An almost quick guide to microbiomes

Most people have heard of the gut microbiome, but few realise that the human body hosts many different microbiomes, each playing a vital role in health and disease.

These microbial ecosystems are made up of trillions of bacteria, fungi, viruses, and other microscopic organisms that live on and within our bodies. Far from being harmful, most of these microbes are essential. They help digest food, train the immune system, produce important nutrients, and protect us from infection.

Unfortunately, microbiomes are easily disrupted. One of the most common causes of disruption is the widespread use of antibiotics.

Antibiotics have saved millions of lives and remain one of medicine’s greatest achievements. However, while they eliminate disease-causing bacteria, they can also damage beneficial microbial communities. Understanding this balance is important if we are to preserve the microbiomes that help keep us healthy.

Six important things to know about antibiotics

1. Antibiotics Save Lives

Since the discovery of penicillin in 1928, antibiotics have revolutionised medicine.

They remain one of the most effective tools for treating bacterial infections and have contributed significantly to increased life expectancy worldwide. Alongside vaccination programmes, antibiotics have prevented countless deaths and transformed modern healthcare.

2. Antibiotics can damage beneficial microorganisms

The human body contains vast communities of microorganisms known collectively as microbiota.

These communities exist throughout the body, including the:

• Gut
• Skin
• Lungs
• Nose and throat
• Urinary tract
• Vagina

Antibiotics are designed to destroy harmful bacteria, but they often affect beneficial bacteria as well. This disruption can alter the balance of microbial communities, a condition known as dysbiosis.

3. Antibiotics can cause side effects

One of the most common consequences of dysbiosis is disruption of normal bowel function.

This may result in antibiotic-associated diarrhoea, which occurs because the gut microbiota is less able to perform its protective and digestive functions.

Studies suggest this affects:

• Up to 35% of adult patients
• Up to 80% of children

Some cases are associated with infection by Clostridioides difficile (C. difficile), a bacterium that can become pathogenic when normal gut microbiota is disrupted.

Clinical outcomes range from mild diarrhoea to severe illness and, occasionally, death.

4. Antibiotics may have long-term effects

Researchers increasingly believe that antibiotic-induced dysbiosis may have consequences beyond short-term digestive symptoms.

Early life appears to be particularly important because the gut microbiota and immune system are still developing.

Studies have linked early disruption of the microbiome to an increased risk of:

• Obesity
• Diabetes
• Asthma
• Inflammatory bowel disease

Although research is ongoing, these findings reinforce the importance of careful antibiotic use.

5. Misuse of antibiotics drives antibiotic resistance

Antibiotic resistance occurs when bacteria evolve mechanisms that allow them to survive treatment.

Antibiotics are effective only against bacterial infections and have no effect on viruses such as influenza or the common cold.

Overuse and inappropriate use of antibiotics in humans, animals, and agriculture accelerate the development of resistant bacteria.

The consequences include:

• Longer hospital stays
• Higher healthcare costs
• More difficult-to-treat infections
• Increased mortality

Antimicrobial resistance is now regarded as one of the most significant public health challenges facing the world.

6. World AMR Awareness Week

Each year, from 18 to 24 November, the World Health Organization (WHO) coordinates World AMR Awareness Week.

The campaign aims to raise awareness of antimicrobial resistance and encourage responsible use of antibiotics and other antimicrobial medicines.

What are microbiota and microbiomes?

The terms microbiota and microbiome are often used interchangeably, but they are not exactly the same.

Microbiota

Microbiota refers to the microorganisms themselves, including:

• Bacteria
• Viruses
• Fungi
• Archaea
• Other microbes

For example, the gut microbiota consists of all the microorganisms living within the digestive tract.

Microbiome

The microbiome includes:

• The microorganisms
• Their genetic material
• Their interactions with one another
• Their surrounding environment

In simple terms:

Microbiota = the organisms

Microbiome = the organisms plus everything associated with them

The remarkable human gut microbiome

The gut microbiome is the largest and most extensively studied microbiome in the human body.

Current estimates suggest that an average adult carries approximately:

Importantly, there is no single “normal” microbiome.

Two healthy individuals may share fewer than half of their microbial species yet both enjoy excellent health.

What often matters most is not the exact species present but the functions those microbes perform.

These functions include:

• Digesting food
• Producing vitamins
• Generating short-chain fatty acids
• Training the immune system
• Preventing colonisation by pathogens

This has led some scientists to suggest that humans are best viewed as ecosystems rather than individual organisms.

Dysbiosis: When the balance is lost

A healthy microbiome depends on balance.

Dysbiosis occurs when microbial communities become disrupted and can arise through:

• Loss of beneficial microbes
• Overgrowth of harmful microbes
• Excessive numbers of microbes performing the same function
• Loss of microbes performing essential functions

Dysbiosis has been associated with numerous conditions, including digestive disorders, metabolic disease, allergies, autoimmune disorders, and some mental health conditions.

Diversity is important, but functional diversity may be even more important than the number of species present.

The major human microbiomes

Scientists recognise dozens of microbial ecosystems throughout the body. The following are generally considered the most important.

1. Gut microbiome

Location: Large intestine

Functions:

• Digests dietary fibre
• Produces short-chain fatty acids
• Synthesises vitamin K and certain B vitamins
• Trains the immune system
• Protects against pathogens
• Influences metabolism

The gut microbiome is generally regarded as the body’s most important microbiome because of its extensive influence on health.

2. Oral microbiome

Location: Mouth, tongue, teeth, gums, saliva

Functions:

• Begins digestion
• Helps control harmful microbes
• Supports oral health

Changes in the oral microbiome have been linked to tooth decay, gum disease, cardiovascular disease, and diabetes.

3. Skin microbiome

Location: Entire skin surface

Functions:

• Creates a protective barrier
• Produces antimicrobial compounds
• Helps regulate inflammation

The skin microbiome has been associated with conditions such as eczema, acne, psoriasis, and wound healing.

4. Nasal microbiome

Location: Nasal passages and sinuses

Functions:

• Filters incoming microbes
• Supports respiratory immunity
• Limits pathogen colonisation

Research suggests it may influence susceptibility to respiratory infections, allergies, and sinus disease.

5. Lung microbiome

Location: Lower respiratory tract

For many years scientists believed the lungs were sterile. We now know they host their own microbiome.

Functions:

• Regulates inflammation
• Interacts with immune cells
• Supports respiratory health

Alterations have been associated with asthma, COPD, pneumonia, and lung cancer.

6. Vaginal microbiome

In healthy individuals, the vaginal microbiome is usually dominated by Lactobacillus species.

Functions:

• Maintains an acidic environment
• Suppresses pathogens
• Supports fertility and pregnancy

Changes in the vaginal microbiome have been linked to bacterial vaginosis, yeast infections, and adverse pregnancy outcomes.

Pre-eclampsia and the vaginal microbiome

Pre-eclampsia is a pregnancy complication characterised by high blood pressure and signs of organ dysfunction after 20 weeks of pregnancy.

Researchers have observed differences in the vaginal microbiomes of women who develop pre-eclampsia, including:

• Reduced Lactobacillus dominance
• Increased microbial diversity
• Greater abundance of potentially inflammatory organisms

However, it remains unclear whether these microbial changes are a cause, a consequence, or simply a marker of increased risk.

7. Urinary microbiome

Location: Bladder and urinary tract

For decades, urine was considered sterile. Modern techniques have shown that healthy urinary tracts contain their own microbial communities.

Functions:

• Helps prevent infection
• Supports mucosal health
• Maintains microbial balance

8. Eye microbiome

Location: Eyelids, conjunctiva, and tear film

Functions:

• Protects against infection
• Supports immune balance
• Helps maintain eye surface health

Disturbances have been linked to dry eye disease, conjunctivitis, and corneal infections.

9. Ear microbiome

Location: External ear canal

Functions:

• Competes with pathogens
• Supports skin health

Research suggests it may influence susceptibility to ear infections.

10. Reproductive tract microbiome

Location: Various reproductive tissues

This remains an active area of scientific investigation.

Researchers are studying how microbial communities may influence:

• Fertility
• Pregnancy outcomes
• Foetal development
• Immune system maturation

Some proposed microbiomes, particularly within the uterus and placenta, remain subjects of ongoing debate.

The often overlooked microbiomes

Scientists are increasingly studying microbial communities associated with:

• Hair follicles
• Scalp
• Armpits
• Belly button
• Hands
• Feet
• Breast tissue
• Semen
• Breast milk
• Tonsils

Many of these are considered specialised sub-communities of larger microbiome systems.

Which microbiome matters most?

All microbiomes interact with one another, making it difficult to rank them definitively.

However, most researchers would place the gut microbiome at the top because it contains:

• The largest microbial population
• The greatest genetic diversity
• Extensive interactions with the immune system
• Major influences on digestion and metabolism

The oral, skin, vaginal, respiratory, and urinary microbiomes also play critical roles in maintaining health.

Conclusion

The human body is not a single organism but a complex ecosystem containing trillions of microorganisms.

These microbial communities help digest food, produce nutrients, regulate immunity, protect against infection, and influence many aspects of health.

Although each microbiome performs specialised functions, the gut microbiome appears to have the broadest influence and has therefore become the primary focus of microbiome research.

As our understanding grows, microbiome science is reshaping how we think about health, disease, nutrition, immunity, and even what it means to be human.