Name: gut microbes and brain health
Uploaded: 2026-03-12T13:36:11.000Z
Duration: 1 min 22 s
Channel: JoVE

The gut&#8211;brain axis is a two-way communication system linking the gut and brain via host-derived signals from neurons and immune cells, as well as microbial metabolites produced in the gut.After birth, maternal and environmental microbes rapidly colonize the gut. Research suggests this early colonization may be linked to immune and some aspects of neural development.By three years of age, the gut microbiome stabilizes, supporting nutrient absorption and maintaining physical and chemical homeostasis.Additionally, the gut microbiome can produce immune-modulating metabolites like tryptophan derivatives, which enter the bloodstream and help support the blood&#8211;brain barrier&#8217;s structure and function.Microbial imbalance, or dysbiosis, can alter the production of these metabolites and may weaken blood&#8211;brain barrier integrity, affecting gut&#8211;brain communication.In mouse models, dysbiosis-associated compounds such as 4-ethylphenylsulfate have been shown to trigger anxiety-like behaviors.Specific probiotics, like Bacteroides fragilis, can restore microbial balance and reverse these effects.

gut-brain axis

Gut-Brain Axis

The gut&#8211;brain axis is a bidirectional communication system that connects the gastrointestinal tract and the brain. This interaction is mediated through multiple pathways, including the vagus nerve, hormonal signals, immune responses, and chemical messengers produced by gut microbes.Microbial Contributions to Brain Function Gut microbiota contributes significantly to brain function by producing neuroactive compounds. These include neuroactive compounds that influence neurotransmitters such as serotonin and gamma-aminobutyric acid (GABA), as well as short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate. These metabolites can influence brain activity by modulating neural signaling, reducing inflammation, and preserving the integrity of the blood&#8211;brain barrier.Microbiome Development in Early Life The gut is rapidly colonized after birth by maternal and environmental microbes. This early microbial exposure plays a key role in shaping the development of the immune system and influencing early brain maturation. By the age of three, the gut microbiome typically stabilizes into a relatively consistent community that supports nutrient absorption, immune balance, and physiological homeostasis.Homeostasis and Brain Support A well-balanced gut microbiome helps maintain systemic equilibrium by regulating inflammation, reinforcing the blood&#8211;brain barrier, and influencing the development and function of brain glial cells, especially microglia. These cells are critical for immune surveillance and neural maintenance within the central nervous system.Dysbiosis and Neurological Impacts A disruption in the microbial balance&#8212;known as dysbiosis&#8212;can impair these regulatory functions. It may lead to chronic inflammation and produce harmful metabolic byproducts that negatively affect brain development and function. Dysbiosis has been associated with several neurological disorders, including Alzheimer&#8217;s disease, Parkinson&#8217;s disease, and autism spectrum disorder.Experimental Insights from Animal Studies Animal studies have shown that dysbiosis-associated compounds, such as 4-ethylphenylsulfate, can induce anxiety-like and repetitive behaviors. Conversely, restoring microbial balance using beneficial bacteria like Bacteroides fragilis has been shown to normalize metabolite levels and reverse these behavioral abnormalities.

The gut&#8211;brain axis is a bidirectional communication system that connects the gastrointestinal tract and the brain. This interaction is mediated ...

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Education

JoVE Core

Microbiology

Unit

Human Microbiome and Virome

KEY TERMS AND CONCEPTS

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 acetate, propionate, and butyrate. These metabolites can support brain activity by changing neural signaling, lowering inflammation, and helping protect the blood-brain barrier.

The microbiome starts forming soon after birth. Maternal and environmental microbes quickly colonize the gut, and this early exposure helps guide immune system development and early brain maturation. By about age three, the gut microbiome usually becomes a more stable community. That stable community supports nutrient absorption, immune balance, and overall body homeostasis, which means internal conditions stay in balance.

A balanced microbiome also supports the brain by controlling inflammation and strengthening the blood-brain barrier. It can influence glial cells, especially microglia. Microglia are immune cells in the central nervous system that help with immune surveillance and neural maintenance.

When microbial balance is disrupted, it is called dysbiosis. Dysbiosis can weaken these protective roles. It may cause chronic inflammation and create harmful metabolic byproducts that affect brain development and function. Dysbiosis has been linked with Alzheimer’s disease, Parkinson’s disease, and autism spectrum disorder.

Animal studies give more detail on these effects. Some dysbiosis-related compounds, such as 4-ethylphenylsulfate, can cause anxiety-like and repetitive behaviors. Studies also show that restoring balance with helpful bacteria like Bacteroides fragilis can normalize metabolite levels and reverse these behavioral changes.

Gut Microbes and Brain 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,...

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...

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 microbes send signals to the brain, shape early development, and how dysbiosis may affect inflammation and behavior.

Gut Microbes and Brain 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 Microbes and Brain Health

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