Human flora
The human body contains a large number of microrganisms, such as bacteria, fungi and archaea, some of these organisms perform tasks that are useful, while the majority have no beneficial or harmful effect.  Those that are expected to be present, and that under normal circumstances do not cause disease, are termed normal flora.

# Bacterial flora
It is estimated that 500 to 100,000 species of bacteria live in the human body . Bacterial cells are much smaller than human cells, and there are about ten times as many bacteria as human cells in the body (1000 trillion (1015) versus 100 trillion (1014)). Though normal flora are found on all surfaces exposed to the environment (on the skin and eyes, in the mouth, nose, small intestine, and colon), the vast majority of bacteria live in the large intestine.
Many of the bacteria in the digestive tract, collectively referred to as gut flora, are able to break down certain nutrients such as carbohydrates that humans otherwise could not digest. The majority of these commensal bacteria are anaerobes, meaning they survive in an environment with no oxygen.  Bacteria of the normal flora can act as opportunistic pathogens at times of lowered immunity. 
Escherichia coli is a bacterium that lives in the colon; it is an extensively studied model organism and probably the best understood bacterium of all.  Certain mutated strands of these gut bacteria do cause disease; an example is E. coli O157:H7.
A number of types of bacteria, such as Actinomyces viscosus and A. naeslundii, live in the mouth, where they are part of a sticky substance called plaque. If this is not removed by brushing, it hardens into calculus (also called tartar).  The same bacteria also secrete acids that dissolve tooth enamel, causing tooth decay.
The vaginal microflora consist mostly of various lactobacillus species. It was long thought that the most common of these species was Lactobacillus acidophilus, but it has later been shown that the most common one is L. iners followed by L. crispatus. Other lactobacilli found in the vagina are L. delbruekii and L. gasseri. Disturbance of the vaginal flora can lead to bacterial vaginosis.

## Bacteria and human health
Bacteria are vital for the maintenance of human health, but some also pose a significant health threat by causing diseases. Large numbers of bacteria live on the skin and in the digestive tract. Their growth can be increased by warmth and sweat. Large populations of these organisms on humans are the cause of body odor and thought to play a part in acne.  There are more than 500 bacterial species present in the normal human gut and are generally beneficial: they synthesize vitamins such as folic acid, vitamin K and biotin, and they ferment complex indigestible carbohydrates. Other beneficial bacteria in the normal flora include Lactobacillus species, which convert milk protein to lactic acid in the gut. The presence of such bacterial colonies also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and some beneficial bacteria are consequently sold as probiotic dietary supplements.
Although the vast majority of bacteria are harmless or beneficial, a few pathogenic bacteria cause infectious diseases.  The most common bacterial disease is tuberculosis, caused by the bacterium Mycobacterium tuberculosis, which kills about 2 million people a year, mostly in sub-Saharan Africa.  Pathogenic bacteria contribute to other globally important diseases, such as pneumonia, which can be caused by bacteria such as Streptococcus and Pseudomonas, and foodborne illnesses, which can be caused by bacteria such as Shigella, Campylobacter and Salmonella. Pathogenic bacteria also cause infections such as tetanus, typhoid fever, diphtheria, syphilis and leprosy.
Koch's postulates, proposed by Robert Koch in 1890, are criteria designed to establish a causal relationship between a causative microbe and a disease. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease.
Each pathogenic species has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and even overwhelming sepsis, a systemic inflammatory response producing shock, massive vasodilation and death. Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease. Finally, some species, such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium, are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis.
Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. For example, the antibiotics, chloramphenicol and tetracyclin inhibit the bacterial ribosome, but not the structurally-different eukaryotic ribosome, and so exhibit selective toxicity. Antibiotics are used both in treating human disease and in intensive farming to promote animal growth. Both uses may be contributing to the rapid development of antibiotic resistance in bacterial populations. Infections can be prevented by antiseptic measures such as sterilizating the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilized to prevent contamination and infection by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection. Most bacteria in food are killed by cooking to temperatures above 60C (140F).

# Archean flora
Archaea are present in the human gut, but in contrast to the enormous variety of bacteria in this organ, the number of archaeal species are much more limited. The dominant group is the methanogens, particularly Methanobrevibacter smithii and Methanosphaera stadtmanae. However, colonization by methanogens is variable and only about 50% of humans have easily-detectable populations or these organisms.

## Archaea and human health
As of 2007, no clear examples of archaeal pathogens are known, although a relationship has been proposed between the presence of some methanogens and human periodontal disease.

# Fungal flora
Fungi, particularly yeasts are present in the human gut. The best studied of these are Candida species, due to their ability to become pathogenic in immunocompromised hosts. Yeasts are also present on the skin, particularly Malassezia species, where they consume oils secreted from the sebaceous glands.