Types of microbiota: understanding the different microbiomes of the human body

Long relegated to the idea of ​​"germs" to be eliminated, microorganisms are now seen as functional partners. Humans coexist with bacteria, yeasts, viruses, and other microorganisms that form a unique signature: the human microbiota. This "biological signature" is not limited to the gut. There are several types of microbiota , distributed across different surfaces and mucous membranes: gut microbiota, oral microbiota, skin microbiota, vaginal microbiota, and respiratory microbiota.

Understanding the different types of microbiota means understanding that each area of ​​the body imposes its own ecological rules: oxygen level, pH, humidity, temperature, sebum presence, cell turnover, and nutrient flow. These parameters select for different communities, capable of producing useful molecules (metabolites), supporting the local barrier, and interacting with natural defenses. Conversely, when the environment becomes unbalanced, dysbiosis can develop: reduced diversity, unsuitable dominant species, impaired functions, local discomfort, and broader repercussions depending on the context.

The objective of this guide on microbiota types is twofold: to map the main microbiotas of the human body and to explain, in a precise and accessible way, their role, their influencing factors and the most relevant actions to preserve the balance of the microbiota.

What is the microbiota?

The microbiota refers to all the microorganisms living in a given environment. In the human body, it is primarily established at interfaces with the outside world: skin, mouth, intestines, upper respiratory tract, and urogenital area. The term "flora," such as " gut flora ," is often used, but microbiota is more accurate as it includes bacteria, fungi (mycobiota), viruses (virome), and other microorganisms. The term microbiome is sometimes used to refer to all the genes and functions carried by these communities, or more broadly, the ecosystem and its capabilities.

Structuring research (particularly large-scale mapping programs) has shown that composition varies considerably from one individual to another, and even from one area of ​​the body to another within the same person. Communities are distinguished not only by species, but also by their functions: production of molecules, utilization of nutrients, and communication with the host.

Microbiota: composition, functions, stability

A "balanced" microbiota does not imply a universal list of "good bacteria" that is identical for everyone. Microbiota balance is better understood as a combination of:

• Diversity (ability to occupy multiple ecological niches)
• Stability (resilience to lifestyle changes)
• Functions (metabolites produced, barrier support, competition with opportunistic species)

As such, a change in the microbiota can be neutral, adaptive, or detrimental depending on the context. Dysbiosis describes a state where the composition and/or functions become less compatible with optimal ecosystem functioning and host comfort. Review studies remind us that dysbiosis is not always the sole cause: it can also be a consequence or a marker of a disturbed environment.

The main types of microbiota in humans

It is useful to think in terms of microbiota types because the biological constraints differ greatly between an oxygen-poor gut, skin exposed to air, and a vaginal mucosa regulated by pH and hormones. Each type of microbiota fulfills "local" roles (barrier, metabolites, comfort) but also "systemic" roles via circulating signals (metabolites, bacterial fragments, immune mediators).

Comparative table of microbiota types (overview)

Types of microbiota	Location	Ecosystem (pH/oxygen/humidity)	Key functions (examples)	Sensitive factors
Gut microbiota	Intestine (especially colon)	Low oxygen, fermentable nutrients	Metabolites (e.g., SCFAs), intestinal barrier, immune dialogue	Diet, fiber, stress, sleep, medication
Oral microbiota	Tongue, gums, saliva, teeth	Biofilms, post-meal acidity cycles	Biofilm balance, metabolites, interaction with mucous membranes	Hygiene, saliva, tobacco, alcohol, mouthwash
Skin microbiota	Skin (dry, oily, moist areas)	Air, variable sebum, UV, perspiration	Skin barrier, microbial competition, tolerance	Skin type, cosmetics, climate, washing, textiles
Vaginal microbiota	Vagina	pH often acidic (depending on profiles), hormones	Local protective ecosystem, pH stability	Menstrual cycle, contraception, intimate hygiene, sexuality
respiratory microbiota	Nose, throat, sometimes lower passages	Airflow, mucins, local immunity	Mucosal barrier, immune interactions	Pollution, infections, tobacco, seasonality

This table highlights a central idea: discussing types of microbiota means discussing different ecological environments. Therefore, the strategies for supporting microbiota balance must be adapted to the specific area.

The gut microbiota

The gut microbiota is often the most studied because it reaches a very high density, especially in the colon, where oxygen is low and fermentable substrates (fiber, resistant starch, certain polyphenols) arrive. It participates in the transformation of nutrients and the production of metabolites, including short-chain fatty acids (SCFAs) resulting from the fermentation of fibers, which are frequently discussed for their role in the intestinal ecosystem.

A metabolic ecosystem: gut bacteria and "function"

Talking about gut bacteria solely by species is reductive. Two microbiomes can be very similar in composition but perform comparable functions (fermentation, metabolite production, mucus maintenance). This is one of the reasons why the microbiome (in the functional sense) is gaining importance: it describes biological capacities, not just species names.

Intestinal barrier, mucus and dialogue with the host

The role of the gut microbiota is expressed in particular through competition with opportunistic species (occupation of niches), influence on mucus and contact surface, and the production of metabolites that locally modulate the ecosystem.

In non-medical terms, it can be summarized as follows: a balanced gut microbiota supports intestinal health by contributing to digestive comfort and good food tolerance in many people, without this implying that it applies to all profiles.

Inter-individual variations: age, geography, diet

Large-scale mapping studies have revealed significant variability between individuals, influenced by lifestyle and diet. Thus, two people can have very different gut microbiomes while still functioning in a state compatible with their physiology.

The oral microbiota

The oral microbiota lives in a very specific environment: constant humidity, the presence of saliva, hard surfaces (teeth) and mucous membranes, and above all, the formation of biofilms. After a meal, variations in acidity occur, which selects for species capable of tolerating or producing a more acidic environment.

Biofilms, saliva and local balance

The goal is not sterilization. In the mouth, a stable microbiota contributes to the balance of biofilms. Oral hygiene primarily aims to limit plaque accumulation and support a composition more compatible with local comfort, rather than to "eradicate" all microbial life.

When hygiene becomes too "aggressive" for the ecosystem

Some potent antiseptics can significantly alter the composition of the oral microbiota. Controlled and reviewed studies report measurable changes in the salivary microbiota after the use of antiseptics such as chlorhexidine, illustrating that a hygiene practice is also an ecological intervention.

The skin microbiota

The skin microbiota colonizes the most exposed organ: the skin. It varies considerably depending on the area (the forehead is rich in sebum, the forearms are drier, and skin folds are more moist). Foundational work in skin microbiology describes a complex ecology: the location on the body, the level of sebum, humidity, UV exposure, and washing habits all shape its composition.

Dry skin, oily skin, moist areas: different niches

The skin is not a uniform "terrain". Three main categories of niches are often described:

• Seborrheic (oilier) areas : selection of lipophilic bacteria
• Dry areas : often higher diversity
• Wet areas (folds): humidity, friction, higher temperature

This diversity explains why different types of skin microbiota can react differently to the same cosmetic product, routine, or climate.

Skin barrier and immune dialogue

The role of the skin microbiota is often explained through "competition" and the production of molecules that influence the ecosystem. Reviews also emphasize its interaction with the local immune system and the development of tolerance: the skin learns to distinguish between compatible signals and ecological irritation.

Interconnection: the gut-skin axis

The concept of the gut-skin axis explores how signals from the gut microbiota (metabolites, mediators) can be reflected on the skin, and vice versa. Recent reviews describe a developing field that is promising but heterogeneous depending on the populations and parameters measured.

The vaginal microbiota

The vaginal microbiota (or intimate microbiota ) is a classic example in human ecology: it depends on pH, hormones, and lifestyle factors. Classification studies describe several "profiles" (community state types) often dominated by Lactobacillus species in many women, although there is significant inter-individual variability.

pH, Lactobacillus and ecological stability

The dominance of certain Lactobacillus species is frequently associated with a lower pH, which contributes to the stability of the local ecosystem. It is essential to avoid a simplistic interpretation: physiological variations exist, and the goal is not to impose a single model, but to support an environment consistent with intimate comfort.

Menstrual cycle, contraception, intimate hygiene: a faster pace

Compared to other types of microbiota, the vaginal microbiota can change more rapidly (cycle, sexuality, hygiene products). Follow-up studies describe fluctuations throughout the cycle, which serves as a reminder that "stability" often means "resilience" rather than "immutability".

The respiratory microbiota

The respiratory microbiota has long remained understudied, partly due to sampling difficulties in certain areas. Today, numerous reviews describe a continuum between the ENT sphere (nose, throat) and the respiratory tract, highlighting the role of microbial exchange, mucins, and local immunity.

An ecosystem influenced by air, mucus, and the environment

Pollution, tobacco smoke, seasonality, infections, allergies: all these factors can alter the local ecology. The reviews also highlight the importance of the gut-lung axis , where the state of the gut microbiota can influence immune responses in distant areas, and vice versa. In this context, the link between the microbiota and allergies deserves closer attention, as microbial imbalances can influence allergic sensitivity and the severity of symptoms.

What factors influence the different types of microbiota?

Microbiota types are sensitive to shared factors (diet, stress, sleep) and to factors specific to each area (vaginal pH, skin sebum, oral hygiene). Rather than searching for a "single factor," it is more realistic to think in terms of "ecological pressures" which, cumulatively, influence the composition and function of the microbiome.

Diet: the strongest argument for the gut microbiota

Diet has a significant influence on the gut microbiota because it provides fermentable substrates . Dietary fibers and certain plant matrices are associated with changes in diversity and variations in metabolites (including SCFAs) discussed in the literature.

At the level of microbiota types, diet also acts indirectly: circulating metabolites, hormonal variations, effects on the skin via the gut-skin axis, and modifications of the oral terrain via the frequency of sugar intake and acidity.

Stress, sleep, activity: the "neuro-immune" terrain

Without overinterpreting, reviews and physiological models describe a link between chronic stress, sleep quality, and barrier balance. This can translate into increased vulnerability to dysbiosis in certain profiles, particularly at the intestinal or cutaneous level, through changes in permeability, local immunity, or secretions.

Medications, antiseptics and exposures

Some antibiotics have a major impact on gut diversity (and sometimes on other sites). Other, less obvious exposures can also alter the local microbiota: oral antiseptics, harsh hygiene products, and pollution. For example, experimental studies show that some antiseptic mouthwashes can lead to measurable shifts in the salivary microbiota.

Hormones, cycle, age

Hormones strongly influence the vaginal microbiota, and age modulates different types of microbiota (skin, gut, mouth). These variations are not "defects": they reflect changes in the biological environment.

Hygiene: a balance between cleanliness and respect for the ecosystem

Appropriate hygiene is a key factor. However, not all types of microbiota have the same tolerance for repeated interventions:

• The skin can suffer from excessive stripping (weakened lipid barrier)
• The mouth can be affected by overly frequent use of antiseptics.
• The intimate area can be sensitized by products that are not pH-balanced and not suitable for mucous membranes.

Why the balance of microbiota types is essential for health

The balance of the microbiota is often presented as a "shield". To remain rigorous, it is more accurate to say that a stable microbiota limits the space available for opportunistic species, contributes to local functions (barrier, metabolites) and modulates immune signals in a contextual manner.

These mechanisms are described in numerous journals, but their expression depends on the site: the intestine does not have the same objectives as a respiratory mucosa. This is precisely the advantage of thinking in terms of microbiota types.

Dysbiosis: a functional concept, not a single label

Dysbiosis is not a universally applicable "standard" diagnosis in everyday life. Reviews highlight that there are several forms of dysbiosis: decreased diversity, loss of function, overrepresentation of certain species, or metabolic changes.

Interconnection: Why one site can influence another

The different types of microbiota communicate indirectly:

• Gut-skin : via metabolites, nutrition, immune signals
• Gut-lung : via immune mediators and interactions
• Systemic mouth : via biofilms, passage of bacterial products, and gingival context, with caution regarding causality.

This interconnectedness explains why it is possible to observe dysbiosis on several sites, or cascading repercussions, depending on the terrain and lifestyle.

How to take care of your different microbiomes

Taking care of the microbiota types is not about "adding bacteria" everywhere. The most robust approach is to optimize the environment (substrates, pH, hydration, barrier) and to use targeted tools when relevant: prebiotics, probiotics, adapted hygiene routines, limiting avoidable aggressions.

In a modern nutricosmetic approach, some brands like Biocyte rely on a formulation methodology and targeted active ingredients to offer food supplement programs focused on comfort and balance, particularly around the skin and the skin ecosystem, in line with the growing interest in the microbiome.

Diet and microbiota

Diet remains fundamental, especially for the gut microbiota and intestinal health. The link between diet and microbiota is crucial: the more varied and fiber-rich the diet, the more it supports a diverse intestinal ecosystem.

Focus on plant diversity and fibers

Fiber nourishes certain fermentation pathways and is associated with increased production of metabolites such as SCFAs (depending on the type of fiber, the food matrix, and the initial gut microbiota). Reviews on fiber and microbiota describe variable but consistent effects on the gut.

Examples of foods often used to diversify intake:

• vegetables (cruciferous vegetables, roots, leaves)
• legumes (lentils, chickpeas)
• whole grains (if tolerated)
• whole fruits
• seeds and oilseeds

Prebiotics: definition and benefits

Prebiotics are not limited to "fibers" in the broad sense. The consensus definition describes a prebiotic as a substrate selectively used by host microorganisms, conferring a benefit (scientific definition, which frames the vocabulary).

In practice, the idea is to provide substrates that promote certain microbial functions. Tolerance is individual: too rapid an increase can cause discomfort, hence the importance of a gradual progression.

Probiotics: definition, strains and objectives

Probiotics are defined as live microorganisms which, when administered in adequate amounts, provide a benefit. The key point is precision: identified strain, dosage, documented use.

Probiotics do not all act in the same way, nor do they affect all types of gut microbiota. Some strains are studied for digestive comfort , others for skin/gut health or women's health. Caution is advised: the effect depends on the strain, the matrix, the duration of use, and the individual's constitution.

Proteins, polyphenols, fats: global ecology matters

Beyond fiber, the overall quality of food influences the ecosystem: frequency of ultra-processed products, excess of fermentable oral sugars, or insufficient intake of vegetables can modify ecological pressures, in the intestine as well as in the mouth.

Hygiene and lifestyle

Hygiene practices should support barriers without "overcorrecting" the ecosystem.

Skin: protect the barrier before trying to "purify" it

For the skin microbiota, the barrier is often the priority: overly harsh cleansers, excessive exfoliation, and overuse of irritating active ingredients can alter the skin's environment (pH, lipids, hydration) and, through a domino effect, the microbiota. Adapting your routine to your skin type (dry, combination, oily) is a concrete way to stabilize the skin microbiota.

Mouth: mechanical hygiene, antiseptics used judiciously

Brushing, flossing/interdental brushes, hydration, and limiting sugary snacks all have an effect on the oral cavity. Strong antiseptics, when used too frequently, can disrupt the balance of the salivary microbiota, according to experimental studies.

Intimate area: respecting pH, mucous membranes and actual needs

For the vaginal microbiota, perfumed products, internal douching, and unsuitable cleansers can disrupt the environment. Gentle external hygiene and respecting the pH balance are simple and often effective principles.

Respiratory system: air, environment, habits

For the respiratory microbiota, air quality, tobacco use, and pollution are major factors. Hydration, regular physical activity, and sleep also support the balance of the mucous membranes.

Stress and sleep: the "invisible" basis

Chronic stress and insufficient sleep influence the body's internal environment (immunity, barrier function, eating habits). While not promising a universal direct effect, these factors are consistent with a comprehensive strategy that promotes a balanced gut microbiota.

FAQs about types of microbiota

What are the main types of microbiota in humans?

The main types of microbiota described in this guide are: gut microbiota, skin microbiota, oral microbiota, vaginal microbiota (in women), and respiratory microbiota. Each has a different composition and function, as the biological environment (pH, oxygen, humidity, sebum) varies depending on the site.

What type of microbiota is the most important?

There is no simple hierarchy among the types of microbiota. The gut microbiota is extensively studied and very complex, but a stable skin or oral microbiota is just as essential locally. The most "important" is often the one most weakened by an individual's constitution, habits, and environment.

Is it possible to have an imbalance of several types of microbiota at the same time?

Yes. Dysbiosis can affect several types of microbiota if common factors are present: stress, lack of sleep, a diet low in fiber, overly aggressive hygiene, smoking, and certain medications. The interconnectedness between sites (e.g., gut-skin) also helps explain these cross-reactions.

How can you tell if your gut microbiota is unbalanced?

The concept of dysbiosis is not limited to a single sign. Manifestations can be local and nonspecific. Only a structured approach allows for the guidance of appropriate actions. Reviews remind us that dysbiosis can be a cause, a consequence, or a marker, depending on the situation.

Do probiotics act on all types of microbiota?

Not necessarily. Probiotics have effects that depend on the strains, the dosage, and the individual's constitution. Some effects are primarily documented for the gut microbiota. Other areas are being studied, but extrapolation should remain cautious. The consensus definition emphasizes the need for identified strains and well-supported use.

Sources

• NIH - Human Microbiome Project (overview, site mapping)
• Grice & Segre - The skin microbiome (review, skin ecology)
• Ravel et al. - Vaginal microbiome of reproductive-age women (classification into profiles/CST, 16S methodology)
• Cho et al. - The oral microbiome in the pathophysiology of cardiovascular disease (review, mechanisms discussed)
• Hill et al. (ISAPP) - Consensus on the definition and use of the term probiotic
• Gibson et al. (ISAPP) - Consensus on the definition and scope of prebiotics
• Review of the lung microbiota (ecology, functions, axes)