Name: how antibiotics change gut bacteria
Uploaded: 2026-05-20T13:45:57.448Z
Duration: 1 min 21 s
Channel: JoVE

Antibiotics eliminate pathogenic bacteria but may also kill beneficial gut microbes, disrupting gut ecosystem balance.This imbalance, called dysbiosis, can reduce the diversity of normal gut bacteria and allow opportunistic pathogens to flourish.Continued use of antibiotics also encourages the growth of antibiotic-resistant bacteria in the gut.During antibiotic treatment, alterations in the gut microbiota change microbial metabolic activity, including the production of short-chain fatty acids and the transformation of bile acids, which are vital for digestion and immunity.As a result, supporting the recovery of the gut microbiota after antibiotic treatment helps to reestablish these metabolic and immune functions.Probiotics, such as Lactobacillus, help restore balance by competing with harmful microbes.Meanwhile, prebiotics, which are non-digestible fibers, nourish these beneficial bacteria and promote the production of short-chain fatty acids. Together, these agents accelerate restoration of healthy gut microbiota.

microbiota modulation by antibiotics

Microbiota Modulation by Antibiotics

Antibiotics have revolutionized modern medicine by saving countless lives from bacterial infections. However, their widespread use has inadvertently harmed the delicate balance of the human gut microbiota. The gut microbiota, a complex community of bacteria, archaea, viruses, and fungi, plays a vital role in regulating metabolism, immune responses, and maintaining intestinal health. Antibiotics, especially broad-spectrum types, disrupt this ecosystem by eradicating both harmful and beneficial microbes, leading to a state known as gut dysbiosis.Disruption of the gut microbiota can begin as early as during pregnancy. Antibiotic use during pregnancy and lactation alters the maternal microbiota and affects the infant&#x2019;s initial microbial colonization. Studies in animals and humans have shown that infants exposed to antibiotics either prenatally or postnatally experience reduced microbial diversity, increased susceptibility to infections, and may have a higher risk of developing asthma, allergies, obesity, and metabolic disorders later in life. Preterm infants, often treated prophylactically with antibiotics, are particularly vulnerable to these effects, including necrotizing enterocolitis and sepsis.In adults, antibiotic treatment also causes long-lasting shifts in gut microbial composition. Even short courses can lead to reduced levels of beneficial species such as Bifidobacterium and Lactobacillus, with changes persisting for weeks to years. Additionally, antibiotic exposure promotes the selection of antibiotic-resistant strains. The gut microbiota becomes a reservoir of antibiotic resistance genes (ARGs), facilitating their spread to pathogens through horizontal gene transfer.The metabolic consequences of dysbiosis are far-reaching. Antibiotics alter the production of key metabolites like short-chain fatty acids and bile acids, disrupting energy homeostasis and glucose metabolism. This microbial imbalance has been linked to insulin resistance, inflammatory bowel diseases, and even mood disorders through the gut-brain axis.To counteract these effects, therapeutic strategies such as probiotics, prebiotics, fecal microbiota transplantation (FMT), and bacteriophage therapy are being explored. These approaches aim to restore microbial balance, enhance immune function, and prevent the spread of antibiotic resistance.Ultimately, careful stewardship of antibiotic use and a deeper understanding of host-microbe interactions are essential. Protecting the diversity and resilience of the gut microbiota is critical not only for individual health but also for combating the global threat of antibiotic resistance.

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Education

JoVE Core

Microbiology

Unit

Human Microbiome and Virome

KEY TERMS AND CONCEPTS

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 microbiota and affect the first microbes that colonize an infant. Studies in animals and humans show that infants exposed to antibiotics before or after birth often have lower microbial diversity. They may also have a higher risk of infections, asthma, allergies, obesity, and metabolic disorders later in life.

Preterm infants are especially vulnerable because they are often given antibiotics to prevent infection. In these infants, antibiotic exposure can increase the risk of necrotizing enterocolitis and sepsis. In adults, antibiotic treatment can also cause long-lasting changes in gut microbial composition. Even short courses can lower beneficial species such as Bifidobacterium and Lactobacillus, and these shifts may last from weeks to years.

Antibiotic exposure can also favor antibiotic-resistant strains. The gut microbiota can become a reservoir of antibiotic resistance genes, or ARGs. These genes can spread to pathogens through horizontal gene transfer, which is the transfer of genetic material between microbes. Antibiotic-related dysbiosis also changes key metabolites such as short-chain fatty acids and bile acids. This can disrupt energy balance and glucose metabolism and has been linked to insulin resistance, inflammatory bowel diseases, and mood disorders through the gut-brain axis.

Researchers are studying ways to restore microbial balance after antibiotic use. These approaches include probiotics, prebiotics, fecal microbiota transplantation, or FMT, and bacteriophage therapy. The goal is to support immune function and reduce the spread of antibiotic resistance. Careful antibiotic use and a better understanding of host-microbe interactions are important for protecting gut microbiota diversity and overall health.

How Antibiotics Change Gut Bacteria

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the oral microbiota

Oral Bacteria and Mouth Health

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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...

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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...

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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...

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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,...

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Gut Microbiota and Human Health

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dysbiosis of the gut microbiota

How Gut Imbalance Affects Health

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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...

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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

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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 antibiotics can disrupt gut microbiota, affect infants and adults, change metabolism, and contribute to antibiotic resistance and dysbiosis.

How Antibiotics Change Gut Bacteria | 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 Antibiotics Change Gut Bacteria

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