Human Microbiome and Virome

Human microbiota are the microorganisms that live on and inside the body. They colonize the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells may range from 10¹³ to 10¹⁴. That means microbes can match or even outnumber human somatic cells.

This host-microbiome relationship has led scientists to describe humans as supraorganisms. In this view, microbial communities help shape development, immunity, and disease risk. Studying the...

The human microbiota starts forming at birth and changes as a person grows. The first years are a sensitive time for microbial colonization. During this period, helpful microbes support immune system maturity. By about age three, children usually have a more stable and diverse microbial community.

Newborns get microbes from the environment around them. Vaginal delivery tends to expose infants to maternal vaginal microbes. Cesarean delivery, or C-section, usually leads to more skin and...

The skin hosts bacteria, fungi, and viruses that help protect the body. This microbial community is called the skin microbiome. Its makeup changes from one body region to another because moisture and sebum, the oily skin secretions, differ across the skin surface.

Oily areas such as the forehead are often colonized by Cutibacterium acnes. These bacteria break down sebum and make propionic acid. That lowers skin pH and helps create a harsh environment for many harmful microbes. Moist and oily...

The eye has a small but specialized microbiota that helps support ocular surface defense. This microbial community is shaped by the eye’s unique anatomy and immune environment. It mostly lives on the conjunctiva and along the eyelid margins.

The conjunctival surface carries fewer microbial species than nearby facial skin. Common members include Staphylococcus epidermidis, Cutibacterium acnes, and Corynebacterium species. Blinking helps wash microbes away, and tears add another layer of...

The oral microbiome is a complex community of bacteria and other microbes that live in the mouth. More than 700 microbial species have been identified so far through genomic sequencing and culture-based studies. Some microbes form a core microbiome that is found in most people, while others vary with diet, lifestyle, and host genetics.

Different parts of the mouth create different habitats for these microbes. The tongue surface has papillae, or small bumps, that trap food and lower oxygen...

Infant oral microbes begin to take hold before birth and continue to change after delivery. The oral cavity was once thought to be sterile in the fetus, but microbes such as Streptococcus and Fusobacterium have been found in amniotic fluid. This suggests that early microbial exposure may occur in utero through transfer from the maternal oral or gastrointestinal tract.

This prenatal exposure may help prime the newborn immune system. Maternal health can also matter, especially if the mother has...

The respiratory tract contains microbes that help shape health and disease. It includes the upper respiratory tract, such as the nostrils, sinuses, pharynx, and oropharynx, and the lower respiratory tract, which includes the larynx, trachea, bronchi, and lungs. The upper tract is heavily colonized by microbes, while the lower tract was once thought to be sterile.

Recent molecular studies show that the lungs are not microbe-free. Instead, they seem to act as transient reservoirs, meaning...

Gut conditions shape which microbes can live in the stomach and small intestine. The human gastrointestinal (GI) tract has different physical and chemical settings that affect microbial communities. These settings help explain why some regions hold very few microbes while others support more growth.

The stomach is one of the hardest places for microbes to colonize because it is highly acidic. Its pH is usually between 1 and 3, which keeps microbial density low. Even so, some acid-tolerant...

The large intestine contains the most densely populated microbial ecosystem in the human body. Most of these microbes are anaerobic bacteria, which grow best without oxygen. The main groups are Bacillota, once called Firmicutes, and Bacteroidota, once called Bacteroidetes.

Microbes are not spread evenly through the large intestine. Their mix changes from one region to another because oxygen levels and nutrients are different in each area. The cecum, at the start of the large intestine,...

The gut microbiota is the community of trillions of microorganisms that live in the human gastrointestinal tract. It includes bacteria, archaea, viruses, and fungi. Most of these microbes live in the large intestine, where they form a stable and diverse ecosystem that supports gut homeostasis, or balance.

These microbes help break down food components that the body cannot digest on its own. Dominant groups such as Bacteroidota and Bacillota ferment indigestible dietary polysaccharides, which...

Gut microbiota imbalance, or dysbiosis, can affect many parts of human health. The gut microbiome includes helpful commensal microbes and opportunistic pathogens that work together to support nutrient metabolism, immune control, and the intestinal barrier. When this balance changes, microbial diversity often drops and the mix of major bacterial groups shifts.

Diet strongly shapes these changes. High-fiber diets support Bacteroidota, which are linked to anti-inflammatory effects and the...

The gut microbiome helps shape brain health through the gut-brain axis. This bidirectional communication system links the gastrointestinal tract and the brain. It uses the vagus nerve, hormones, immune signals, and chemical messengers made by gut microbes.

Gut microbes produce compounds that affect the nervous system. These include neuroactive molecules that can influence neurotransmitters such as serotonin and gamma-aminobutyric acid, or GABA. They also make short-chain fatty acids, including...

The urogenital tract contains a natural community of microorganisms, and healthy kidneys and bladder are not sterile. Molecular sequencing has shown that these microbes are present even in healthy adults. Their numbers are low compared with the distal urethra, but they still form part of the normal microbial habitat.

Most of these resident microbes are harmless, but they can become opportunistic pathogens when the urogenital environment changes. Shifts in pH and disruptions in microbial...

The human virome is the collection of viruses that live in and on the human body. It includes bacteriophages, which infect bacteria, and eukaryotic viruses, which infect human cells. Viruses from food and the environment can also be part of this shifting community. Estimates suggest the body may contain around 10^13 viral particles, but the number changes by body site and by the method used to detect them.

Scientists have learned much more about the virome through untargeted shotgun...

Bacteriophages are viruses that infect bacteria, and they are found throughout the human body. They are a major part of the human virome. In the gut, they can reach very high numbers, and many belong to the orders Caudovirales and Microviridae. A large fraction still cannot be classified and is often described as viral "dark matter."

Some bacteriophages integrate their genetic material into bacterial DNA. This process is called lysogeny, and the phage genome then becomes a prophage. During...

Antibiotics can change the balance of gut bacteria and other microbes in the human digestive tract. The gut microbiota is a community of bacteria, archaea, viruses, and fungi. It helps control metabolism, immune responses, and intestinal health. Broad-spectrum antibiotics can remove both harmful and helpful microbes and create gut dysbiosis, which means an unbalanced microbiota.

These changes can start before birth. Antibiotic use during pregnancy and lactation can alter the mother’s...