Human microbiota

The term human microbiota refers to an ecosystem made up of trillions of microorganisms that inhabit the human body. These microbial communities consist mostly of bacteria but also include viruses, fungi, and other microorganisms. They reside both in and on the body in such diverse locations as the mouth, lungs, skin, genitals, and digestive tract. While attaining an accurate count of human microbiota is difficult, a 2012 study by the National Institutes of Health (NIH) estimated that the body contains thousands of different species of microbes. Many of these microorganisms exist in a symbiotic relationship with humans, helping in the digestion of food and protecting against attacks by other bacteria. Negatively altering the human-microbe ecosystem may lead to certain diseases or medical conditions.

Background

Dutch scientist Antonie van Leeuwenhoek was the first person to use a microscope to observe single-celled organisms in the late 1600s. He later observed that these tiny organisms he called animalcules were also inside his mouth. In the late nineteenth century, Austrian pediatrician Theodor Escherich was the first to discover that microorganisms were a natural part of the human body. He observed a type of bacteria living in the intestines of both healthy and sick children. He called this bacteria Bacillus communis coli. After his death, it was renamed Escherichia coli in his honor. E. coli is a common bacterium in humans and is normally harmless. However, some strains of the bacteria found outside the body can cause severe food poisoning and intestinal illnesses.

The most numerous form of human microbiota by far is bacteria. Bacteria are single-celled microscopic organisms that can live in almost any environment. Bacteria come in three shapes—spherical, rod-like, or spiral—and replicate themselves by dividing into two identical cells. This gives them the ability to change their genetic makeup and possibly evolve to resist drugs used to treat them. Most bacteria are harmless, with fewer than one hundred species capable of causing infectious diseases in humans. Viruses are microorganisms that consist of strands of DNA or RNA surrounded by a protein shell. They are inert organisms until they invade a living cell and use the cell to reproduce. Viruses can be disease-causing agents, but many viruses in humans do not cause disease except in the very young, elderly, or those with damaged immune systems. Fungi are single or multicellular organisms that reproduce by emitting spores into the environment. Other microorganisms found in human microbiota are protozoa, parasites, and archaea—primitive single-celled organisms similar to bacteria.

Overview

In 2007, the NIH in the United States began the first phase of the Human Microbiome Project, an attempt to identify and categorize the microorganisms that live in or on the human body. In findings released in 2012, the NIH determined that humans contain more than ten thousand different species of microbes and that these outnumber human cells by a ten-to-one ratio. Further research suggested that the number of microorganisms in the body may be just slightly more than the number of human cells—an estimated thirty-nine trillion microbes to thirty trillion cells. The study also found the type and number of microbes in one person—the person's microbial "signature"—is different from the next person's. This may explain why some people are more prone to certain infections and respond differently to bacterial-fighting medicines such as antibiotics. A second phase of the project resulted in findings released in 2019 pertaining to microbiome and host biological properties in three different conditions: inflammatory bowel disease, pregnancy and preterm birth, and type 2 diabetes.

The human gut, or gastrointestinal tract—the part of the digestive system consisting of the stomach and intestines—contains most of the body's microbiota. Many of the microorganisms in the gut aid in the process of digestion. Bacteria called Bacteroides are responsible for breaking down carbohydrates while Lactobacillus acidophilus breaks down sugars in dairy products. The microbial environment of the human gut can change over time and is affected by factors such as diet, age, lifestyle, and personal hygiene. For example, a stomach bacterium called Helicobacter pylori regulates levels of a hormone that stimulates hunger. Scientists have suggested that hygiene changes may bring about a lack of H. pylori in the stomach that may lead to obesity. The use of antibiotics may also kill off some helpful bacteria, resulting in gastrointestinal issues such as diarrhea and irritable bowel syndrome.

People experience a change in their microbial content during pregnancy, and research suggests that they may pass on those microbes to their children in the womb. As babies leave the birth canal, they acquire more microbes from their mother. Studies have shown children born by Caesarean section have different microbiota than children born vaginally. In the first few years of their lives, children acquire their own microbiota at an accelerated rate. As their immune systems develop along with them, their bodies come to recognize helpful microbes from harmful ones.

Microbiota are also common in the mouth, where they inhabit the mucus lining and saliva. Some of these microbes are passed along to other parts of the body, such as the lungs and gastrointestinal tract. While the lungs do not offer microbes as welcoming an environment as the mouth, several species of bacteria can be found there. On the skin, human microbiota, such as the bacterium Staphylococcus epidermidis, act as a protective shield to keep the bacteria of the outside world at bay.

While much of the human microbiota are beneficial, the body also contains some potentially dangerous microorganisms. These normally coexist with the body's other microbes and do not cause serious illnesses. Some researchers believe these harmful organisms have adjusted to the human ecosystem or are kept in check by helpful bacteria. If the body's immune system becomes compromised or the natural balance of helpful microbiota is altered, these microbes can lead to health issues. The bacterium Staphylococcus aureus, which is normally found on the skin, can cause a potentially serious MRSA infection if it enters the body through a cut or wound. A species of fungus called Cladosporium can trigger asthma, while another fungus, Candida, can cause a mouth infection known as thrush. Human papillomaviruses, commonly found on the skin, can lead to skin infections or cervical cancer.

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