Name: how gut microbes support human health
Uploaded: 2026-03-12T13:36:13.000Z
Duration: 1 min 22 s
Channel: JoVE

The human body hosts a vast number of microbes, primarily bacteria, that inhabit many regions of the body, including the skin, mouth, gut, and urogenital tract.Together, these microbes form the human microbiota, a community that supports key functions in the body.A portion of these microbes makes up the resident microbiota which are long-term, stable populations, while transient microbiota are present only for short durations.Microbial colonization begins at birth. As a person grows, factors such as diet, age, environment, and antibiotic use influence the diversity and stability of microbial communities.Also, temperature, pH, oxygen levels, and body secretions affect microbial growth.Through a process known as microbial antagonism, the normal microbiota can protect the host by physically occupying binding sites and consuming nutrients, so they outcompete invading pathogens.For example, microorganisms in the gut promote health by synthesizing vitamins and suppressing pathogens through the production of bacteriocins.

introduction to the human microbiota

Introduction to the Human Microbiota

Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10&#185;&#179; to 10&#185;&#8308;&#8212;comparable to, or exceeding, the number of human somatic cells. This host&#8211;microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity, and disease susceptibility.Understanding the human microbiome holds immense promise for clinical advancements. It could lead to biomarkers that forecast disease risk, tailored microbial therapies, personalized medicine, and custom-designed probiotics. Nonetheless, interpreting the complex host&#8211;microbe interactions remains a significant challenge. These interactions are not unidirectional; human lifestyle, diet, and health can influence the microbiota, obscuring causality.The study of the microbiome has revealed extensive microbial diversity, primarily through culture-independent methods such as 16S rRNA gene sequencing and metagenomics. These technologies have facilitated comparisons of microbiomes across individuals and body sites, showing that although species-level composition varies widely, similarities often emerge at higher taxonomic levels.Some studies have reported microbial DNA in the placenta, though whether a true in-utero microbiome exists remains debated. At birth, the newborn's microbiota is shaped by maternal vaginal flora, especially Lactobacillus species in vaginal births, or by skin and environmental microbes in cesarean deliveries. It continues evolving rapidly in the first three years. The gut microbiota stabilizes thereafter but remains responsive to environmental influences.Symbiotic relationships within the microbiota are diverse. Commensals benefit without affecting the host, mutualistic microbes offer reciprocal advantages&#8212;such as E. coli synthesizing essential vitamins&#8212;and parasitic organisms harm the host. However, under certain conditions, normally benign microbes can become opportunistic pathogens.The microbiota also confer protective benefits through microbial antagonism, preventing pathogen overgrowth by competing for resources and altering the local environment. Disruption of this balance, often by antibiotics, can lead to overgrowth of harmful species such as Clostridioides difficile.Recent efforts like the Human Microbiome Project and global metagenomic initiatives have revealed a remarkable genetic capacity in the human microbiome, far exceeding the human genome. This supports the argument that the microbiome functions akin to a vital organ, essential for maintaining health and homeostasis.

Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. ...

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Education

JoVE Core

Microbiology

Unit

Human Microbiome and Virome

KEY TERMS AND CONCEPTS

how gut microbes support human health

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 human microbiome may also lead to biomarkers that predict disease, targeted microbial therapies, personalized medicine, and custom probiotics. Even so, these host-microbe interactions are complex, because diet, lifestyle, and health can also change the microbiota.

Researchers study microbiomes with culture-independent methods. Two key tools are 16S rRNA gene sequencing and metagenomics. These methods make it possible to compare microbiomes from different people and body sites. They show that species can vary a lot, but higher taxonomic levels often look more similar.

The microbiome also changes early in life. Some studies have found microbial DNA in the placenta, but it is still debated whether a true microbiome exists before birth. At birth, the newborn microbiota is shaped by the mother’s vaginal flora in vaginal delivery, especially Lactobacillus species, or by skin and environmental microbes in cesarean delivery. The microbiota then changes quickly during the first three years and becomes more stable after that, although it still responds to the environment.

Microbes in the body can have different relationships with the host. Commensals benefit without affecting the host. Mutualistic microbes help both sides, such as E. coli making essential vitamins. Parasitic organisms harm the host. Some normally harmless microbes can also become opportunistic pathogens under certain conditions.

The microbiota can protect against disease through microbial antagonism. This means microbes compete for resources and change the local environment so harmful pathogens cannot overgrow. When this balance is disrupted, often by antibiotics, harmful species such as Clostridioides difficile can increase. Large projects like the Human Microbiome Project and global metagenomic studies have shown that the human microbiome has a huge genetic capacity, far beyond the human genome. This is why many scientists think of the microbiome as an important organ for health and homeostasis.

How Gut Microbes Support Human Health

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...

development of human microbiota

How Early Feeding Shapes the Gut Microbiota

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 microbiota

How Skin Microbes Protect the Body

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...

microbiome of the eye

Eye Microbiota and Ocular Defense

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 microbiota

Oral Bacteria and Mouth Health

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...

development of the oral microbiota

How Infant Oral Microbes Take Hold

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...

microbiota of the respiratory tract

Respiratory Tract Microbes and Health

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...

microbiota of the stomach and small intestine

microbiota-of-the-stomach-and-small-intestine

How Gut Conditions Shape Microbes

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...

microbiota of the large intestine

Large Intestine Microbes and Their Roles

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,...

functions of the gut microbiota

Gut Microbiota and Human Health

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...

dysbiosis of the gut microbiota

How Gut Imbalance Affects Health

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...

gut-brain axis

Gut Microbes and Brain Health

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...

microbiota of the urogenital tract

Urogenital Microbiota and Urinary Health

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...

human virome

Human Virome and Body-Site Differences

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 of the human virome

How Bacteriophages Shape Human Microbes

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...

microbiota modulation by antibiotics

How Antibiotics Change Gut Bacteria

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...

key terms and concepts

Explore how human microbiota develop, defend the body, and shift with birth, diet, antibiotics, and the environment in grades 9–12 biology.

How Gut Microbes Support Human Health | JoVE K12

JoVE Core Microbiology provides an engaging introduction to the microbial world and its influence on health, industry, and the environment. This comprehensive collection covers key concepts such as microbial structure, metabolism, genetics, and ecology. It introduces essential laboratory techniques and microscopy methods through visually engaging animations. Corresponding scientist-in-action videos bridge classroom concepts with real-world research and applications.

microbiology

How Gut Microbes Support Human Health

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