Introduction

The human body is home to an enormous number of microorganisms that live on our skin, in the mouth, throughout the digestive tract and at several other anatomical sites. These microorganisms include bacteria, archaea, fungi, viruses and certain microbial eukaryotes. Although microorganisms are commonly associated with infectious diseases, many live in close association with humans without causing harm. Some also contribute to important biological functions, including digestion, metabolism, protection against pathogens and regulation of immune responses.

For many years, microbiology textbooks and educational materials commonly stated that microbial cells outnumber human cells by approximately ten to one. However, this estimate has been revised. A study published in PLOS Biology in 2016 estimated that a reference adult male contains approximately 38 trillion bacterial cells and 30 trillion human cells. Although these numbers vary with body size, age and other individual characteristics, they suggest that bacterial and human cell numbers are of a similar order of magnitude.

The relationship between humans and microorganisms is more complex than simply sharing the same environment. Microorganisms obtain nutrients and suitable conditions from the body, while the host may benefit from their metabolic activities and interactions with the immune system. However, not every microorganism is beneficial, and the same microbial species may behave differently depending on its location and the condition of the host.

The composition of these microbial communities also varies considerably across the body. The intestinal tract contains large populations of bacteria adapted to oxygen-limited environments, whereas the skin supports organisms that tolerate changes in moisture, oxygen availability and exposure to the external environment. The mouth, nasal cavity, vagina and urinary tract each provide different ecological conditions that influence which microorganisms can survive and multiply.

Modern DNA sequencing and other molecular techniques have transformed our understanding of these communities. Researchers can now investigate microbial diversity, identify genetic pathways involved in metabolism and examine how microorganisms interact with human physiology. These developments have made the human microbiome an important area of research in microbiology, immunology, nutrition, medicine and biotechnology.

Figure 1. Human microbiota associated with different anatomical sites, including the oral cavity, skin, gastrointestinal tract, and urinary tract. Conceptual scientific illustration by Microbes World, created through AI.

What are the human microbiota and human microbiome?

The terms microbiota and microbiome are closely related but have slightly different meanings.

Microbiota generally refers to the microorganisms living in a particular environment. For example, the gut microbiota consists of microorganisms inhabiting the gastrointestinal tract, while the skin microbiota refers to those associated with the skin.

The term microbiome is often used to describe these microorganisms together with their collective genetic information. In broader ecological definitions, it also includes their activities, interactions and environmental conditions.

In older microbiology textbooks, the microorganisms commonly associated with healthy individuals were called normal flora or indigenous flora. However, microbiota is now the preferred term because these organisms are not plants, and their biological diversity extends beyond bacteria alone.

Human-associated microorganisms may be described as resident or transient. Resident microorganisms can persist in particular anatomical locations over time, while transient microorganisms may enter through food, environmental exposure, contact with other people or other routes without becoming established members of the community.

Nevertheless, these categories are not always permanent. A microorganism that persists in one individual may be detected only temporarily in another, and the composition of resident communities can change with diet, medication, ageing and other influences.

What types of microorganisms live in the human body?

Bacteria are the most extensively studied members of the human microbiota. They belong to numerous taxonomic groups and have different metabolic capabilities, nutrient requirements and ecological functions. Their distribution depends strongly on the anatomical location.

Archaea are also found in human-associated environments. For example, the methanogenic archaeon Methanobrevibacter smithii can occur in the intestine, where it participates in microbial metabolic networks by consuming hydrogen and producing methane.

Fungi form another component of human microbial communities, sometimes called the mycobiota. Yeasts belonging to genera such as Candida and Malassezia can inhabit different body sites. Some coexist with the host without causing disease, while others may become opportunistic pathogens under particular conditions.

Viruses are important members of the human virome. Some infect human cells, while bacteriophages infect bacteria. These bacterial viruses can influence microbial population dynamics and contribute to the movement of genetic material among bacteria.

Certain microbial eukaryotes, including protists, may also inhabit the human intestinal tract. Their biological relationships with the host vary, and detecting them does not automatically indicate infection or disease.

Together, these organisms form complex microbial ecosystems. Their interactions with one another can influence their ability to colonize particular habitats and perform biological functions.

Relationships between the host and its microorganisms

The associations between humans and microorganisms are commonly described using ecological concepts such as mutualism, commensalism and parasitism.

Mutualism refers to a relationship in which both organisms benefit. For example, some intestinal microorganisms obtain nutrients from the host while producing metabolites that contribute to intestinal functions.

Commensalism describes an association in which one organism benefits without a clearly demonstrated benefit or harm to the other. Many microorganisms traditionally described as commensals may have functions that are not yet fully understood.

Parasitism involves a relationship in which one organism benefits while causing harm to another. Disease-causing microorganisms may damage tissues, produce toxins or disrupt normal physiological functions.

These relationships are not always fixed. Some microorganisms that normally inhabit the body without causing symptoms can become opportunistic pathogens when they enter normally protected tissues or when host immune defences are weakened.

For example, certain Escherichia coli strains live in the intestine without causing disease. However, some strains can produce urinary tract infections, bloodstream infections or other illnesses when they possess appropriate virulence factors and reach susceptible anatomical sites.

Therefore, microorganisms should not simply be divided into good and bad organisms. Their effects depend on their genetic characteristics, location, interactions with other microbes and the physiological condition of the host.

Microbial composition varies across different human body sites

The human body does not contain one uniform microbial community. Instead, each anatomical site provides a distinct environment that supports microorganisms adapted to its physical, chemical and biological conditions.

Oxygen availability, temperature, pH, moisture, nutrients, host secretions and local immune responses help determine which microorganisms can persist.

For example, many intestinal bacteria grow under oxygen-limited conditions, while some skin bacteria tolerate exposure to oxygen and changing environmental conditions. Oral microorganisms may form structured biofilms on teeth, whereas vaginal microbial communities are often influenced by acidity and reproductive hormones.

These differences explain why certain bacterial phyla or genera dominate particular body sites.

When interpreting microbiome composition, it is important to understand that published percentages usually represent the relative abundance of sequencing reads assigned to particular microorganisms. They are not necessarily equivalent to the percentage of living microbial cells.

The following sections describe major microbial groups found at different body sites, their approximate relative abundances where reliable studies provide them, and their main biological roles.

Figure 2. Microbial ecosystems across the human body. Conceptual illustration based on the Human Microbiome Project Consortium (2012) and created by AI.

Composition of the human gut microbiota

The gastrointestinal tract contains one of the most densely populated microbial ecosystems associated with the human body.

However, microorganisms are not distributed uniformly along the digestive tract. The stomach and upper small intestine generally contain fewer bacteria than the large intestine because of differences in acidity, intestinal movement, bile exposure and other environmental conditions.

The colon provides favourable conditions for dense microbial growth, including abundant dietary residues, mucus-derived nutrients and largely oxygen-limited environments.

Major bacterial phyla in the gut

In healthy adults, faecal bacterial communities are commonly dominated by two phyla: Bacillota, historically called Firmicutes, and Bacteroidota, formerly known as Bacteroidetes.

A systematic review and meta-analysis published in 2025 examined 86 studies involving 20,748 participants and reported the following approximate phylum-level abundances. These are median values across different groups of studies, not fixed reference ranges for every healthy individual.

These figures summarize study-group medians calculated using different sample-processing approaches. They are not simultaneous measurements from one population and should not be added together to calculate the composition of an individual sample.

These broad taxonomic groups contain many organisms with different physiological and metabolic characteristics.

Important gut bacterial genera and their functions

Members of Bacillota include several well-studied intestinal genera such as Faecalibacterium, Roseburia, Blautia and other organisms capable of fermenting dietary compounds. Some members, including Faecalibacterium prausnitzii and certain Roseburia species, are associated with the production of butyrate, an important short-chain fatty acid involved in colonocyte metabolism and intestinal barrier functions.

Bacteroidota includes genera such as Bacteroides and Prevotella. Many members possess extensive enzymatic pathways for breaking down complex carbohydrates and other dietary or host-derived substrates. Their abundance varies with diet, lifestyle and individual characteristics.

Actinomycetota includes Bifidobacterium, which is particularly important during early life. Certain Bifidobacterium species can utilize human milk oligosaccharides and often become prominent members of the intestinal microbiota of breastfed infants.

Verrucomicrobiota includes Akkermansia muciniphila, a bacterium capable of utilizing intestinal mucin. Its interactions with the mucus layer and host metabolism have attracted considerable research interest, although its abundance should not be interpreted as a universal indicator of intestinal health.

Pseudomonadota includes Escherichia and several other genera. These bacteria often occur at relatively low abundance in many healthy adults but may become more prominent under certain conditions, including intestinal inflammation or antibiotic-associated disturbances.

At the genus level, the intestinal microbiota differs considerably between individuals. Some communities contain relatively high abundances of Bacteroides, while others are enriched in Prevotella or other genera. Consequently, there is no single genus-level percentage that defines a healthy gut microbiota.

Is Escherichia coli an essential member of every human gut microbiota?

Escherichia coli is one of the most familiar bacteria in microbiology, largely because of its extensive use in molecular biology and infectious disease research.

Although many E. coli strains can live harmlessly in the intestinal tract, the species is not necessarily present at the same abundance in every individual. It generally represents a relatively small fraction of the intestinal community in many healthy adults, compared with abundant obligately anaerobic bacteria.

Some intestinal microorganisms synthesize vitamins, including certain B vitamins and vitamin K-related compounds. However, the extent to which these compounds contribute to human nutrition depends on the microorganisms involved, their location in the intestine and the availability of the vitamins for absorption.

Therefore, it would be inaccurate to suggest that humans depend primarily on E. coli for their vitamin requirements or that the species performs the same functions in every host.

Composition of the human oral microbiota

The oral cavity contains a highly diverse microbial ecosystem distributed across teeth, tongue, gingiva, saliva and other mucosal surfaces.

These surfaces differ in oxygen availability, nutrient conditions and their capacity to support microbial attachment. Teeth provide stable, non-shedding surfaces where complex bacterial biofilms can develop, while saliva contains microorganisms originating from several oral habitats.

Major bacterial phyla in saliva

A study published in Frontiers in Microbiology in 2022 reported the following average relative abundances in its human saliva dataset.

These percentages are representative of the particular study population and samples, rather than universal values for all oral sites.

At the genus level, the same study identified Streptococcus as the most abundant genus, accounting for approximately 22.62% of reads, followed by Neisseria at 13.86% and Haemophilus at 13.76%.

Biological roles of oral microorganisms

Streptococcus species are common early colonizers of oral surfaces. They participate in dental biofilm development and contribute to interactions between different bacterial populations. Some are normal residents, while certain species, including Streptococcus mutans, can contribute to dental caries when ecological conditions favour acid-producing microbial communities.

Neisseria species are commonly found in the oral cavity, where some participate in nitrate reduction and other metabolic processes. These activities are part of the broader nitrogen metabolism occurring within oral microbial communities.

Veillonella species can utilize lactate produced by other oral bacteria. This is an example of metabolic cross-feeding, in which one microorganism uses compounds produced by another.

Actinomyces species are important in the formation of dental biofilms, particularly on tooth surfaces. Fusobacterium nucleatum can interact with multiple bacterial groups and contributes to the organization of some mixed-species oral biofilms.

The microbial composition of dental plaque differs from that of saliva. Dental plaque communities change as biofilms mature and environmental conditions become more favourable for organisms adapted to lower oxygen concentrations.

These ecological changes are important in oral health. Dental caries involves microbial acid production and tooth demineralization, while periodontal diseases involve interactions between microbial communities, host immunity and inflammatory processes.

The presence of one particular bacterial species does not necessarily indicate disease. The activities of the wider microbial community and the host response are often more informative.

Figure 4. Oral microbial communities in health and disease. Based on Marsh (2003) and Lamont et al. (2018) and created by AI.

Composition of the human skin microbiota

The skin is one of the largest interfaces between the human body and the external environment. Its microbial composition varies markedly between different anatomical locations because of differences in moisture, sebum production, temperature, pH and exposure to environmental microorganisms.

The three major skin environments commonly described in microbiome research are sebaceous or oily sites, moist sites and relatively dry sites.

Major bacterial phyla across skin environments

A study published in Frontiers in Microbiology in 2023 investigated bacterial communities from 579 skin samples collected from 129 healthy adults. The sampled regions included the area behind the ears, the belly button, between the toes, the calves and the forearms.

The researchers reported substantial differences between these sites.

These values are mean relative abundances from the specified study. The oily category represented the sampled area behind the ears; it should not be assumed to describe every sebaceous site, such as the forehead or upper back.

The same study reported that Staphylococcus represented approximately 67.4% of reads in its oily-site group, whereas Corynebacterium represented about 36.4% in the moist-site group.

Other studies have reported strong Cutibacterium dominance in selected sebaceous regions, demonstrating why composition cannot be generalized from one oily skin location to all others.

Important skin microorganisms and their functions

Cutibacterium acnes is commonly associated with sebum-rich regions, including the face and upper back. It can metabolize skin lipids and participates in local microbial interactions. Although certain strains and host responses are involved in acne development, C. acnes is also a normal member of the skin microbiota.

Staphylococcus epidermidis is another important skin-associated organism. Some strains produce substances that inhibit competing microorganisms or influence local immune responses. However, the same species may behave as an opportunistic pathogen, particularly in infections involving implanted medical devices.

Corynebacterium species are frequently found in moist skin environments, including the armpits and skin folds. Certain species metabolize compounds present in sweat and skin secretions, contributing to the production of substances associated with body odour.

Dry skin sites generally contain more variable bacterial communities. Their composition can be influenced by environmental contact, washing practices, clothing, skin physiology and other exposures.

The skin microbiota contributes to barrier-associated microbial interactions and competition against potentially harmful organisms. However, changes in microbial composition are also associated with skin diseases such as acne, atopic dermatitis and some chronic wound infections.

These relationships are influenced by host immunity and skin conditions, and no single bacterial percentage reliably determines skin health.

Composition of the vaginal microbiota

The vaginal microbiota is a specialized microbial ecosystem influenced by hormones, reproductive stage, epithelial physiology and local chemical conditions.

In many healthy women of reproductive age, vaginal bacterial communities are dominated by members of the genus Lactobacillus. However, different community compositions can occur among individuals without obvious symptoms.

A major study by Ravel and colleagues investigated 396 asymptomatic women and described five principal vaginal microbial community patterns, commonly called community state types (CSTs).

The percentages above describe the proportion of women assigned to each community state type in the study, not the percentage abundance of the named bacterial species. Values are approximate and do not sum to exactly 100% because of rounding.

Functions of dominant vaginal microorganisms

Lactobacillus crispatus is particularly interesting because it contributes to lactic acid production and an acidic vaginal environment. Low vaginal pH can restrict the growth of some microorganisms associated with vaginal infections.

Lactobacillus iners is also frequently detected but has different physiological characteristics from L. crispatus. It can be associated with several vaginal community conditions, including periods of microbial transition.

Other lactobacilli, such as L. gasseri and L. jensenii, also occur in some vaginal communities and contribute to local microbial interactions.

Communities classified within CST IV contain a broader range of anaerobic bacteria, including members of Gardnerella, Prevotella, Sneathia, Megasphaera and other genera.

Some of these organisms are associated with bacterial vaginosis, a condition involving characteristic changes in vaginal microbial communities. However, a relatively diverse vaginal community does not automatically establish bacterial vaginosis, particularly when an individual has no symptoms.

The vaginal microbiota may also change during menstruation, pregnancy, menopause and other hormonal transitions. This makes reproductive stage an important consideration when comparing microbial composition between individuals.

Composition of the nasal and respiratory microbiota

The nose and upper respiratory tract provide habitats for microorganisms that tolerate exposure to inhaled air, mucus, immune factors and changing environmental conditions.

Common bacterial genera associated with the anterior nares include Staphylococcus, Corynebacterium, Dolosigranulum, Moraxella and Cutibacterium.

A study of healthy adults in Santiago, Chile, published in Microorganisms in 2023, reported Staphylococcus in approximately 89.1% of participants and Corynebacterium in approximately 82.7%. The reported median relative abundances were about 17.2% for Staphylococcus and 18.1% for Corynebacterium.

These two types of percentages should be distinguished. Detection in 89.1% of participants means that the genus was found in that proportion of sampled individuals; it does not mean that the genus represented 89.1% of all bacterial sequences.

Functions of nasal microorganisms

Staphylococcus epidermidis and related organisms can occur as common residents of the nasal and skin-associated microbiota. Certain strains may influence local microbial competition.

Staphylococcus aureus can also colonize the nose without causing symptoms. However, nasal carriage may be relevant to the epidemiology of some S. aureus infections, particularly in susceptible individuals.

Corynebacterium and Dolosigranulum have attracted attention because of their associations with certain respiratory microbial community patterns. Researchers are investigating whether interactions among these organisms influence colonization by other bacteria.

The lower respiratory tract has a much lower microbial biomass than the oral cavity or colon. Modern molecular studies have detected microbial material in lower airway samples, but their interpretation requires careful control for contamination originating from the mouth, upper airways or sampling procedures.

In relatively healthy lower respiratory samples, microorganisms belonging to genera such as Prevotella, Veillonella and Streptococcus may be detected, often reflecting microbial exchange with the upper respiratory tract.

However, there is no reliable universal percentage of a particular bacterial genus that defines a healthy lung microbiota. Microbial biomass, immigration, elimination and local growth conditions must all be considered.

Composition of the urinary microbiota

For many years, the urinary bladder was considered sterile in healthy individuals. Modern culture techniques and molecular approaches have demonstrated that microorganisms can sometimes be detected in urine collected from people without urinary symptoms.

Commonly reported genera include Lactobacillus, Streptococcus, Corynebacterium, Staphylococcus, Gardnerella and several others.

Their relative abundances vary considerably according to sex, age, hormonal status, individual characteristics and collection method.

Some urinary microbial communities contain relatively high proportions of lactobacilli, whereas others contain more diverse bacterial populations.

An important methodological distinction concerns catheter-collected urine versus voided urine. Voided samples may contain microorganisms originating from surrounding anatomical sites, making interpretation of the bladder microbiota more difficult.

For these reasons, it would be scientifically misleading to assign one fixed set of phylum- or genus-level percentages to the urinary tract of all healthy adults.

Detecting bacteria in urine also does not automatically indicate a urinary tract infection. Diagnosis requires consideration of symptoms, clinical findings, bacterial identification and other relevant information.

The urinary microbiota is an active research area, but the biological roles of many detected microorganisms are not yet fully understood.

How does the human microbiota develop throughout life?

Human-associated microbial communities begin developing early in life and undergo substantial changes as the host grows and encounters new environmental conditions.

Birth is associated with major microbial exposure and colonization. Delivery mode, gestational age, feeding practices, antibiotic treatment, environmental contact and other factors can influence the early microbiota.

The intestinal microbiota of breastfed infants often contains substantial populations of Bifidobacterium. Certain species possess enzymes that allow them to utilize human milk oligosaccharides, complex carbohydrates that the infant cannot digest efficiently.

These compounds provide substrates that can favour the growth of particular bacteria and influence the developing microbial ecosystem.

As infants begin consuming solid foods, the intestinal environment changes and supports a wider range of microbial metabolic activities. Organisms capable of degrading plant polysaccharides and other dietary components become increasingly important.

During childhood, microbial communities generally develop toward more adult-like compositions, although considerable variation remains between individuals.

In adulthood, some microbiota characteristics may remain relatively stable over time. However, diet, antibiotic exposure, infections, medication use, travel and other factors can produce temporary or persistent changes.

Ageing is also associated with shifts in microbial composition. Nevertheless, these changes are influenced by health status, diet, medications and living conditions, rather than chronological age alone.

The microbiota is therefore a dynamic system that develops alongside the host throughout life.

How do microorganisms contribute to digestion and metabolism?

One of the most extensively studied functions of the intestinal microbiota is the metabolism of dietary compounds that human digestive enzymes cannot fully break down.

Several intestinal bacteria possess pathways for degrading complex carbohydrates, including certain dietary fibres and plant-derived polysaccharides.

When these compounds reach the large intestine, microorganisms can ferment them and produce metabolites such as acetate, propionate and butyrate.

These short-chain fatty acids participate in several biological processes. Butyrate is an important energy source for colon epithelial cells, while acetate and propionate contribute to metabolic pathways and signalling processes involving intestinal and other tissues.

Microorganisms also participate in the transformation of bile acids, amino acids and other dietary or host-derived compounds.

Some intestinal microbes synthesize vitamins or modify compounds that influence nutrient availability. However, the nutritional contribution of microbial vitamin production varies according to the compound, microbial activity and absorption site.

Microbial metabolism can also affect certain medications. Some microorganisms possess enzymes capable of transforming drugs or influencing their availability within the digestive tract.

These activities demonstrate that the intestinal microbiota is not merely a collection of bacteria living alongside the host. It contributes to biochemical processes that interact with human metabolism.

Microbiota and the human immune system

The immune system is continuously exposed to microorganisms and their products at several body surfaces. The intestine, skin, respiratory tract and other mucosal environments contain physical and immunological barriers that help regulate these interactions.

In the intestine, epithelial cells, mucus, antimicrobial peptides and immune cells contribute to maintaining separation between many microorganisms and sensitive host tissues.

At the same time, microbial signals can influence immune-cell development and activity. Some microbial metabolites participate in signalling pathways that affect local inflammation, epithelial barrier functions and immune regulation.

The intestinal microbiota also contributes to colonization resistance, a process through which established microorganisms and host responses help prevent invading pathogens from becoming established.

Colonization resistance may involve competition for nutrients, occupation of ecological niches, production of inhibitory substances or changes in the intestinal environment.

However, microbiota–immune interactions are not universally protective. Certain microorganisms may contribute to inflammation under particular conditions, while changes in host immunity can alter which bacteria survive and multiply.

Therefore, immune regulation depends on interactions between microorganisms, host tissues and environmental conditions rather than on the presence of one supposedly beneficial bacterial species.

What is microbial dysbiosis?

The term dysbiosis is commonly used to describe microbial community changes associated with a disturbed relationship between microorganisms and their host.

Studies have reported differences in microbial composition in several conditions, including inflammatory bowel disease, recurrent infections, metabolic disorders and certain inflammatory skin diseases.

However, dysbiosis is not a single, universally defined microbial state. It does not necessarily mean that microbial diversity has decreased or that one particular bacterial group has become abundant.

For example, increased abundance of certain facultatively anaerobic bacteria may occur during intestinal inflammation. This can result partly from changes in oxygen availability, nutrient conditions and the intestinal environment.

Consequently, an altered microbiota can be a consequence of disease, a contributor to disease processes or both.

This creates an important challenge in microbiome research. When researchers observe a difference between healthy individuals and patients, they must determine whether the microbial change is biologically meaningful or simply associated with other factors.

Antibiotic use, diet, age, medication, geography and underlying health conditions may all influence microbial composition.

Therefore, a statistically significant association between a microorganism and a disease does not automatically establish causation.

The gut–brain axis and other microbiome connections

Researchers are increasingly investigating communication between intestinal microorganisms and other physiological systems.

The gut–brain axis refers to interactions involving the gastrointestinal tract, nervous system, immune system, endocrine signalling and microbial metabolites.

Experimental research has demonstrated that microbial products can influence signalling pathways relevant to host physiology. However, many mechanistic findings originate from animal models, and their relevance to human diseases requires further investigation.

Human studies have reported associations between microbial composition and several neurological or psychological conditions. Nevertheless, these associations do not establish that altering the microbiota will necessarily prevent or treat such conditions.

Similar caution is needed when discussing obesity, diabetes, cardiovascular disease and cancer.

Microbial metabolism may influence biological pathways associated with these conditions, but human health outcomes also depend on genetics, diet, medication, lifestyle and many other factors.

The microbiota should therefore be considered one component of a complex biological system rather than an independent explanation for every disease.

The Human Microbiome Project: A major scientific milestone

One of the most important developments in human microbiome research was the Human Microbiome Project (HMP), launched by the United States National Institutes of Health in 2007.

The project was designed to characterize microbial communities associated with healthy humans and develop scientific resources for investigating their relationships with health and disease.

A major publication appeared in Nature in 2012, describing the structure, function and diversity of microbial communities across multiple anatomical habitats.

The study analysed 4,788 specimens collected from 242 screened adults, including 129 men and 113 women. The samples represented five major body regions: the gastrointestinal tract, oral cavity, skin, nasal passages and vagina.

Researchers sampled 18 anatomical habitats in women and 15 in men, with the difference reflecting the inclusion of vaginal sites.

Bacterial communities were characterized using 16S rRNA gene sequencing. A subset of samples was also analysed using shotgun metagenomic sequencing to investigate microbial genetic and functional potential.

One of the project's most important findings was that microbial communities differ substantially between anatomical sites. The mouth, skin, gut and vagina contain distinct microbial populations adapted to their local environments.

The study also demonstrated considerable variation between healthy individuals. Two people could possess different microbial compositions while sharing some broadly similar microbial functional capabilities.

These findings challenged the idea that every healthy person should harbour an identical set of bacterial species.

The HMP also produced reference datasets, sequencing resources and analytical methods that contributed to the development of modern microbiome research.

From the Human Microbiome Project to the Integrative Human Microbiome Project

The initial Human Microbiome Project focused primarily on describing microorganisms and their collective genetic characteristics.

Its second phase, known as the Integrative Human Microbiome Project (iHMP), expanded this approach by combining microbial information with host biological measurements and longitudinal sampling.

The iHMP investigated three major areas: inflammatory bowel disease, pregnancy and preterm birth, and physiological responses in individuals with prediabetes.

Researchers used approaches including metagenomics, transcriptomics, metabolomics and host-associated measurements.

This allowed them to examine changes in microbial composition and function alongside changes in host physiology.

The project helped establish the importance of studying microbial communities over time rather than relying solely on one sample collected at a single time point.

It also demonstrated why identifying microorganisms is only one step toward understanding their biological significance.

How do scientists study human microbial communities?

The methods used to investigate the human microbiota have changed substantially with advances in molecular biology and sequencing technology.

Traditional culture-based methods remain important because they allow researchers to isolate viable organisms, investigate their physiology and experimentally test their functions.

However, many microbial species are difficult to recover under conventional laboratory conditions. Molecular methods have therefore become essential for characterizing complex communities.

16S rRNA gene sequencing

The 16S rRNA gene is widely used to investigate bacterial and archaeal communities because it contains conserved and variable regions that can support taxonomic classification.

Researchers amplify selected gene regions or sequence longer fragments and compare them with reference databases.

This approach provides information about microbial community composition, but its taxonomic resolution depends on the target region, sequencing method and reference database.

Closely related species may not always be distinguishable. For example, 16S rRNA sequencing often cannot reliably separate Escherichia coli from closely related Shigella populations.

It also does not directly establish whether an organism is alive, metabolically active or capable of causing disease.

Shotgun metagenomic sequencing

Shotgun metagenomics examines DNA recovered from microbial communities without specifically targeting the 16S rRNA gene.

It can provide information about microbial species, strains and genetic pathways, depending on sample quality, sequencing depth and analytical methods.

This approach can also support investigation of antimicrobial resistance genes, virulence-associated factors and other genomic characteristics.

However, identifying a gene in metagenomic data does not automatically mean that the gene is expressed or that the corresponding biological activity occurs.

Metatranscriptomics, metaproteomics and metabolomics

Metatranscriptomics investigates RNA molecules and can provide information about microbial gene expression.

Metaproteomics examines proteins produced within microbial communities, while metabolomics investigates small molecules associated with microbial and host metabolism.

These approaches can be combined with sequencing data to study microbial activity and functional pathways.

However, each method has limitations, and interpretation requires careful consideration of analytical procedures, sample collection and biological context.

Why sampling and data analysis matter

Microbiome results can be influenced by DNA extraction methods, sequencing platforms, reference databases, laboratory contamination and bioinformatic decisions.

For example, different extraction procedures may recover DNA from some bacterial groups more efficiently than from others. Similarly, different 16S rRNA regions may produce different taxonomic profiles.

Relative abundance data also have compositional properties. An increase in the proportion of one bacterial group can make another group appear less abundant even when its absolute cell count has not changed.

This is particularly important when comparing samples from different people, body sites or time points.

Appropriate experimental controls, clear metadata, suitable statistical methods and independent validation are therefore essential for reliable microbiome research.

Modern clinical applications of microbiome research

Research on the human microbiome has progressed from describing microbial communities to investigating whether particular microorganisms or microbial functions can be used to prevent or treat disease.

Several approaches are being studied, including dietary interventions, probiotics, prebiotics, microbiota transplantation and other live microbial products.

Dietary interventions may influence the availability of substrates used by intestinal microorganisms. Changes in dietary fibre, protein, fat and other food components can alter microbial metabolism and community composition. However, responses vary considerably between individuals.

Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Their effects depend on the particular strain, dose, product and clinical indication. A microorganism should not be considered clinically beneficial merely because it belongs to a genus frequently used in probiotic products.

Prebiotics are substrates selectively utilized by host microorganisms that confer a health benefit. Certain dietary fibres and related compounds have been investigated for these properties.

One important area of established clinical progress involves recurrent Clostridioides difficile infection. Antibiotic-associated disruption of intestinal microbial communities can reduce colonization resistance and facilitate infection or recurrence.

In the United States, the Food and Drug Administration has approved microbiota-based products, including REBYOTA and VOWST, for preventing recurrence of C. difficile infection in specified adults following antibiotic treatment.

These developments demonstrate that microbiota-based interventions can provide clinical benefits in defined situations. However, they also require appropriate quality control and screening because products containing live microorganisms may carry biological risks.

For many other conditions, microbiome-targeted treatments remain experimental or have not yet demonstrated sufficiently consistent clinical benefits.

Is there a single healthy human microbiome?

One of the most important questions in microbiome research is whether there is a standard microbial composition that can be considered healthy.

Current evidence indicates that there is no single microbial community shared by all healthy individuals.

Microbial composition varies with anatomical location, age, diet, environment, medication use, hormonal status and many other characteristics.

A gut microbiota containing a relatively high proportion of Bacteroides is not automatically healthier than one containing more Prevotella. Similarly, greater microbial diversity does not always indicate better health at every body site.

For example, a lactobacilli-dominated vaginal community may have relatively low diversity while being compatible with healthy physiological conditions.

Microbial functions, interactions and relationships with the host may therefore be more informative than the abundance of individual organisms alone.

This is also why commercial microbiome tests that label particular bacterial percentages as good or bad should be interpreted cautiously. Many reported associations are not sufficiently established to serve as individual clinical diagnostic criteria.

Understanding a healthy microbiome requires considering the whole microbial community, its functions and the biological context in which it exists.

Current research and future directions

Human microbiome research continues to expand because many questions about microbial diversity, function and host interactions remain unresolved.

One major direction is the study of strain-level diversity. Different strains belonging to the same bacterial species can possess different metabolic pathways, colonization characteristics or virulence factors.

Researchers are also investigating microbial interactions within complex communities. These include nutrient sharing, competition, bacteriophage infection and changes in the chemical conditions of microbial habitats.

Another important area is spatial organization. Microorganisms are not distributed uniformly throughout the intestine or other body surfaces. Their proximity to mucus layers, epithelial tissues and neighbouring microorganisms can influence their biological activities.

Longitudinal studies are helping scientists understand how microbial populations change during dietary interventions, antibiotic treatment, infections, ageing and disease progression.

Multi-omics research is becoming increasingly important because it allows investigators to combine taxonomic, genetic, metabolic and host physiological information.

There is also growing interest in improving the geographical and demographic representation of microbiome research. Many early studies focused on selected populations, and their findings cannot automatically be generalized to people with different diets, environments and lifestyles.

Future microbiome research will increasingly depend on identifying microbial functions, understanding causal mechanisms and demonstrating whether targeted interventions produce meaningful health benefits.

The human body is therefore best understood as a complex biological environment containing multiple microbial ecosystems. These communities contribute to digestion, metabolism, immune interactions and ecological processes throughout life. Their activities can be beneficial, neutral or harmful depending on the organism and its biological context.

Understanding the composition and functions of these communities provides an important foundation for studying human physiology, infectious diseases, immunology, nutrition and the development of microbiome-based medicine.

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