How do people know what germs do, and how many of them live with us? The NIH Human Microbiome Project studied the microbes that live in and on the human body and their roles in health and disease. Before it began, this community was largely unstudied. The human microbiome includes both helpful and potentially harmful microbes; most are helpful partners, while some, in smaller numbers, can cause disease. As of November 2026, here is where the count stands. NIH once described microbial cells in the body as outnumbering human cells by about ten to one, but a 2016 study re-counted and estimated about one microbial cell for each human cell. Open question: as of November 2026, researchers do not yet know how much each microbe in the body changes health. Before the Human Microbiome Project, the influence of these microbes on development, immunity and nutrition was almost entirely unknown.
Germs come in several kinds. Bacteria are tiny living things made of just one cell, and under a microscope they look like balls, rods or spirals. A virus is a germ made of genetic material inside a coat of protein. The greatest number of viruses are phages, viruses that infect bacteria, and studying viruses that infect many kinds of organisms also helps scientists understand human disease. Parasites are living things that use other living things, like the human body, for food and a place to live; they range from one-celled protozoa to worms you can see.
Most germs do not hurt people, and some germs even help, so the question is how the few that do harm cause sickness. A germ makes you sick when it gets into your body and your body reacts. When germs get inside the body they take energy from it and can damage healthy cells; some bacteria multiply quickly in the body and give off toxins, which are poisons that damage cells. A virus cannot make copies of itself alone, so it has to get inside a living cell and use that cell to make copies; often a virus ends up killing the cell it infected while making copies, which is how it damages the body.
The body defends itself in layers; skin is a barrier that blocks germs from getting into the body, and everyone is born with this general protection, called innate immunity. White blood cells are part of the body's defense, and they go after germs and fight them; some white blood cells, called phagocytes, chew up invading organisms, and one kind, the neutrophil, fights bacteria. After you have met a germ, your immune system usually remembers it, and your antibodies stay in your body in case that germ comes back. Sneezing, coughing, diarrhea and a high fever come partly from the immune system fighting germs, not only from the germs themselves. In 1882, Ilya Mechnikov proposed that some white blood cells work by capturing and destroying harmful bacteria; he called the process phagocytosis and shared the 1908 Nobel Prize for work on immunity.
Most fevers are caused by infections, and a fever helps the immune system kick into action against the germs. A fever is a body temperature of 100.4 degrees Fahrenheit (38 degrees Celsius) or higher. A cold is caused by a virus, and more than 200 viruses can cause one. In the United States, rhinoviruses cause the most colds; colds spread through tiny droplets in the air and on things people touch.
Antonie van Leeuwenhoek of Delft, Holland, was a cloth merchant with no university degree; he made simple microscopes and became one of the most important discoverers in the history of biology. His microscopes were single powerful lenses, not the compound microscopes used today, and his lenses magnified over 200 times, with clearer images than his colleagues could make. He is often called the inventor of the microscope, but compound microscopes were invented around 1595, nearly forty years before he was born; his gift was grinding lenses and describing carefully what he saw. He was the first to see bacteria, and he also saw blood cells and tiny animals called rotifers and nematodes.
Louis Pasteur showed that yeast, a living organism, causes alcoholic fermentation, and that living organisms turn milk sugar into lactic acid; this pointed to tiny living things as causes of change, including disease. Pasteur was not the first to say that germs cause disease, but his experiments gave the idea strong support against the older miasma theory, which held that bad air caused disease. His swan-neck flasks let air in but kept dust and airborne microbes out, and sterilized broth in them stayed clear, which helped show that air alone cannot create life. In 1864 he found that heating wine to 50 to 60 degrees Celsius (122 to 140 degrees Fahrenheit) killed the microbes that spoiled it; the process is called pasteurization, and it later became common for milk.
In 1876 Robert Koch proved that one bacterium, Bacillus anthracis, causes anthrax, and he was the first to prove that a specific bacterium causes a specific disease. In 1882 he discovered the bacterium that causes tuberculosis, and in 1905 he won the Nobel Prize in Physiology or Medicine. Koch's postulates are four criteria for deciding whether a particular bacterium causes a particular disease, and as of 2025 many researchers still use them as a guide. Science also corrects itself. Koch did not believe human and animal tuberculosis were connected, but the Nobel Foundation notes he was not entirely correct.
In the 1840s two hospital clinics in Vienna had very different results. From 1840 through 1846, deaths of mothers in the doctors' clinic were 98.4 per 1,000 births, compared with 36.2 per 1,000 in the midwives' clinic. Ignaz Semmelweis noticed that medical students went from handling bodies to examining mothers without washing their hands, while midwives did neither. In 1847 he had students wash in chloride of lime first. After handwashing began, deaths in the doctors' clinic fell in 1848 to 12.7 per 1,000 births, about the same as the 13.3 per 1,000 in the midwives' clinic.
Patients went to the two clinics on alternate days, which by accident made a controlled trial; with so many births, 42,795 from 1840 to 1846, chance could confidently be ruled out; no one knew about germs in 1847, so Semmelweis could not explain why handwashing worked. His idea had little effect at the time, and antisepsis became routine in childbirth care only in the 1880s, after bacteria were discovered. The usual story that Semmelweis was simply ignored is too simple; he refused to publish for years and insisted one cause explained all cases, while others such as Oliver Wendell Holmes also urged handwashing.
For an infection to happen, germs must travel from a source, enter a body, invade tissues, multiply and cause a reaction, and handwashing breaks the chain at the travel step; germs spread when someone coughs or sneezes, and when you touch something that has germs on it. A single gram of human poop, about the weight of a paper clip, can hold one trillion germs, which is why washing after the toilet matters. Germs can get into your body through your eyes, nose and mouth, so try not to touch your face with unwashed hands. When you sneeze or cough, cover your mouth and nose with a tissue and then throw the tissue away.
Handwashing education in communities has been measured to cut diarrhea by 23 to 40 percent, colds and other respiratory illness by 16 to 21 percent, and school absences from stomach illness by 29 to 57 percent. Soap works better than water alone because soap lifts dirt and microbes off the skin, and people also scrub longer when they use soap. The temperature of the water does not seem to change how many germs a wash removes; handwashing for about 15 to 30 seconds removes more germs than washing for less time, and as of November 2026, many countries recommend about 20 seconds. Most 20-second studies counted how many microbes were removed, not how many people stayed healthy; only a small share of microbes cause illness, so as of November 2026 the best washing time is still not settled. If you cannot use soap and water, a hand sanitizer with at least 60 percent alcohol can help.
Edward Jenner used cowpox in 1796 to protect a boy from smallpox, an early vaccine, and by the mid-1800s scientists such as Pasteur were making vaccines from weakened versions of disease-causing germs. A vaccine teaches your immune system to recognize a germ before the real germ arrives. Vaccines work by imitating an infection, so the immune system practices without the person getting the real illness, and a vaccine can make you feel tired or sore for a day or two while your body learns. When enough people are vaccinated, it is harder for a disease to spread to people who cannot have vaccines, such as those with weakened immune systems.
In 1928 Alexander Fleming saw that a mold had grown on a plate of staphylococcus bacteria and that the bacteria had stopped growing near the mold; he concluded the mold made a substance that works against bacteria. Fleming named the substance penicillin, and it became the basis for medicines that treat bacterial infections. Antibiotics are medicines that kill bacteria or stop them from growing, but they do not work on viruses, so they do not help a cold. Take antibiotics exactly the way a doctor tells you to, and never share them. Taking antibiotics when they are not needed does not help and can cause side effects and add to antibiotic resistance.
Antibiotic resistance happens when bacteria change so that an antibiotic no longer kills them, and they keep growing; it is the germs that become resistant to a medicine, not the person's body. Bacteria that survive a drug through genetic changes multiply and spread, so each use of an antibiotic selects for resistant survivors. Resistant germs can pass their resistance genes to other germs that were never exposed to the drug. The World Health Organization estimated that about 1 in 6 lab-confirmed bacterial infections worldwide were resistant to antibiotics in 2023; it also estimated that bacterial resistance was associated with more than 4.7 million deaths worldwide in 2021. Both are estimates as of November 2026.
The CDC's 2026 report estimates more than 9.3 million drug-resistant infections a year in the United States, with more than 39,000 deaths. As of November 2026 these are estimates, and they change with each report. Handwashing helps fight antibiotic resistance, because fewer infections means fewer antibiotics used, and overuse of antibiotics is the single most important factor behind resistance worldwide. Open question: new antibiotics are scarce. As of November 2026 the World Health Organization describes a research and development crisis with few new medicines in the pipeline.
Words to know
- microbiome: body's microbe community
- postulates: required criteria
- phages: bacteria-infecting viruses
- pasteurization: heat treatment
- antisepsis: germ prevention
