Name: gut microbiota and human health
Uploaded: 2026-03-12T13:36:08.000Z
Duration: 1 min 18 s
Channel: JoVE

The gut microbiota is the community of microbes that live along the digestive tract.Dominant gut colonizers, such as members of the Bacteroidota and Bacillota phyla, ferment complex dietary polysaccharides.This process produces short-chain fatty acids, like acetate, butyrate, and propionate, which support gut homeostasis.Also, certain members of Bacteroidota can trigger the activation of regulatory T cells and boost the host&#8217;s defenses.Some gut bacteria produce antimicrobial compounds, like bacteriocins, that kill harmful microbes.Select members of Bacillota and Actinomycetota, synthesize essential vitamins such as vitamin K and certain B vitamins.Certain gut bacteria convert cholesterol and bile acids into secondary bile acids. These metabolites act as signaling molecules that regulate lipid and glucose metabolism in the gut.Gut bacteria also compete with pathogens like Clostridioides difficile for nutrients and space, reducing the risk of infections.

functions of the gut microbiota

Functions of the Gut Microbiota

The gut microbiota includes trillions of microorganisms that colonize the human gastrointestinal tract, including bacteria, archaea, viruses, and fungi. This complex ecosystem plays a critical role in maintaining intestinal and systemic health. Most of these microbes inhabit the large intestine, establishing a relatively stable and diverse community that contributes to gut homeostasis through various metabolic, immunological, and protective mechanisms.Dominant bacterial phyla, such as Bacteroidota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes), facilitate the fermentation of indigestible dietary polysaccharides. This fermentation yields short-chain fatty acids (SCFAs), notably butyrate, propionate, and acetate. Butyrate is a primary energy source for colonocytes and exhibits anti-inflammatory properties, while propionate influences gluconeogenesis and lipid metabolism in the liver.Specific Bacteroidota species modulate the host immune system by stimulating dendritic and regulatory T cells, thereby enhancing mucosal immunity and maintaining immune tolerance. Additionally, various gut bacteria produce bacteriocins and other antimicrobial peptides that inhibit the growth of pathogenic microorganisms. These functions are vital for controlling opportunistic pathogens, such as Clostridioides difficile, by competing for nutrients and colonization sites.Members of the Actinomycetota phylum, including genera such as Bifidobacterium, contribute to the biosynthesis of essential micronutrients like vitamin B12 (cobalamin) and vitamin K. Certain gut microbes participate in the biotransformation of bile acids and cholesterol into bioactive metabolites that influence lipid digestion, glucose homeostasis, and systemic metabolic regulation. Some bacterial species also metabolize xenobiotics, including pharmaceutical compounds and dietary toxins, resulting in the modulation and management of their bioavailability and excretion.The gut microbiota is an intricate interface between diet, host physiology, and environmental exposures. Its metabolic versatility and immunomodulatory capabilities play a fundamental role in health and disease prevention.

The gut microbiota includes trillions of microorganisms that colonize the human gastrointestinal tract, including bacteria, archaea, viruses, and fungi. ...

https://cloudfront.jove.com/files/ftp_upload/40799/40799_article_thumb_40799.jpg

Education

JoVE Core

Microbiology

Unit

Human Microbiome and Virome

KEY TERMS AND CONCEPTS

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 are complex carbohydrates. This process produces short-chain fatty acids, or SCFAs, including butyrate, propionate, and acetate. Butyrate serves as a main energy source for colonocytes, the cells that line the colon, and it also has anti-inflammatory effects. Propionate helps influence gluconeogenesis and lipid metabolism in the liver.

The gut microbiota also helps shape the immune system. Some Bacteroidota species stimulate dendritic cells and regulatory T cells, which support mucosal immunity and immune tolerance. In addition, many gut bacteria make bacteriocins and other antimicrobial peptides. These compounds help block harmful microbes by limiting their growth and by competing for nutrients and space. This is especially important for controlling opportunistic pathogens such as Clostridioides difficile.

Another key role of gut microbes is nutrient production. Members of the Actinomycetota phylum, including Bifidobacterium, help synthesize essential micronutrients such as vitamin B12 and vitamin K. Gut bacteria also change bile acids and cholesterol into bioactive metabolites. These products can affect lipid digestion, glucose balance, and overall metabolic regulation.

Some gut microbes also metabolize xenobiotics, which are foreign compounds such as medicines and dietary toxins. This can change how these substances are absorbed, used, and removed from the body. Together, the gut microbiota links diet, host physiology, and environmental exposures. Its metabolic, immune, and protective roles are important for health and disease prevention.

Gut Microbiota and Human Health

introduction to the human microbiota

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,...

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

Learn how gut microbiota support digestion, immunity, vitamin production, and protection against pathogens in the human digestive system.

Gut Microbiota and 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

Gut Microbiota and Human Health

Description

Transcript

Tags