique and reflects your genetic inheritance, where and how you live, and what you eat. Research on the microbiome is a rapidly expanding research field, offering us insights into our constant interactions with the microbes within, and without.

micrometre (µm)

Often called a micron, a micrometre or micrometer is a size that is one millionth of a metre. Microns and micrometre are often used to describe the size of cells and microbes.


A very small living organism visible with a microscope is called a microorganism, or a microbe. Microbes include viruses, bacteria, archaea, fungi, plants like algae, and protozoa, among others.


A type of white blood cell with a big appetite. Produced like other blood products in bone marrow, monocytes spend their young life circulating in the blood stream before maturing into macrophages ("big eater") within tissues of the body. As a phagocyte, monocytes and macrophages engulf cellular debris, damaged cells, and infectious agents.


A major type of white blood cell. Neutrophils are the first responders of the adaptive immune system, and attack and consume infectious agents.

MRSA bacteria being phagocytized by neutrophil (white blood cell) that is colored blue. Image via National Institute of Allergy and Infectious Diseases (NIAID)


Specialized compartments within a cell are called organelles. Seen only though a microscope, each cell has a distinct function to support survival of the cell. For example, the nucleus of the cell regulates the activity of the cell. Cell compartments are to the cell, what your internal organs are to your body.


An outbreak occurs when a disease or illness in a geographic area occurs at a higher rate than expected for the area or circumstances.

Image by Athalia Christie at CDC Global/Flickr


Refers to a global outbreak of a disease or illness. The European Centre for Disease Prevention and Control (ECDC) defines a pandemic as "an epidemic occurring worldwide, or over a very wide area, crossing international boundaries and usually affecting a large number of people."


Residing on or in a living organism, parasites cause damage and disease by drawing nutrients from its host. Parasites can be large or small and are found in every kingdom of life. The relationship between a parasite and a host is called parasitism, in which one organism is harmed and one benefits.


A disease-causing microorganism that is sometimes called a germ.


See "bacteriophage" above.


A type of cell that ingests by engulfing foreign substances and pathogens. Different types of phagocytes in the human immune system include neutrophils, monocytes, and macrophages.


Certain undigestible substances that promote and sustain the health of probiotics and bacteria in the intestinal tract (gut microbiome).


A type of infectious protein that acts like a virus but doesn't contain DNA. Prions are infections because misfolded versions of the prion protein can misfold normal version of the prion protein to spread disease. Misfolded proteins aren't able to do their job correctly. Normal prion proteins are found throughout the kingdom of life and have important roles.


Microorganisms used in food and other products intended to bolster health. Research continues to develop around how probiotics work, and how they could be helpful for supporting the human microbiome.


Cells that do not contain internal structures called organelles. Prokaryotes include the Archaea and Bacteria domains.


Composed of chains of amino acids, proteins are larger molecules that perform many different functions essential to biological life. Depending on their composition, proteins could act as antibodies in the immune system or help with signaling between cells and organs in the body. DNA, a cell's genetic code, serves as the blueprint for all of the proteins in the cell.

protein folding

Created from long chains of amino acids, proteins take on distinct shapes that enable them to carry out a specific function. When a protein folds into its native three-dimensional shape, it is called protein folding.

Conversely, a misfolded protein is one that does not fold into its native structure, which can be caused by mutations in the amino acid sequence or errors in the folding process. This can can cause the misfolded protein to be inactive, modified, or even toxic.


In biology, a reservoir is a primary host of a pathogen, where infections spread outward from. The host may suffer few symptoms or eventually die as a result. For example, certain kinds of birds are considered to be the natural reservoirs of West Nile virus in the US. The virus spreads amongst the birds throughout the year, and infections in humans come from contact with this reservoir of infected animals.

respiratory tract

Composed of the upper airways, nose and nasal cavity, sinuses, throat, and larynx. It's lined with a mucous membrane, part of the innate immune system that wards off infectious agents. Several common viruses, like the cold and flu, take hold of the respiratory tract when they infect a human.

ribonucleic acid (RNA)

A large molecule made of smaller molecular units called nucleotides. RNA transcribes genetic information from DNA and is used as a template to create proteins, among other functions. RNA differs from DNA in structure (RNA generally has one strand, DNA has two), function, and composition.

stem cell

Undifferentiated cells that grow into specialized cells early in life. Later in life, stem cell growth slows, but stem cells are capable of assisting with wound repair and healing. Research around stem cells, using reprogrammed adult stem cells, is in its infancy and holds real promise for tissue and even organ regeneration. Bone marrow is full of stem cells that give rise to our adaptive immune system.

Embryonic stem cells. Image by Nissim Benvensity/Wikimedia Commons


A certain type or variant of a specific species of microorganism. For example, the annual flu vaccination contains the predominant strains of flu that are circulating around the world before the beginning of the flu season.


The term superbug is used to describe bacteria that have become resistant to antibiotics and other drugs used to treat their infection. These multi-drug resistant (MDR) bacteria are a serious threat to public health.

symbiotic (symbiosis)

The reliance of two organisms upon each other to stay alive is called a symbiosis. Symbiosis is also called mutualism, a relationship between two lifeforms in which both organisms benefit.


As an indicator of disease, illness, or dysfunction, there are many kinds of symptoms. The symptoms of a respiratory infection with a cold (like a rhinovirus or coronavirus) include headache, runny nose, and sneezing.


A micro-animal also called moss piglets or water bears that can live in extreme environments such as 10,000 feet below sea level and in the highest altitudes of the Himalayas. They can even survive in space. When in an extreme environment, they dry up in a "tun" state that mimics death, and they can return to a healthy life when the opportunity arises. More info can be found at the link below.

T cells

Named for the shape of receptor on their surface, T cells (or CD4 cells) are manufactured by lymphocytes. T cells are a type of white blood cell that signal and support immune cells as well as continually scan for pathogens or cells that have become damaged or infected. They are specifically targeted by HIV (human immunodeficiency virus), which can cause AIDS (acquired immune deficiency syndrome) if the infection causes their numbers to below 200 cells per microliter (a normal range is about 500-1,500).

tissue culture

See "cell culture" above.


Produced by animals, plants, and microorganisms, toxins are substances that cause cellular and other damage when ingested, absorbed, or breathed in. They are usually proteins, and their danger is linked to how much there is of them.

universal flu vaccine

Not yet a reality, researchers are gaining ground on developing a universal flu vaccine that would confer immunity against a majority of circulating flu viruses, instead of just specific subtypes.


A compound, structure, virus, or bacteria used to protect someone from a dangerous pathogen, vaccines are used in immunization programs to provide protection against infectious agents. Vaccines prime your immune system to be able to react quickly when you come in contact with a dangerous virus or bacteria, keeping them from sickening you. While all vaccines have side effects they are generally mild and rare. Numerous scientific studies have shown that the administration and use of vaccines is not linked to autism.


A disease vector is an agent that carries a pathogen from one host to another. For example, the vector for West Nile virus is the Culex mosquito that carries the virus from infected birds to uninfected birds, and on to humans and mammals. Other major vectors include black flies, fleas, ticks, other species of mosquito, and can also include humans, birds, and other animals.


A curved, rod-shaped bacteria, vibrio are one of group of bacteria that typically cause food-borne illnesses. The virulent illness cholera is caused by the bacteria Vibrio cholerae.

A number of oblong-shaped Vibrio parahaemolyticus bacteria. Image by James Archer/CDC


The ability or degree of damage or infection caused by a pathogen, or disease-causing microorganism. A highly virulent infection would almost always cause disease and that disease would likely be deadly or very dangerous. A less virulent infection would only cause symptoms in a small percentage of people and those symptoms would be milder.


Smaller than bacteria, a virus is a complex set of proteins and genetic material that must infect a cell in order to copy itself. Many (though not all) viruses cause disease. Different species of virus infect everything from humans and other animals, to plants and even bacteria.

There remains a lively, ongoing debate on whether viruses are "alive" because they are protein shells that contain small amounts of genetic material, like RNA and DNA, but lack characteristics to qualify them as "living." For example, since a virus must invade and hijack the processes in the cells in your body to reproduce itself, it can't survive on its own; But plenty of bacteria, archaea, fungi, plants and animals have similar symbiotic relationships that rely on other organisms for reproduction or survival.

white blood cell (WBC)

An important defensive component of an immune response is the white blood cell or leukocyte. Common types of mammalian white blood cell are neutrophils, lymphocytes, and monocytes (also called B cells and T cells). White blood cells are continually produced from bone marrow and circulate in the bloodstream. When you are injured, white blood cells are part of the inflammatory response taken by your immune system to to speed healing. Special types of white blood cells create immunity by "remembering" a pathogen you've already come into contact with and marshaling the body's defensive forces quickly in response to it.

World Health Organization (WHO)

With headquarters in Geneva, Switzerland, the WHO is an agency of the United Nations with a leadership role in supporting and sustaining international public health.


Microbes capable of living in extremely dry environments, xerophiles live in conditions with very low water activity.

Zika virus

Spread through mosquito bites, sexual contact, blood transfusion, laboratory exposure, and before birth from mother to child. While the symptoms of the virus may are not usually serious in healthy people, Zika is known to cause serious birth defects and may cause long-term damage to male fertility.


Diseases and infections transmitted from an animal to a human. A zoonotic agent could be bacteria, virus, or other infectious agent. Zoonoses diseases include toxoplasmosis, often transmitted by cats, and E. coli and Salmonella infections transmitted by handling infected animals or reptiles. In the last decade, zoonotic diseases represented three-quarters of emergent pathogens.

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