By Larry M. Bush, MD, Charles E. Schmidt College of Medicine, Florida Atlantic University;University of Miami-Miller School of Medicine/JFK Medical Center

Bacteria are microscopic, single-celled organisms. There are thousands of different kinds, and they live in every conceivable environment all over the world. They live in soil, seawater, and deep within the earth’s crust. Some bacteria have been reported even to live in radioactive waste. Many bacteria live in the bodies of people and animals—on the skin and in the airways, mouth, and digestive, reproductive, and urinary tracts—without causing any harm. Such bacteria are called resident flora, or the microbiome. Many resident flora are actually helpful to people—for example by helping them digest food or by preventing the growth of other, more dangerous bacteria.

Only a few kinds of bacteria cause disease. They are called pathogens. Sometimes bacteria that normally reside harmlessly in the body cause disease. Bacteria can cause disease by producing harmful substances (toxins), invading tissues, or doing both.


Bacteria can be classified in several ways:

  • Scientific names: Bacteria, like other living things, are classified by genus (based on having one or several similar characteristics) and, within the genus, by species. Their scientific name is genus followed by species (for example, Clostridium botulinum). Within a species, there may be different types, called strains. Strains differ in genetic makeup and chemical components. Sometimes certain drugs and vaccines are effective only against certain strains.Staining: Bacteria may be classified by the color they turn after certain chemicals (stains) are applied to them. A commonly used stain is the Gram stain. Some bacteria stain blue. They are called gram-positive. Others stain red. They are called gram-negative. Gram-positive and gram-negative bacteria stain differently because their cell walls are different. They also cause different types of infections, and different types of antibiotics are effective against them.
  • Shapes: All bacteria may be classified as one of three basic shapes: spheres (cocci), rods (bacilli), and spirals or helixes (spirochetes).
  • Need for oxygen: Bacteria are also classified by whether they need oxygen to live and grow. Those that need oxygen are called aerobes. Those that have trouble living or growing when oxygen is present are called anaerobes. Some bacteria, called facultative bacteria, can live and grow with or without oxygen.

Bacteria in the Body

The body normally contains several hundred different species of bacteria but many trillions of individual bacteria. The bacteria outnumber the cells of the body by about 10 to 1.
Most of these bacteria reside on the skin and teeth, in the spaces between teeth and gums, and in the mucous membranes that line the throat, intestine, and vagina. The species differ at each site, reflecting the different environment at each site.
Many of them are anaerobes—that is, they do not require oxygen. Usually, these anaerobes do not cause disease. Many have useful functions, such as helping break down food in the intestine.

However, these bacteria can cause disease if the mucous membranes are damaged. Then, bacteria can enter tissues that are usually off-limits to them and that have no defenses against them. The bacteria may infect nearby structures (such as the sinuses, middle ear, lungs, brain, abdomen, pelvis, and skin) or enter the bloodstream and spread.

Bacterial Defenses

Bacteria have many ways of defending themselves.


Some bacteria secrete a substance that helps them attach to other bacteria, cells, or objects. This substance combines with the bacteria to form a sticky layer called biofilm. For example, certain bacteria form a biofilm on teeth (called dental plaque). The biofilm traps food particles, which the bacteria process and use, and in this process, they probably cause tooth decay. Biofilms also help protect bacteria from antibiotics.


Some bacteria are enclosed in a protective capsule. This capsule helps prevent white blood cells, which fight infection, from ingesting the bacteria. Such bacteria are described as encapsulated.

Outer membrane

Under the capsule, gram-negative bacteria have an outer membrane that protects them against certain antibiotics. When disrupted, this membrane releases toxic substances called endotoxins. Endotoxins contribute to the severity of symptoms during infections with gram-negative bacteria.


Some bacteria produce spores, which are an inactive (dormant) form. Spores can enable bacteria to survive when environmental conditions are difficult. When conditions are favorable, each spore germinates into an active bacterium.


Flagella are long, thin filaments that protrude from the cell surface and enable bacteria to move. Bacteria without flagella cannot move on their own.

Antibiotic resistance

Some bacteria are naturally resistant to certain antibiotics.
Other bacteria develop resistance to drugs because they acquire genes from other bacteria that have become resistant or because their genes mutate. For example, soon after the drug penicillin was introduced in the mid-1940s, a few individual Staphylococcus aureus bacteria acquired genes that made penicillin ineffective against them. The strains that possessed these special genes had a survival advantage when penicillin was commonly used to treat infections. Strains of Staphylococcus aureus that lacked these new genes were killed by penicillin, allowing the remaining penicillin-resistant bacteria to reproduce and over time become more common. Chemists then altered the penicillin molecule, making a different but similar drug, methicillin, which could kill the penicillin-resistant bacteria. Soon after methicillin was introduced, strains of Staphylococcus aureus developed genes that made them resistant to methicillin and related drugs. These strains are called methicillin-resistant Staphylococcus aureus (MRSA).
The genes that encode for drug resistance can be passed to following generations of bacteria or sometimes even to other species of bacteria.
The more often antibiotics are used, the more likely resistant bacteria are to develop. Therefore, doctors try to use antibiotics only when they are necessary. Giving antibiotics to people who probably do not have a bacterial infection, such as those who have cough and cold symptoms, does not make people better but does help create resistant bacteria. Because antibiotics have been so widely used (and misused), many bacteria are resistant to certain antibiotics.
Resistant bacteria can spread from person to person. Because international travel is so common, resistant bacteria can spread to many parts of the world in a short time. Spread of these bacteria in hospitals is a particular concern. Resistant bacteria are common in hospitals because antibiotics are so often necessary and hospital personnel and visitors may spread the bacteria if they do not strictly follow appropriate sanitary procedures. Also, many hospitalized patients have a weakened immune system, making them more susceptible to infection.
Resistant bacteria can also spread to people from animals. Resistant bacteria are common among farm animals because antibiotics are often routinely given to healthy animals to prevent infections that can impair growth or cause illness.